============================================================================= Reading config file: /home/ubuntu/rna-tools/rna_tools/tools/webserver-engine/media/jobs/a01028d0/tmp/C11_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/a01028d0/tmp/C11_refx/C11.pdb ============================================================================= Atom's 462 N1 residue renamed to RG3 Atom's 461 C2 residue renamed to RG3 Atom's 460 N3 residue renamed to RG3 Atom's 459 C4 residue renamed to RG3 Atom's 458 N9 residue renamed to RG3 Atom's 457 C8 residue renamed to RG3 Atom's 456 N7 residue renamed to RG3 Atom's 455 C5 residue renamed to RG3 Atom's 454 C6 residue renamed to RG3 Atom's 453 O6 residue renamed to RG3 Atom's 452 N2 residue renamed to RG3 Atom's 451 O2' residue renamed to RG3 Atom's 450 O4' residue renamed to RG3 Atom's 449 C5' residue renamed to RG3 Atom's 448 C4' residue renamed to RG3 Atom's 447 C3' residue renamed to RG3 Atom's 446 C2' residue renamed to RG3 Atom's 445 C1' residue renamed to RG3 Atom's 444 O3' residue renamed to RG3 Atom's 443 O5' residue renamed to RG3 Atom's 442 OP2 residue renamed to RG3 Atom's 441 OP1 residue renamed to RG3 Atom's 440 P residue renamed to RG3 Error: recognition of atom ATOM 1 OP3 A B 1 ... failed. Atom erased. Missing atom added: ATOM 23 H5'1 A B 1 53.829 -28.060 27.767 1.00 0.00 H Missing atom added: ATOM 24 H5'2 A B 1 52.918 -26.653 26.975 1.00 0.00 H Missing atom added: ATOM 25 H4' A B 1 53.103 -28.695 25.704 1.00 0.00 H Missing atom added: ATOM 26 H3' A B 1 53.754 -28.324 24.823 1.00 0.00 H Missing atom added: ATOM 29 H1' A B 1 50.307 -29.505 24.416 1.00 0.00 H Missing atom added: ATOM 27 H2' A B 1 53.083 -28.531 23.262 1.00 0.00 H Missing atom added: ATOM 28 HO'2 A B 1 53.544 -29.657 22.932 1.00 0.00 H Missing atom added: ATOM 30 H8 A B 1 50.741 -26.064 24.283 1.00 0.00 H Missing atom added: ATOM 31 H61 A B 1 47.063 -25.974 21.088 1.00 0.00 H Missing atom added: ATOM 32 H62 A B 1 46.121 -27.205 20.372 1.00 0.00 H Missing atom added: ATOM 33 H2 A B 1 47.505 -31.507 21.865 1.00 0.00 H Missing atom added: ATOM 23 H5'1 A B 2 55.446 -32.297 27.218 1.00 0.00 H Missing atom added: ATOM 24 H5'2 A B 2 54.963 -30.523 27.454 1.00 0.00 H Missing atom added: ATOM 25 H4' A B 2 56.869 -31.454 28.658 1.00 0.00 H Missing atom added: ATOM 26 H3' A B 2 57.926 -30.118 26.017 1.00 0.00 H Missing atom added: ATOM 29 H1' A B 2 59.615 -33.098 27.567 1.00 0.00 H Missing atom added: ATOM 27 H2' A B 2 60.160 -30.542 26.874 1.00 0.00 H Missing atom added: ATOM 28 HO'2 A B 2 58.815 -30.588 29.203 1.00 0.00 H Missing atom added: ATOM 30 H8 A B 2 57.303 -32.769 24.775 1.00 0.00 H Missing atom added: ATOM 31 H61 A B 2 60.480 -33.686 21.186 1.00 0.00 H Missing atom added: ATOM 32 H62 A B 2 62.173 -33.907 21.171 1.00 0.00 H Missing atom added: ATOM 33 H2 A B 2 64.024 -33.249 25.508 1.00 0.00 H Missing atom added: ATOM 23 H5'1 A B 3 60.340 -28.399 28.515 1.00 0.00 H Missing atom added: ATOM 24 H5'2 A B 3 60.459 -26.569 28.243 1.00 0.00 H Missing atom added: ATOM 25 H4' A B 3 62.526 -27.740 28.399 1.00 0.00 H Missing atom added: ATOM 26 H3' A B 3 61.873 -26.770 25.610 1.00 0.00 H Missing atom added: ATOM 29 H1' A B 3 63.785 -30.008 26.095 1.00 0.00 H Missing atom added: ATOM 27 H2' A B 3 64.083 -27.501 24.930 1.00 0.00 H Missing atom added: ATOM 28 HO'2 A B 3 64.597 -27.293 27.487 1.00 0.00 H Missing atom added: ATOM 30 H8 A B 3 60.391 -29.167 24.990 1.00 0.00 H Missing atom added: ATOM 31 H61 A B 3 60.924 -30.746 20.402 1.00 0.00 H Missing atom added: ATOM 32 H62 A B 3 62.272 -31.329 19.531 1.00 0.00 H Missing atom added: ATOM 33 H2 A B 3 66.224 -31.176 22.179 1.00 0.00 H Missing atom added: ATOM 21 H5'1 U B 4 65.499 -25.256 26.865 1.00 0.00 H Missing atom added: ATOM 22 H5'2 U B 4 65.553 -23.404 26.830 1.00 0.00 H Missing atom added: ATOM 23 H4' U B 4 67.503 -24.779 26.185 1.00 0.00 H Missing atom added: ATOM 24 H3' U B 4 66.298 -23.661 23.689 1.00 0.00 H Missing atom added: ATOM 27 H1' U B 4 67.605 -27.156 23.623 1.00 0.00 H Missing atom added: ATOM 25 H2' U B 4 67.992 -24.748 22.408 1.00 0.00 H Missing atom added: ATOM 26 HO'2 U B 4 69.265 -24.794 24.686 1.00 0.00 H Missing atom added: ATOM 29 H6 U B 4 64.360 -25.799 23.968 1.00 0.00 H Missing atom added: ATOM 30 H3 U B 4 65.333 -28.158 19.413 1.00 0.00 H Missing atom added: ATOM 28 H5 U B 4 62.451 -26.217 22.431 1.00 0.00 H Missing atom added: ATOM 24 H5'1 G B 5 70.017 -23.053 22.938 1.00 0.00 H Missing atom added: ATOM 25 H5'2 G B 5 70.401 -21.283 22.547 1.00 0.00 H Missing atom added: ATOM 26 H4' G B 5 71.252 -22.903 21.029 1.00 0.00 H Missing atom added: ATOM 27 H3' G B 5 68.925 -21.380 19.820 1.00 0.00 H Missing atom added: ATOM 30 H1' G B 5 69.436 -25.000 18.966 1.00 0.00 H Missing atom added: ATOM 28 H2' G B 5 69.334 -22.578 17.769 1.00 0.00 H Missing atom added: ATOM 29 HO'2 G B 5 71.715 -22.936 18.889 1.00 0.00 H Missing atom added: ATOM 31 H8 G B 5 67.064 -23.389 21.192 1.00 0.00 H Missing atom added: ATOM 34 H1 G B 5 64.482 -26.568 15.711 1.00 0.00 H Missing atom added: ATOM 32 H21 G B 5 68.045 -26.195 14.960 1.00 0.00 H Missing atom added: ATOM 33 H22 G B 5 66.473 -26.348 14.407 1.00 0.00 H Missing atom added: ATOM 24 H5'1 G B 6 71.178 -20.941 16.816 1.00 0.00 H Missing atom added: ATOM 25 H5'2 G B 6 71.297 -19.161 16.317 1.00 0.00 H Missing atom added: ATOM 26 H4' G B 6 70.708 -20.637 14.598 1.00 0.00 H Missing atom added: ATOM 27 H3' G B 6 68.342 -18.938 15.459 1.00 0.00 H Missing atom added: ATOM 30 H1' G B 6 67.972 -22.542 14.123 1.00 0.00 H Missing atom added: ATOM 28 H2' G B 6 67.204 -19.944 13.516 1.00 0.00 H Missing atom added: ATOM 29 HO'2 G B 6 69.664 -20.291 12.677 1.00 0.00 H Missing atom added: ATOM 31 H8 G B 6 67.451 -21.172 17.498 1.00 0.00 H Missing atom added: ATOM 34 H1 G B 6 61.738 -23.291 14.343 1.00 0.00 H Missing atom added: ATOM 32 H21 G B 6 64.228 -23.027 11.673 1.00 0.00 H Missing atom added: ATOM 33 H22 G B 6 62.624 -22.975 12.145 1.00 0.00 H Missing atom added: ATOM 23 H5'1 A B 7 68.634 -18.294 11.451 1.00 0.00 H Missing atom added: ATOM 24 H5'2 A B 7 68.441 -16.482 11.114 1.00 0.00 H Missing atom added: ATOM 25 H4' A B 7 67.091 -17.548 9.712 1.00 0.00 H Missing atom added: ATOM 26 H3' A B 7 65.692 -16.008 12.025 1.00 0.00 H Missing atom added: ATOM 29 H1' A B 7 64.087 -18.974 10.331 1.00 0.00 H Missing atom added: ATOM 27 H2' A B 7 63.615 -16.320 10.810 1.00 0.00 H Missing atom added: ATOM 28 HO'2 A B 7 65.257 -16.525 8.755 1.00 0.00 H Missing atom added: ATOM 30 H8 A B 7 65.757 -18.597 13.558 1.00 0.00 H Missing atom added: ATOM 31 H61 A B 7 61.814 -19.430 16.312 1.00 0.00 H Missing atom added: ATOM 32 H62 A B 7 60.164 -19.647 15.929 1.00 0.00 H Missing atom added: ATOM 33 H2 A B 7 59.398 -19.084 11.265 1.00 0.00 H Missing atom added: ATOM 23 H5'1 A B 8 63.905 -14.286 9.140 1.00 0.00 H Missing atom added: ATOM 24 H5'2 A B 8 63.889 -12.439 9.300 1.00 0.00 H Missing atom added: ATOM 25 H4' A B 8 61.793 -13.419 8.863 1.00 0.00 H Missing atom added: ATOM 26 H3' A B 8 62.021 -12.406 11.728 1.00 0.00 H Missing atom added: ATOM 29 H1' A B 8 59.886 -15.469 10.783 1.00 0.00 H Missing atom added: ATOM 27 H2' A B 8 59.622 -12.919 11.907 1.00 0.00 H Missing atom added: ATOM 28 HO'2 A B 8 59.744 -12.631 9.303 1.00 0.00 H Missing atom added: ATOM 30 H8 A B 8 62.928 -14.814 12.771 1.00 0.00 H Missing atom added: ATOM 31 H61 A B 8 61.081 -16.529 16.949 1.00 0.00 H Missing atom added: ATOM 32 H62 A B 8 59.524 -17.078 17.386 1.00 0.00 H Missing atom added: ATOM 33 H2 A B 8 56.492 -16.720 13.733 1.00 0.00 H Missing atom added: ATOM 23 H5'1 A B 9 58.654 -10.835 10.554 1.00 0.00 H Missing atom added: ATOM 24 H5'2 A B 9 58.491 -9.117 11.230 1.00 0.00 H Missing atom added: ATOM 25 H4' A B 9 56.644 -10.392 11.707 1.00 0.00 H Missing atom added: ATOM 26 H3' A B 9 58.346 -9.596 14.076 1.00 0.00 H Missing atom added: ATOM 29 H1' A B 9 56.282 -12.904 13.962 1.00 0.00 H Missing atom added: ATOM 27 H2' A B 9 56.521 -10.482 15.461 1.00 0.00 H Missing atom added: ATOM 28 HO'2 A B 9 55.129 -9.887 13.382 1.00 0.00 H Missing atom added: ATOM 30 H8 A B 9 59.843 -11.760 14.221 1.00 0.00 H Missing atom added: ATOM 31 H61 A B 9 60.935 -14.129 18.341 1.00 0.00 H Missing atom added: ATOM 32 H62 A B 9 60.002 -15.074 19.414 1.00 0.00 H Missing atom added: ATOM 33 H2 A B 9 55.462 -15.291 18.002 1.00 0.00 H Missing atom added: ATOM 24 H5'1 G B 10 55.715 -7.373 15.888 1.00 0.00 H Missing atom added: ATOM 25 H5'2 G B 10 56.739 -5.883 16.291 1.00 0.00 H Missing atom added: ATOM 26 H4' G B 10 56.349 -5.958 18.020 1.00 0.00 H Missing atom added: ATOM 27 H3' G B 10 59.256 -6.178 16.741 1.00 0.00 H Missing atom added: ATOM 30 H1' G B 10 58.729 -7.300 20.082 1.00 0.00 H Missing atom added: ATOM 28 H2' G B 10 60.550 -6.539 17.657 1.00 0.00 H Missing atom added: ATOM 29 HO'2 G B 10 60.855 -5.356 18.154 1.00 0.00 H Missing atom added: ATOM 31 H8 G B 10 59.470 -9.752 17.643 1.00 0.00 H Missing atom added: ATOM 34 H1 G B 10 59.027 -10.867 24.400 1.00 0.00 H Missing atom added: ATOM 32 H21 G B 10 58.365 -7.290 24.005 1.00 0.00 H Missing atom added: ATOM 33 H22 G B 10 58.934 -8.545 24.954 1.00 0.00 H Missing atom added: ATOM 24 H5'1 G B 11 57.808 -2.324 20.612 1.00 0.00 H Missing atom added: ATOM 25 H5'2 G B 11 57.458 -0.809 19.605 1.00 0.00 H Missing atom added: ATOM 26 H4' G B 11 58.698 -0.407 21.569 1.00 0.00 H Missing atom added: ATOM 27 H3' G B 11 60.350 -0.165 19.012 1.00 0.00 H Missing atom added: ATOM 30 H1' G B 11 61.960 -1.406 22.217 1.00 0.00 H Missing atom added: ATOM 28 H2' G B 11 62.172 0.626 20.354 1.00 0.00 H Missing atom added: ATOM 29 HO'2 G B 11 60.247 1.275 21.980 1.00 0.00 H Missing atom added: ATOM 31 H8 G B 11 60.975 -3.248 19.248 1.00 0.00 H Missing atom added: ATOM 34 H1 G B 11 67.734 -2.321 19.957 1.00 0.00 H Missing atom added: ATOM 32 H21 G B 11 66.222 0.108 22.240 1.00 0.00 H Missing atom added: ATOM 33 H22 G B 11 67.504 -0.328 21.258 1.00 0.00 H Missing atom added: ATOM 21 H5'1 C B 12 61.650 3.162 20.234 1.00 0.00 H Missing atom added: ATOM 22 H5'2 C B 12 61.493 4.426 18.888 1.00 0.00 H Missing atom added: ATOM 23 H4' C B 12 63.658 4.191 19.577 1.00 0.00 H Missing atom added: ATOM 24 H3' C B 12 63.146 3.240 16.759 1.00 0.00 H Missing atom added: ATOM 27 H1' C B 12 65.775 1.567 18.900 1.00 0.00 H Missing atom added: ATOM 25 H2' C B 12 65.554 2.959 16.560 1.00 0.00 H Missing atom added: ATOM 26 HO'2 C B 12 65.567 4.685 18.538 1.00 0.00 H Missing atom added: ATOM 30 H6 C B 12 62.508 0.810 17.924 1.00 0.00 H Missing atom added: ATOM 28 H41 C B 12 62.824 -2.764 14.810 1.00 0.00 H Missing atom added: ATOM 29 H42 C B 12 64.505 -2.807 14.486 1.00 0.00 H Missing atom added: ATOM 31 H5 C B 12 61.460 -1.203 16.399 1.00 0.00 H Missing atom added: ATOM 23 H5'1 A B 13 65.719 4.503 15.381 1.00 0.00 H Missing atom added: ATOM 24 H5'2 A B 13 65.416 5.709 14.007 1.00 0.00 H Missing atom added: ATOM 25 H4' A B 13 66.750 3.843 13.450 1.00 0.00 H Missing atom added: ATOM 26 H3' A B 13 64.041 3.762 12.148 1.00 0.00 H Missing atom added: ATOM 29 H1' A B 13 65.646 0.531 13.192 1.00 0.00 H Missing atom added: ATOM 27 H2' A B 13 64.714 1.788 10.970 1.00 0.00 H Missing atom added: ATOM 28 HO'2 A B 13 67.112 2.651 11.453 1.00 0.00 H Missing atom added: ATOM 30 H8 A B 13 62.829 2.530 14.683 1.00 0.00 H Missing atom added: ATOM 31 H61 A B 13 59.146 -0.427 13.446 1.00 0.00 H Missing atom added: ATOM 32 H62 A B 13 59.069 -1.838 12.486 1.00 0.00 H Missing atom added: ATOM 33 H2 A B 13 63.319 -2.866 10.605 1.00 0.00 H Missing atom added: ATOM 23 H5'1 A B 14 65.647 2.740 9.037 1.00 0.00 H Missing atom added: ATOM 24 H5'2 A B 14 65.067 3.778 7.615 1.00 0.00 H Missing atom added: ATOM 25 H4' A B 14 64.595 1.563 7.269 1.00 0.00 H Missing atom added: ATOM 26 H3' A B 14 62.234 3.379 7.546 1.00 0.00 H Missing atom added: ATOM 29 H1' A B 14 61.975 -0.148 8.849 1.00 0.00 H Missing atom added: ATOM 27 H2' A B 14 60.798 1.563 7.017 1.00 0.00 H Missing atom added: ATOM 28 HO'2 A B 14 62.928 0.526 5.968 1.00 0.00 H Missing atom added: ATOM 30 H8 A B 14 62.262 2.999 10.717 1.00 0.00 H Missing atom added: ATOM 31 H61 A B 14 57.917 2.793 12.929 1.00 0.00 H Missing atom added: ATOM 32 H62 A B 14 56.590 1.729 12.773 1.00 0.00 H Missing atom added: ATOM 33 H2 A B 14 57.354 -1.465 9.326 1.00 0.00 H Missing atom added: ATOM 23 H5'1 A B 15 60.984 1.641 4.562 1.00 0.00 H Missing atom added: ATOM 24 H5'2 A B 15 60.705 2.752 3.105 1.00 0.00 H Missing atom added: ATOM 25 H4' A B 15 58.924 1.266 3.743 1.00 0.00 H Missing atom added: ATOM 26 H3' A B 15 58.289 4.130 4.509 1.00 0.00 H Missing atom added: ATOM 29 H1' A B 15 57.166 1.279 6.731 1.00 0.00 H Missing atom added: ATOM 27 H2' A B 15 56.170 3.438 5.294 1.00 0.00 H Missing atom added: ATOM 28 HO'2 A B 15 56.361 1.498 3.712 1.00 0.00 H Missing atom added: ATOM 30 H8 A B 15 59.863 3.807 6.944 1.00 0.00 H Missing atom added: ATOM 31 H61 A B 15 58.373 6.005 11.040 1.00 0.00 H Missing atom added: ATOM 32 H62 A B 15 56.985 5.811 12.017 1.00 0.00 H Missing atom added: ATOM 33 H2 A B 15 54.034 2.560 10.179 1.00 0.00 H Missing atom added: ATOM 24 H5'1 G B 16 54.941 2.916 2.968 1.00 0.00 H Missing atom added: ATOM 25 H5'2 G B 16 54.412 3.821 1.441 1.00 0.00 H Missing atom added: ATOM 26 H4' G B 16 52.645 3.768 2.697 1.00 0.00 H Missing atom added: ATOM 27 H3' G B 16 54.031 6.527 2.294 1.00 0.00 H Missing atom added: ATOM 30 H1' G B 16 52.437 6.193 5.333 1.00 0.00 H Missing atom added: ATOM 28 H2' G B 16 53.756 7.825 3.163 1.00 0.00 H Missing atom added: ATOM 29 HO'2 G B 16 52.444 8.195 2.804 1.00 0.00 H Missing atom added: ATOM 31 H8 G B 16 56.075 5.993 4.858 1.00 0.00 H Missing atom added: ATOM 34 H1 G B 16 53.291 8.249 10.705 1.00 0.00 H Missing atom added: ATOM 32 H21 G B 16 50.439 7.606 8.503 1.00 0.00 H Missing atom added: ATOM 33 H22 G B 16 51.106 8.481 9.764 1.00 0.00 H Missing atom added: ATOM 21 H5'1 U B 17 51.174 8.879 1.700 1.00 0.00 H Missing atom added: ATOM 22 H5'2 U B 17 50.053 8.928 0.226 1.00 0.00 H Missing atom added: ATOM 23 H4' U B 17 50.660 10.852 0.221 1.00 0.00 H Missing atom added: ATOM 24 H3' U B 17 50.318 9.159 -2.046 1.00 0.00 H Missing atom added: ATOM 27 H1' U B 17 53.269 11.669 -2.010 1.00 0.00 H Missing atom added: ATOM 25 H2' U B 17 50.881 11.005 -3.466 1.00 0.00 H Missing atom added: ATOM 26 HO'2 U B 17 50.184 12.433 -1.527 1.00 0.00 H Missing atom added: ATOM 29 H6 U B 17 52.951 8.191 -1.953 1.00 0.00 H Missing atom added: ATOM 30 H3 U B 17 55.487 10.455 -5.920 1.00 0.00 H Missing atom added: ATOM 28 H5 U B 17 54.225 6.737 -3.520 1.00 0.00 H Missing atom added: ATOM 21 H5'1 C B 18 48.686 12.662 -2.865 1.00 0.00 H Missing atom added: ATOM 22 H5'2 C B 18 47.030 12.441 -3.668 1.00 0.00 H Missing atom added: ATOM 23 H4' C B 18 48.262 13.864 -4.915 1.00 0.00 H Missing atom added: ATOM 24 H3' C B 18 47.664 11.146 -6.177 1.00 0.00 H Missing atom added: ATOM 27 H1' C B 18 50.853 12.999 -7.029 1.00 0.00 H Missing atom added: ATOM 25 H2' C B 18 48.591 11.952 -8.234 1.00 0.00 H Missing atom added: ATOM 26 HO'2 C B 18 48.011 14.285 -7.269 1.00 0.00 H Missing atom added: ATOM 30 H6 C B 18 50.106 10.285 -4.892 1.00 0.00 H Missing atom added: ATOM 28 H41 C B 18 52.372 6.487 -6.632 1.00 0.00 H Missing atom added: ATOM 29 H42 C B 18 52.881 7.049 -8.167 1.00 0.00 H Missing atom added: ATOM 31 H5 C B 18 51.019 7.711 -4.760 1.00 0.00 H Missing atom added: ATOM 24 H5'1 G B 19 46.567 13.795 -8.907 1.00 0.00 H Missing atom added: ATOM 25 H5'2 G B 19 44.985 13.286 -9.724 1.00 0.00 H Missing atom added: ATOM 26 H4' G B 19 46.508 13.771 -11.321 1.00 0.00 H Missing atom added: ATOM 27 H3' G B 19 45.691 10.835 -11.090 1.00 0.00 H Missing atom added: ATOM 30 H1' G B 19 49.162 11.779 -12.275 1.00 0.00 H Missing atom added: ATOM 28 H2' G B 19 46.916 10.390 -13.101 1.00 0.00 H Missing atom added: ATOM 29 HO'2 G B 19 46.548 12.910 -13.566 1.00 0.00 H Missing atom added: ATOM 31 H8 G B 19 47.939 10.408 -9.057 1.00 0.00 H Missing atom added: ATOM 34 H1 G B 19 51.697 5.949 -12.677 1.00 0.00 H Missing atom added: ATOM 32 H21 G B 19 50.875 8.613 -15.049 1.00 0.00 H Missing atom added: ATOM 33 H22 G B 19 51.240 7.004 -14.773 1.00 0.00 H Missing atom added: ATOM 23 H5'1 A B 20 45.224 11.723 -14.921 1.00 0.00 H Missing atom added: ATOM 24 H5'2 A B 20 43.678 10.953 -15.594 1.00 0.00 H Missing atom added: ATOM 25 H4' A B 20 45.402 10.442 -16.960 1.00 0.00 H Missing atom added: ATOM 26 H3' A B 20 44.198 8.113 -15.390 1.00 0.00 H Missing atom added: ATOM 29 H1' A B 20 47.862 8.095 -16.347 1.00 0.00 H Missing atom added: ATOM 27 H2' A B 20 45.549 6.609 -16.680 1.00 0.00 H Missing atom added: ATOM 28 HO'2 A B 20 45.555 8.534 -18.414 1.00 0.00 H Missing atom added: ATOM 30 H8 A B 20 46.139 8.673 -13.115 1.00 0.00 H Missing atom added: ATOM 31 H61 A B 20 47.684 4.694 -10.747 1.00 0.00 H Missing atom added: ATOM 32 H62 A B 20 48.574 3.325 -11.247 1.00 0.00 H Missing atom added: ATOM 33 H2 A B 20 49.575 3.531 -15.895 1.00 0.00 H Missing atom added: ATOM 24 H5'1 RG3 B 21 44.231 6.889 -19.157 1.00 0.00 H Missing atom added: ATOM 25 H5'2 RG3 B 21 42.675 5.971 -19.567 1.00 0.00 H Missing atom added: ATOM 26 H4' RG3 B 21 44.448 4.722 -20.201 1.00 0.00 H Missing atom added: ATOM 27 H3' RG3 B 21 42.804 3.634 -17.866 1.00 0.00 H Missing atom added: ATOM 30 H1' RG3 B 21 46.513 2.908 -18.111 1.00 0.00 H Missing atom added: ATOM 28 H2' RG3 B 21 44.074 1.605 -17.984 1.00 0.00 H Missing atom added: ATOM 29 HO'2 RG3 B 21 44.500 2.331 -20.434 1.00 0.00 H Missing atom added: ATOM 31 H8 RG3 B 21 44.587 5.204 -15.927 1.00 0.00 H Missing atom added: ATOM 34 H1 RG3 B 21 47.289 -0.144 -12.577 1.00 0.00 H Missing atom added: ATOM 32 H21 RG3 B 21 47.543 -1.040 -16.116 1.00 0.00 H Missing atom added: ATOM 33 H22 RG3 B 21 47.396 -1.528 -14.522 1.00 0.00 H Missing atom added: ATOM 35 H3T RG3 B 21 43.081 2.885 -20.520 1.00 0.00 H Missing atom added: ATOM 4 OP3 A B 1 53.830 -26.980 30.502 1.00 15.13 Number of atoms: 692 Number of residues: 21 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: 750 Number of angles built: 1336 Number of dihedrals built: 2030 Number of impropers built: 150 ----------------------------------------------------------------------------- End of molecule (chain) ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Building interresidual nonbonded pairs & H-bonds (it may take a while)... Number of electrostatic pairs: 237000 Number of van der Waals pairs: 48484 Number of H-bonds built: 0 Number of spring restraints: 0 Number of positional restraints: 0 Number of base pairs built: 0 Number of molecules (chains) read: 1 ----------------------------------------------------------------------------- Performing minimization step: 1. Total energy = 4412.6340 kcal/mol (4409.5453 without restraints) Performing minimization step: 2. Total energy = 4386.9262 kcal/mol (4383.9454 without restraints) Performing minimization step: 3. Total energy = 4362.1114 kcal/mol (4359.2335 without restraints) Performing minimization step: 4. Total energy = 4338.1473 kcal/mol (4335.3675 without restraints) Performing minimization step: 5. Total energy = 4314.9937 kcal/mol (4312.3072 without restraints) Performing minimization step: 6. Total energy = 4292.6119 kcal/mol (4290.0143 without restraints) Performing minimization step: 7. Total energy = 4270.9653 kcal/mol (4268.4523 without restraints) Performing minimization step: 8. Total energy = 4250.0187 kcal/mol (4247.5864 without restraints) Performing minimization step: 9. Total energy = 4229.7387 kcal/mol (4227.3831 without restraints) Performing minimization step: 10. Total energy = 4210.0933 kcal/mol (4207.8108 without restraints) Performing minimization step: 11. Total energy = 4191.0520 kcal/mol (4188.8391 without restraints) Performing minimization step: 12. Total energy = 4172.5857 kcal/mol (4170.4390 without restraints) Performing minimization step: 13. Total energy = 4154.6667 kcal/mol (4152.5830 without restraints) Performing minimization step: 14. Total energy = 4137.2684 kcal/mol (4135.2447 without restraints) Performing minimization step: 15. Total energy = 4120.3657 kcal/mol (4118.3990 without restraints) Performing minimization step: 16. Total energy = 4103.9344 kcal/mol (4102.0219 without restraints) Performing minimization step: 17. Total energy = 4087.9515 kcal/mol (4086.0907 without restraints) Performing minimization step: 18. Total energy = 4072.3952 kcal/mol (4070.5834 without restraints) Performing minimization step: 19. Total energy = 4057.2446 kcal/mol (4055.4795 without restraints) Performing minimization step: 20. Total energy = 4042.4798 kcal/mol (4040.7591 without restraints) Performing minimization step: 21. Total energy = 4028.0819 kcal/mol (4026.4035 without restraints) Performing minimization step: 22. Total energy = 4014.0329 kcal/mol (4012.3946 without restraints) Performing minimization step: 23. Total energy = 4000.3156 kcal/mol (3998.7155 without restraints) Performing minimization step: 24. Total energy = 3986.9137 kcal/mol (3985.3499 without restraints) Performing minimization step: 25. Total energy = 3973.8117 kcal/mol (3972.2825 without restraints) Performing minimization step: 26. Total energy = 3960.9951 kcal/mol (3959.4986 without restraints) Performing minimization step: 27. Total energy = 3948.4495 kcal/mol (3946.9842 without restraints) Performing minimization step: 28. Total energy = 3936.1617 kcal/mol (3934.7261 without restraints) Performing minimization step: 29. Total energy = 3924.1191 kcal/mol (3922.7117 without restraints) Performing minimization step: 30. Total energy = 3912.3097 kcal/mol (3910.9292 without restraints) Performing minimization step: 31. Total energy = 3900.7222 kcal/mol (3899.3672 without restraints) Performing minimization step: 32. Total energy = 3889.3459 kcal/mol (3888.0152 without restraints) Performing minimization step: 33. Total energy = 3878.1704 kcal/mol (3876.8628 without restraints) Performing minimization step: 34. Total energy = 3867.1859 kcal/mol (3865.9003 without restraints) Performing minimization step: 35. Total energy = 3856.3833 kcal/mol (3855.1187 without restraints) Performing minimization step: 36. Total energy = 3845.7541 kcal/mol (3844.5094 without restraints) Performing minimization step: 37. Total energy = 3835.2897 kcal/mol (3834.0641 without restraints) Performing minimization step: 38. Total energy = 3824.9826 kcal/mol (3823.7750 without restraints) Performing minimization step: 39. Total energy = 3814.8253 kcal/mol (3813.6350 without restraints) Performing minimization step: 40. Total energy = 3804.8108 kcal/mol (3803.6370 without restraints) Performing minimization step: 41. Total energy = 3794.9326 kcal/mol (3793.7745 without restraints) Performing minimization step: 42. Total energy = 3785.1844 kcal/mol (3784.0413 without restraints) Performing minimization step: 43. Total energy = 3775.5604 kcal/mol (3774.4315 without restraints) Performing minimization step: 44. Total energy = 3766.0548 kcal/mol (3764.9397 without restraints) Performing minimization step: 45. Total energy = 3756.6626 kcal/mol (3755.5605 without restraints) Performing minimization step: 46. Total energy = 3747.3786 kcal/mol (3746.2890 without restraints) Performing minimization step: 47. Total energy = 3738.1981 kcal/mol (3737.1205 without restraints) Performing minimization step: 48. Total energy = 3729.1168 kcal/mol (3728.0506 without restraints) Performing minimization step: 49. Total energy = 3720.1304 kcal/mol (3719.0752 without restraints) Performing minimization step: 50. Total energy = 3711.2349 kcal/mol (3710.1901 without restraints) Performing minimization step: 51. Total energy = 3702.4265 kcal/mol (3701.3918 without restraints) Performing minimization step: 52. Total energy = 3693.7017 kcal/mol (3692.6767 without restraints) Performing minimization step: 53. Total energy = 3685.0571 kcal/mol (3684.0414 without restraints) Performing minimization step: 54. Total energy = 3676.4896 kcal/mol (3675.4827 without restraints) Performing minimization step: 55. Total energy = 3667.9960 kcal/mol (3666.9978 without restraints) Performing minimization step: 56. Total energy = 3659.5737 kcal/mol (3658.5837 without restraints) Performing minimization step: 57. Total energy = 3651.2198 kcal/mol (3650.2378 without restraints) Performing minimization step: 58. Total energy = 3642.9319 kcal/mol (3641.9575 without restraints) Performing minimization step: 59. Total energy = 3634.7075 kcal/mol (3633.7404 without restraints) Performing minimization step: 60. Total energy = 3626.5447 kcal/mol (3625.5847 without restraints) Performing minimization step: 61. Total energy = 3618.4405 kcal/mol (3617.4874 without restraints) Performing minimization step: 62. Total energy = 3610.3934 kcal/mol (3609.4468 without restraints) Performing minimization step: 63. Total energy = 3602.4017 kcal/mol (3601.4616 without restraints) Performing minimization step: 64. Total energy = 3594.4628 kcal/mol (3593.5289 without restraints) Performing minimization step: 65. Total energy = 3586.5754 kcal/mol (3585.6474 without restraints) Performing minimization step: 66. Total energy = 3578.7378 kcal/mol (3577.8156 without restraints) Performing minimization step: 67. Total energy = 3570.9484 kcal/mol (3570.0318 without restraints) Performing minimization step: 68. Total energy = 3563.2058 kcal/mol (3562.2946 without restraints) Performing minimization step: 69. Total energy = 3555.5084 kcal/mol (3554.6025 without restraints) Performing minimization step: 70. Total energy = 3547.8550 kcal/mol (3546.9542 without restraints) Performing minimization step: 71. Total energy = 3540.2443 kcal/mol (3539.3485 without restraints) Performing minimization step: 72. Total energy = 3532.6751 kcal/mol (3531.7841 without restraints) Performing minimization step: 73. Total energy = 3525.1461 kcal/mol (3524.2598 without restraints) Performing minimization step: 74. Total energy = 3517.6564 kcal/mol (3516.7746 without restraints) Performing minimization step: 75. Total energy = 3510.2048 kcal/mol (3509.3275 without restraints) Performing minimization step: 76. Total energy = 3502.7904 kcal/mol (3501.9174 without restraints) Performing minimization step: 77. Total energy = 3495.4121 kcal/mol (3494.5433 without restraints) Performing minimization step: 78. Total energy = 3488.0692 kcal/mol (3487.2045 without restraints) Performing minimization step: 79. Total energy = 3480.7607 kcal/mol (3479.9000 without restraints) Performing minimization step: 80. Total energy = 3473.4857 kcal/mol (3472.6290 without restraints) Performing minimization step: 81. Total energy = 3466.2436 kcal/mol (3465.3907 without restraints) Performing minimization step: 82. Total energy = 3459.0336 kcal/mol (3458.1844 without restraints) Performing minimization step: 83. Total energy = 3451.8549 kcal/mol (3451.0094 without restraints) Performing minimization step: 84. Total energy = 3444.7069 kcal/mol (3443.8650 without restraints) Performing minimization step: 85. Total energy = 3437.5889 kcal/mol (3436.7505 without restraints) Performing minimization step: 86. Total energy = 3430.5002 kcal/mol (3429.6653 without restraints) Performing minimization step: 87. Total energy = 3423.4404 kcal/mol (3422.6088 without restraints) Performing minimization step: 88. Total energy = 3416.4088 kcal/mol (3415.5805 without restraints) Performing minimization step: 89. Total energy = 3409.4048 kcal/mol (3408.5797 without restraints) Performing minimization step: 90. Total energy = 3402.4280 kcal/mol (3401.6061 without restraints) Performing minimization step: 91. Total energy = 3395.4778 kcal/mol (3394.6590 without restraints) Performing minimization step: 92. Total energy = 3388.5538 kcal/mol (3387.7380 without restraints) Performing minimization step: 93. Total energy = 3381.6555 kcal/mol (3380.8427 without restraints) Performing minimization step: 94. Total energy = 3374.7824 kcal/mol (3373.9726 without restraints) Performing minimization step: 95. Total energy = 3367.9341 kcal/mol (3367.1273 without restraints) Performing minimization step: 96. Total energy = 3361.1103 kcal/mol (3360.3063 without restraints) Performing minimization step: 97. Total energy = 3354.3105 kcal/mol (3353.5093 without restraints) Performing minimization step: 98. Total energy = 3347.5344 kcal/mol (3346.7359 without restraints) Performing minimization step: 99. Total energy = 3340.7815 kcal/mol (3339.9858 without restraints) Performing minimization step: 100. Total energy = 3334.0516 kcal/mol (3333.2586 without restraints) Writing PDB file: /home/ubuntu/rna-tools/rna_tools/tools/webserver-engine/media/jobs/a01028d0/tmp/C11_refx/C11_refx.pdb ...Done. Performing minimization step: 101. Total energy = 3327.3443 kcal/mol (3326.5540 without restraints) Performing minimization step: 102. Total energy = 3320.6593 kcal/mol (3319.8716 without restraints) Performing minimization step: 103. Total energy = 3313.9963 kcal/mol (3313.2112 without restraints) Performing minimization step: 104. Total energy = 3307.3550 kcal/mol (3306.5724 without restraints) Performing minimization step: 105. Total energy = 3300.7352 kcal/mol (3299.9552 without restraints) Performing minimization step: 106. Total energy = 3294.1365 kcal/mol (3293.3589 without restraints) Performing minimization step: 107. Total energy = 3287.5586 kcal/mol (3286.7834 without restraints) Performing minimization step: 108. Total energy = 3281.0013 kcal/mol (3280.2285 without restraints) Performing minimization step: 109. Total energy = 3274.4643 kcal/mol (3273.6939 without restraints) Performing minimization step: 110. Total energy = 3267.9472 kcal/mol (3267.1792 without restraints) Performing minimization step: 111. Total energy = 3261.4503 kcal/mol (3260.6846 without restraints) Performing minimization step: 112. Total energy = 3254.9730 kcal/mol (3254.2096 without restraints) Performing minimization step: 113. Total energy = 3248.5151 kcal/mol (3247.7540 without restraints) Performing minimization step: 114. Total energy = 3242.0764 kcal/mol (3241.3177 without restraints) Performing minimization step: 115. Total energy = 3235.6570 kcal/mol (3234.9004 without restraints) Performing minimization step: 116. Total energy = 3229.2563 kcal/mol (3228.5019 without restraints) Performing minimization step: 117. Total energy = 3222.8742 kcal/mol (3222.1220 without restraints) Performing minimization step: 118. Total energy = 3216.5107 kcal/mol (3215.7606 without restraints) Performing minimization step: 119. Total energy = 3210.1654 kcal/mol (3209.4175 without restraints) Performing minimization step: 120. Total energy = 3203.8383 kcal/mol (3203.0926 without restraints) Performing minimization step: 121. Total energy = 3197.5294 kcal/mol (3196.7857 without restraints) Performing minimization step: 122. Total energy = 3191.2380 kcal/mol (3190.4965 without restraints) Performing minimization step: 123. Total energy = 3184.9644 kcal/mol (3184.2249 without restraints) Performing minimization step: 124. Total energy = 3178.7082 kcal/mol (3177.9708 without restraints) Performing minimization step: 125. Total energy = 3172.4695 kcal/mol (3171.7341 without restraints) Performing minimization step: 126. Total energy = 3166.2479 kcal/mol (3165.5146 without restraints) Performing minimization step: 127. Total energy = 3160.0434 kcal/mol (3159.3121 without restraints) Performing minimization step: 128. Total energy = 3153.8559 kcal/mol (3153.1266 without restraints) Performing minimization step: 129. Total energy = 3147.6853 kcal/mol (3146.9579 without restraints) Performing minimization step: 130. Total energy = 3141.5313 kcal/mol (3140.8059 without restraints) Performing minimization step: 131. Total energy = 3135.3940 kcal/mol (3134.6705 without restraints) Performing minimization step: 132. Total energy = 3129.2731 kcal/mol (3128.5516 without restraints) Performing minimization step: 133. Total energy = 3123.1685 kcal/mol (3122.4489 without restraints) Performing minimization step: 134. Total energy = 3117.0802 kcal/mol (3116.3625 without restraints) Performing minimization step: 135. Total energy = 3111.0080 kcal/mol (3110.2923 without restraints) Performing minimization step: 136. Total energy = 3104.9519 kcal/mol (3104.2380 without restraints) Performing minimization step: 137. Total energy = 3098.9117 kcal/mol (3098.1996 without restraints) Performing minimization step: 138. Total energy = 3092.8873 kcal/mol (3092.1771 without restraints) Performing minimization step: 139. Total energy = 3086.8786 kcal/mol (3086.1703 without restraints) Performing minimization step: 140. Total energy = 3080.8856 kcal/mol (3080.1791 without restraints) Performing minimization step: 141. Total energy = 3074.9081 kcal/mol (3074.2035 without restraints) Performing minimization step: 142. Total energy = 3068.9461 kcal/mol (3068.2433 without restraints) Performing minimization step: 143. Total energy = 3062.9994 kcal/mol (3062.2984 without restraints) Performing minimization step: 144. Total energy = 3057.0680 kcal/mol (3056.3688 without restraints) Performing minimization step: 145. Total energy = 3051.1519 kcal/mol (3050.4545 without restraints) Performing minimization step: 146. Total energy = 3045.2508 kcal/mol (3044.5552 without restraints) Performing minimization step: 147. Total energy = 3039.3648 kcal/mol (3038.6709 without restraints) Performing minimization step: 148. Total energy = 3033.4937 kcal/mol (3032.8016 without restraints) Performing minimization step: 149. Total energy = 3027.6376 kcal/mol (3026.9472 without restraints) Performing minimization step: 150. Total energy = 3021.7962 kcal/mol (3021.1076 without restraints) Performing minimization step: 151. Total energy = 3015.9695 kcal/mol (3015.2827 without restraints) Performing minimization step: 152. Total energy = 3010.1576 kcal/mol (3009.4724 without restraints) Performing minimization step: 153. Total energy = 3004.3602 kcal/mol (3003.6768 without restraints) Performing minimization step: 154. Total energy = 2998.5775 kcal/mol (2997.8959 without restraints) Performing minimization step: 155. Total energy = 2992.8092 kcal/mol (2992.1292 without restraints) Performing minimization step: 156. Total energy = 2987.0553 kcal/mol (2986.3770 without restraints) Performing minimization step: 157. Total energy = 2981.3157 kcal/mol (2980.6391 without restraints) Performing minimization step: 158. Total energy = 2975.5901 kcal/mol (2974.9152 without restraints) Performing minimization step: 159. Total energy = 2969.8790 kcal/mol (2969.2058 without restraints) Performing minimization step: 160. Total energy = 2964.1819 kcal/mol (2963.5103 without restraints) Performing minimization step: 161. Total energy = 2958.4990 kcal/mol (2957.8290 without restraints) Performing minimization step: 162. Total energy = 2952.8302 kcal/mol (2952.1619 without restraints) Performing minimization step: 163. Total energy = 2947.1753 kcal/mol (2946.5087 without restraints) Performing minimization step: 164. Total energy = 2941.5344 kcal/mol (2940.8695 without restraints) Performing minimization step: 165. Total energy = 2935.9074 kcal/mol (2935.2441 without restraints) Performing minimization step: 166. Total energy = 2930.2944 kcal/mol (2929.6328 without restraints) Performing minimization step: 167. Total energy = 2924.6951 kcal/mol (2924.0350 without restraints) Performing minimization step: 168. Total energy = 2919.1094 kcal/mol (2918.4509 without restraints) Performing minimization step: 169. Total energy = 2913.5374 kcal/mol (2912.8805 without restraints) Performing minimization step: 170. Total energy = 2907.9790 kcal/mol (2907.3237 without restraints) Performing minimization step: 171. Total energy = 2902.4342 kcal/mol (2901.7805 without restraints) Performing minimization step: 172. Total energy = 2896.9029 kcal/mol (2896.2509 without restraints) Performing minimization step: 173. Total energy = 2891.3852 kcal/mol (2890.7347 without restraints) Performing minimization step: 174. Total energy = 2885.8808 kcal/mol (2885.2319 without restraints) Performing minimization step: 175. Total energy = 2880.3899 kcal/mol (2879.7425 without restraints) Performing minimization step: 176. Total energy = 2874.9123 kcal/mol (2874.2665 without restraints) Performing minimization step: 177. Total energy = 2869.4480 kcal/mol (2868.8038 without restraints) Performing minimization step: 178. Total energy = 2863.9970 kcal/mol (2863.3543 without restraints) Performing minimization step: 179. Total energy = 2858.5592 kcal/mol (2857.9181 without restraints) Performing minimization step: 180. Total energy = 2853.1345 kcal/mol (2852.4950 without restraints) Performing minimization step: 181. Total energy = 2847.7231 kcal/mol (2847.0851 without restraints) Performing minimization step: 182. Total energy = 2842.3247 kcal/mol (2841.6883 without restraints) Performing minimization step: 183. Total energy = 2836.9394 kcal/mol (2836.3045 without restraints) Performing minimization step: 184. Total energy = 2831.5671 kcal/mol (2830.9338 without restraints) Performing minimization step: 185. Total energy = 2826.2078 kcal/mol (2825.5760 without restraints) Performing minimization step: 186. Total energy = 2820.8615 kcal/mol (2820.2312 without restraints) Performing minimization step: 187. Total energy = 2815.5282 kcal/mol (2814.8995 without restraints) Performing minimization step: 188. Total energy = 2810.2077 kcal/mol (2809.5804 without restraints) Performing minimization step: 189. Total energy = 2804.8999 kcal/mol (2804.2742 without restraints) Performing minimization step: 190. Total energy = 2799.6050 kcal/mol (2798.9808 without restraints) Performing minimization step: 191. Total energy = 2794.3229 kcal/mol (2793.7002 without restraints) Performing minimization step: 192. Total energy = 2789.0534 kcal/mol (2788.4322 without restraints) Performing minimization step: 193. Total energy = 2783.7967 kcal/mol (2783.1770 without restraints) Performing minimization step: 194. Total energy = 2778.5527 kcal/mol (2777.9344 without restraints) Performing minimization step: 195. Total energy = 2773.3212 kcal/mol (2772.7045 without restraints) Performing minimization step: 196. Total energy = 2768.1024 kcal/mol (2767.4871 without restraints) Performing minimization step: 197. Total energy = 2762.8961 kcal/mol (2762.2824 without restraints) Performing minimization step: 198. Total energy = 2757.7025 kcal/mol (2757.0902 without restraints) Performing minimization step: 199. Total energy = 2752.5213 kcal/mol (2751.9104 without restraints) Performing minimization step: 200. Total energy = 2747.3525 kcal/mol (2746.7432 without restraints) Writing PDB file: /home/ubuntu/rna-tools/rna_tools/tools/webserver-engine/media/jobs/a01028d0/tmp/C11_refx/C11_refx.pdb ...Done. Performing minimization step: 201. Total energy = 2742.1962 kcal/mol (2741.5883 without restraints) Performing minimization step: 202. Total energy = 2737.0523 kcal/mol (2736.4459 without restraints) Performing minimization step: 203. Total energy = 2731.9208 kcal/mol (2731.3158 without restraints) Performing minimization step: 204. Total energy = 2726.8016 kcal/mol (2726.1981 without restraints) Performing minimization step: 205. Total energy = 2721.6948 kcal/mol (2721.0928 without restraints) Performing minimization step: 206. Total energy = 2716.6002 kcal/mol (2715.9996 without restraints) Performing minimization step: 207. Total energy = 2711.5180 kcal/mol (2710.9188 without restraints) Performing minimization step: 208. Total energy = 2706.4479 kcal/mol (2705.8502 without restraints) Performing minimization step: 209. Total energy = 2701.3901 kcal/mol (2700.7938 without restraints) Performing minimization step: 210. Total energy = 2696.3444 kcal/mol (2695.7496 without restraints) Performing minimization step: 211. Total energy = 2691.3109 kcal/mol (2690.7175 without restraints) Performing minimization step: 212. Total energy = 2686.2895 kcal/mol (2685.6975 without restraints) Performing minimization step: 213. Total energy = 2681.2802 kcal/mol (2680.6896 without restraints) Performing minimization step: 214. Total energy = 2676.2829 kcal/mol (2675.6938 without restraints) Performing minimization step: 215. Total energy = 2671.2977 kcal/mol (2670.7100 without restraints) Performing minimization step: 216. Total energy = 2666.3245 kcal/mol (2665.7382 without restraints) Performing minimization step: 217. Total energy = 2661.3633 kcal/mol (2660.7784 without restraints) Performing minimization step: 218. Total energy = 2656.4141 kcal/mol (2655.8306 without restraints) Performing minimization step: 219. Total energy = 2651.4766 kcal/mol (2650.8945 without restraints) Performing minimization step: 220. Total energy = 2646.5512 kcal/mol (2645.9705 without restraints) Performing minimization step: 221. Total energy = 2641.6372 kcal/mol (2641.0580 without restraints) Performing minimization step: 222. Total energy = 2636.7356 kcal/mol (2636.1578 without restraints) Performing minimization step: 223. Total energy = 2631.8458 kcal/mol (2631.2694 without restraints) Performing minimization step: 224. Total energy = 2626.9678 kcal/mol (2626.3928 without restraints) Performing minimization step: 225. Total energy = 2622.1016 kcal/mol (2621.5279 without restraints) Performing minimization step: 226. Total energy = 2617.2472 kcal/mol (2616.6749 without restraints) Performing minimization step: 227. Total energy = 2612.4044 kcal/mol (2611.8335 without restraints) Performing minimization step: 228. Total energy = 2607.5734 kcal/mol (2607.0039 without restraints) Performing minimization step: 229. Total energy = 2602.7541 kcal/mol (2602.1859 without restraints) Performing minimization step: 230. Total energy = 2597.9464 kcal/mol (2597.3796 without restraints) Performing minimization step: 231. Total energy = 2593.1504 kcal/mol (2592.5850 without restraints) Performing minimization step: 232. Total energy = 2588.3660 kcal/mol (2587.8019 without restraints) Performing minimization step: 233. Total energy = 2583.5932 kcal/mol (2583.0305 without restraints) Performing minimization step: 234. Total energy = 2578.8319 kcal/mol (2578.2706 without restraints) Performing minimization step: 235. Total energy = 2574.0822 kcal/mol (2573.5223 without restraints) Performing minimization step: 236. Total energy = 2569.3440 kcal/mol (2568.7854 without restraints) Performing minimization step: 237. Total energy = 2564.6173 kcal/mol (2564.0601 without restraints) Performing minimization step: 238. Total energy = 2559.9022 kcal/mol (2559.3463 without restraints) Performing minimization step: 239. Total energy = 2555.1984 kcal/mol (2554.6439 without restraints) Performing minimization step: 240. Total energy = 2550.5061 kcal/mol (2549.9529 without restraints) Performing minimization step: 241. Total energy = 2545.8252 kcal/mol (2545.2733 without restraints) Performing minimization step: 242. Total energy = 2541.1556 kcal/mol (2540.6052 without restraints) Performing minimization step: 243. Total energy = 2536.4975 kcal/mol (2535.9483 without restraints) Performing minimization step: 244. Total energy = 2531.8507 kcal/mol (2531.3029 without restraints) Performing minimization step: 245. Total energy = 2527.2152 kcal/mol (2526.6687 without restraints) Performing minimization step: 246. Total energy = 2522.5910 kcal/mol (2522.0458 without restraints) Performing minimization step: 247. Total energy = 2517.9781 kcal/mol (2517.4342 without restraints) Performing minimization step: 248. Total energy = 2513.3764 kcal/mol (2512.8339 without restraints) Performing minimization step: 249. Total energy = 2508.7860 kcal/mol (2508.2448 without restraints) Performing minimization step: 250. Total energy = 2504.2067 kcal/mol (2503.6669 without restraints) Performing minimization step: 251. Total energy = 2499.6387 kcal/mol (2499.1002 without restraints) Performing minimization step: 252. Total energy = 2495.0817 kcal/mol (2494.5445 without restraints) Performing minimization step: 253. Total energy = 2490.5362 kcal/mol (2490.0003 without restraints) Performing minimization step: 254. Total energy = 2486.0016 kcal/mol (2485.4670 without restraints) Performing minimization step: 255. Total energy = 2481.4781 kcal/mol (2480.9449 without restraints) Performing minimization step: 256. Total energy = 2476.9657 kcal/mol (2476.4338 without restraints) Performing minimization step: 257. Total energy = 2472.4644 kcal/mol (2471.9338 without restraints) Performing minimization step: 258. Total energy = 2467.9742 kcal/mol (2467.4448 without restraints) Performing minimization step: 259. Total energy = 2463.4949 kcal/mol (2462.9669 without restraints) Performing minimization step: 260. Total energy = 2459.0267 kcal/mol (2458.4999 without restraints) Performing minimization step: 261. Total energy = 2454.5694 kcal/mol (2454.0440 without restraints) Performing minimization step: 262. Total energy = 2450.1231 kcal/mol (2449.5989 without restraints) Performing minimization step: 263. Total energy = 2445.6878 kcal/mol (2445.1649 without restraints) Performing minimization step: 264. Total energy = 2441.2633 kcal/mol (2440.7417 without restraints) Performing minimization step: 265. Total energy = 2436.8500 kcal/mol (2436.3297 without restraints) Performing minimization step: 266. Total energy = 2432.4474 kcal/mol (2431.9283 without restraints) Performing minimization step: 267. Total energy = 2428.0556 kcal/mol (2427.5378 without restraints) Performing minimization step: 268. Total energy = 2423.6746 kcal/mol (2423.1582 without restraints) Performing minimization step: 269. Total energy = 2419.3045 kcal/mol (2418.7893 without restraints) Performing minimization step: 270. Total energy = 2414.9452 kcal/mol (2414.4313 without restraints) Performing minimization step: 271. Total energy = 2410.5967 kcal/mol (2410.0840 without restraints) Performing minimization step: 272. Total energy = 2406.2589 kcal/mol (2405.7475 without restraints) Performing minimization step: 273. Total energy = 2401.9319 kcal/mol (2401.4218 without restraints) Performing minimization step: 274. Total energy = 2397.6155 kcal/mol (2397.1067 without restraints) Performing minimization step: 275. Total energy = 2393.3099 kcal/mol (2392.8024 without restraints) Performing minimization step: 276. Total energy = 2389.0150 kcal/mol (2388.5087 without restraints) Performing minimization step: 277. Total energy = 2384.7307 kcal/mol (2384.2257 without restraints) Performing minimization step: 278. Total energy = 2380.4574 kcal/mol (2379.9536 without restraints) Performing minimization step: 279. Total energy = 2376.1943 kcal/mol (2375.6917 without restraints) Performing minimization step: 280. Total energy = 2371.9418 kcal/mol (2371.4405 without restraints) Performing minimization step: 281. Total energy = 2367.7000 kcal/mol (2367.2000 without restraints) Performing minimization step: 282. Total energy = 2363.4688 kcal/mol (2362.9700 without restraints) Performing minimization step: 283. Total energy = 2359.2481 kcal/mol (2358.7505 without restraints) Performing minimization step: 284. Total energy = 2355.0377 kcal/mol (2354.5413 without restraints) Performing minimization step: 285. Total energy = 2350.8380 kcal/mol (2350.3429 without restraints) Performing minimization step: 286. Total energy = 2346.6488 kcal/mol (2346.1550 without restraints) Performing minimization step: 287. Total energy = 2342.4701 kcal/mol (2341.9775 without restraints) Performing minimization step: 288. Total energy = 2338.3018 kcal/mol (2337.8105 without restraints) Performing minimization step: 289. Total energy = 2334.1440 kcal/mol (2333.6539 without restraints) Performing minimization step: 290. Total energy = 2329.9966 kcal/mol (2329.5077 without restraints) Performing minimization step: 291. Total energy = 2325.8596 kcal/mol (2325.3719 without restraints) Performing minimization step: 292. Total energy = 2321.7330 kcal/mol (2321.2465 without restraints) Performing minimization step: 293. Total energy = 2317.6167 kcal/mol (2317.1314 without restraints) Performing minimization step: 294. Total energy = 2313.5107 kcal/mol (2313.0267 without restraints) Performing minimization step: 295. Total energy = 2309.4151 kcal/mol (2308.9323 without restraints) Performing minimization step: 296. Total energy = 2305.3298 kcal/mol (2304.8482 without restraints) Performing minimization step: 297. Total energy = 2301.2547 kcal/mol (2300.7743 without restraints) Performing minimization step: 298. Total energy = 2297.1899 kcal/mol (2296.7107 without restraints) Performing minimization step: 299. Total energy = 2293.1353 kcal/mol (2292.6574 without restraints) Performing minimization step: 300. Total energy = 2289.0910 kcal/mol (2288.6142 without restraints) Writing PDB file: /home/ubuntu/rna-tools/rna_tools/tools/webserver-engine/media/jobs/a01028d0/tmp/C11_refx/C11_refx.pdb ...Done. Performing minimization step: 301. Total energy = 2285.0569 kcal/mol (2284.5813 without restraints) Performing minimization step: 302. Total energy = 2281.0329 kcal/mol (2280.5586 without restraints) Performing minimization step: 303. Total energy = 2277.0191 kcal/mol (2276.5460 without restraints) Performing minimization step: 304. Total energy = 2273.0155 kcal/mol (2272.5435 without restraints) Performing minimization step: 305. Total energy = 2269.0220 kcal/mol (2268.5512 without restraints) Performing minimization step: 306. Total energy = 2265.0386 kcal/mol (2264.5690 without restraints) Performing minimization step: 307. Total energy = 2261.0653 kcal/mol (2260.5969 without restraints) Performing minimization step: 308. Total energy = 2257.1021 kcal/mol (2256.6349 without restraints) Performing minimization step: 309. Total energy = 2253.1489 kcal/mol (2252.6829 without restraints) Performing minimization step: 310. Total energy = 2249.2057 kcal/mol (2248.7409 without restraints) Performing minimization step: 311. Total energy = 2245.2726 kcal/mol (2244.8089 without restraints) Performing minimization step: 312. Total energy = 2241.3494 kcal/mol (2240.8870 without restraints) Performing minimization step: 313. Total energy = 2237.4363 kcal/mol (2236.9750 without restraints) Performing minimization step: 314. Total energy = 2233.5331 kcal/mol (2233.0729 without restraints) Performing minimization step: 315. Total energy = 2229.6398 kcal/mol (2229.1808 without restraints) Performing minimization step: 316. Total energy = 2225.7564 kcal/mol (2225.2987 without restraints) Performing minimization step: 317. Total energy = 2221.8830 kcal/mol (2221.4264 without restraints) Performing minimization step: 318. Total energy = 2218.0194 kcal/mol (2217.5640 without restraints) Performing minimization step: 319. Total energy = 2214.1657 kcal/mol (2213.7114 without restraints) Performing minimization step: 320. Total energy = 2210.3219 kcal/mol (2209.8687 without restraints) Performing minimization step: 321. Total energy = 2206.4878 kcal/mol (2206.0359 without restraints) Performing minimization step: 322. Total energy = 2202.6637 kcal/mol (2202.2130 without restraints) Performing minimization step: 323. Total energy = 2198.8493 kcal/mol (2198.3997 without restraints) Performing minimization step: 324. Total energy = 2195.0447 kcal/mol (2194.5962 without restraints) Performing minimization step: 325. Total energy = 2191.2498 kcal/mol (2190.8024 without restraints) Performing minimization step: 326. Total energy = 2187.4646 kcal/mol (2187.0184 without restraints) Performing minimization step: 327. Total energy = 2183.6891 kcal/mol (2183.2441 without restraints) Performing minimization step: 328. Total energy = 2179.9234 kcal/mol (2179.4795 without restraints) Performing minimization step: 329. Total energy = 2176.1673 kcal/mol (2175.7245 without restraints) Performing minimization step: 330. Total energy = 2172.4209 kcal/mol (2171.9792 without restraints) Performing minimization step: 331. Total energy = 2168.6841 kcal/mol (2168.2436 without restraints) Performing minimization step: 332. Total energy = 2164.9569 kcal/mol (2164.5175 without restraints) Performing minimization step: 333. Total energy = 2161.2393 kcal/mol (2160.8011 without restraints) Performing minimization step: 334. Total energy = 2157.5313 kcal/mol (2157.0942 without restraints) Performing minimization step: 335. Total energy = 2153.8329 kcal/mol (2153.3969 without restraints) Performing minimization step: 336. Total energy = 2150.1443 kcal/mol (2149.7094 without restraints) Performing minimization step: 337. Total energy = 2146.4649 kcal/mol (2146.0312 without restraints) Performing minimization step: 338. Total energy = 2142.7953 kcal/mol (2142.3627 without restraints) Performing minimization step: 339. Total energy = 2139.1349 kcal/mol (2138.7034 without restraints) Performing minimization step: 340. Total energy = 2135.4840 kcal/mol (2135.0537 without restraints) Performing minimization step: 341. Total energy = 2131.8426 kcal/mol (2131.4134 without restraints) Performing minimization step: 342. Total energy = 2128.2106 kcal/mol (2127.7825 without restraints) Performing minimization step: 343. Total energy = 2124.5880 kcal/mol (2124.1610 without restraints) Performing minimization step: 344. Total energy = 2120.9748 kcal/mol (2120.5489 without restraints) Performing minimization step: 345. Total energy = 2117.3710 kcal/mol (2116.9462 without restraints) Performing minimization step: 346. Total energy = 2113.7766 kcal/mol (2113.3529 without restraints) Performing minimization step: 347. Total energy = 2110.1915 kcal/mol (2109.7688 without restraints) Performing minimization step: 348. Total energy = 2106.6157 kcal/mol (2106.1941 without restraints) Performing minimization step: 349. Total energy = 2103.0492 kcal/mol (2102.6287 without restraints) Performing minimization step: 350. Total energy = 2099.4920 kcal/mol (2099.0726 without restraints) Performing minimization step: 351. Total energy = 2095.9442 kcal/mol (2095.5259 without restraints) Performing minimization step: 352. Total energy = 2092.4055 kcal/mol (2091.9883 without restraints) Performing minimization step: 353. Total energy = 2088.8762 kcal/mol (2088.4602 without restraints) Performing minimization step: 354. Total energy = 2085.3560 kcal/mol (2084.9410 without restraints) Performing minimization step: 355. Total energy = 2081.8447 kcal/mol (2081.4308 without restraints) Performing minimization step: 356. Total energy = 2078.3430 kcal/mol (2077.9302 without restraints) Performing minimization step: 357. Total energy = 2074.8502 kcal/mol (2074.4385 without restraints) Performing minimization step: 358. Total energy = 2071.3666 kcal/mol (2070.9559 without restraints) Performing minimization step: 359. Total energy = 2067.8920 kcal/mol (2067.4825 without restraints) Performing minimization step: 360. Total energy = 2064.4264 kcal/mol (2064.0179 without restraints) Performing minimization step: 361. Total energy = 2060.9700 kcal/mol (2060.5626 without restraints) Performing minimization step: 362. Total energy = 2057.5228 kcal/mol (2057.1164 without restraints) Performing minimization step: 363. Total energy = 2054.0845 kcal/mol (2053.6792 without restraints) Performing minimization step: 364. Total energy = 2050.6553 kcal/mol (2050.2510 without restraints) Performing minimization step: 365. Total energy = 2047.2350 kcal/mol (2046.8318 without restraints) Performing minimization step: 366. Total energy = 2043.8238 kcal/mol (2043.4216 without restraints) Performing minimization step: 367. Total energy = 2040.4214 kcal/mol (2040.0204 without restraints) Performing minimization step: 368. Total energy = 2037.0281 kcal/mol (2036.6281 without restraints) Performing minimization step: 369. Total energy = 2033.6436 kcal/mol (2033.2447 without restraints) Performing minimization step: 370. Total energy = 2030.2681 kcal/mol (2029.8701 without restraints) Performing minimization step: 371. Total energy = 2026.9014 kcal/mol (2026.5045 without restraints) Performing minimization step: 372. Total energy = 2023.5436 kcal/mol (2023.1478 without restraints) Performing minimization step: 373. Total energy = 2020.1948 kcal/mol (2019.8001 without restraints) Performing minimization step: 374. Total energy = 2016.8547 kcal/mol (2016.4610 without restraints) Performing minimization step: 375. Total energy = 2013.5234 kcal/mol (2013.1307 without restraints) Performing minimization step: 376. Total energy = 2010.2009 kcal/mol (2009.8092 without restraints) Performing minimization step: 377. Total energy = 2006.8871 kcal/mol (2006.4965 without restraints) Performing minimization step: 378. Total energy = 2003.5823 kcal/mol (2003.1927 without restraints) Performing minimization step: 379. Total energy = 2000.2860 kcal/mol (1999.8974 without restraints) Performing minimization step: 380. Total energy = 1996.9987 kcal/mol (1996.6111 without restraints) Performing minimization step: 381. Total energy = 1993.7197 kcal/mol (1993.3332 without restraints) Performing minimization step: 382. Total energy = 1990.4495 kcal/mol (1990.0640 without restraints) Performing minimization step: 383. Total energy = 1987.1880 kcal/mol (1986.8035 without restraints) Performing minimization step: 384. Total energy = 1983.9350 kcal/mol (1983.5516 without restraints) Performing minimization step: 385. Total energy = 1980.6907 kcal/mol (1980.3083 without restraints) Performing minimization step: 386. Total energy = 1977.4550 kcal/mol (1977.0736 without restraints) Performing minimization step: 387. Total energy = 1974.2278 kcal/mol (1973.8474 without restraints) Performing minimization step: 388. Total energy = 1971.0092 kcal/mol (1970.6298 without restraints) Performing minimization step: 389. Total energy = 1967.7991 kcal/mol (1967.4208 without restraints) Performing minimization step: 390. Total energy = 1964.5976 kcal/mol (1964.2202 without restraints) Performing minimization step: 391. Total energy = 1961.4045 kcal/mol (1961.0281 without restraints) Performing minimization step: 392. Total energy = 1958.2200 kcal/mol (1957.8446 without restraints) Performing minimization step: 393. Total energy = 1955.0438 kcal/mol (1954.6695 without restraints) Performing minimization step: 394. Total energy = 1951.8762 kcal/mol (1951.5028 without restraints) Performing minimization step: 395. Total energy = 1948.7169 kcal/mol (1948.3445 without restraints) Performing minimization step: 396. Total energy = 1945.5661 kcal/mol (1945.1946 without restraints) Performing minimization step: 397. Total energy = 1942.4236 kcal/mol (1942.0532 without restraints) Performing minimization step: 398. Total energy = 1939.2895 kcal/mol (1938.9200 without restraints) Performing minimization step: 399. Total energy = 1936.1637 kcal/mol (1935.7952 without restraints) Performing minimization step: 400. Total energy = 1933.0462 kcal/mol (1932.6787 without restraints) Writing PDB file: /home/ubuntu/rna-tools/rna_tools/tools/webserver-engine/media/jobs/a01028d0/tmp/C11_refx/C11_refx.pdb ...Done. Performing minimization step: 401. Total energy = 1929.9370 kcal/mol (1929.5705 without restraints) Performing minimization step: 402. Total energy = 1926.8362 kcal/mol (1926.4706 without restraints) Performing minimization step: 403. Total energy = 1923.7436 kcal/mol (1923.3790 without restraints) Performing minimization step: 404. Total energy = 1920.6592 kcal/mol (1920.2956 without restraints) Performing minimization step: 405. Total energy = 1917.5829 kcal/mol (1917.2203 without restraints) Performing minimization step: 406. Total energy = 1914.5149 kcal/mol (1914.1533 without restraints) Performing minimization step: 407. Total energy = 1911.4552 kcal/mol (1911.0945 without restraints) Performing minimization step: 408. Total energy = 1908.4036 kcal/mol (1908.0438 without restraints) Performing minimization step: 409. Total energy = 1905.3601 kcal/mol (1905.0013 without restraints) Performing minimization step: 410. Total energy = 1902.3250 kcal/mol (1901.9672 without restraints) Performing minimization step: 411. Total energy = 1899.2978 kcal/mol (1898.9409 without restraints) Performing minimization step: 412. Total energy = 1896.2786 kcal/mol (1895.9227 without restraints) Performing minimization step: 413. Total energy = 1893.2676 kcal/mol (1892.9126 without restraints) Performing minimization step: 414. Total energy = 1890.2645 kcal/mol (1889.9106 without restraints) Performing minimization step: 415. Total energy = 1887.2695 kcal/mol (1886.9165 without restraints) Performing minimization step: 416. Total energy = 1884.2824 kcal/mol (1883.9302 without restraints) Performing minimization step: 417. Total energy = 1881.3033 kcal/mol (1880.9521 without restraints) Performing minimization step: 418. Total energy = 1878.3322 kcal/mol (1877.9820 without restraints) Performing minimization step: 419. Total energy = 1875.3691 kcal/mol (1875.0198 without restraints) Performing minimization step: 420. Total energy = 1872.4139 kcal/mol (1872.0656 without restraints) Performing minimization step: 421. Total energy = 1869.4666 kcal/mol (1869.1192 without restraints) Performing minimization step: 422. Total energy = 1866.5272 kcal/mol (1866.1807 without restraints) Performing minimization step: 423. Total energy = 1863.5956 kcal/mol (1863.2501 without restraints) Performing minimization step: 424. Total energy = 1860.6719 kcal/mol (1860.3273 without restraints) Performing minimization step: 425. Total energy = 1857.7561 kcal/mol (1857.4124 without restraints) Performing minimization step: 426. Total energy = 1854.8480 kcal/mol (1854.5052 without restraints) Performing minimization step: 427. Total energy = 1851.9477 kcal/mol (1851.6058 without restraints) Performing minimization step: 428. Total energy = 1849.0552 kcal/mol (1848.7142 without restraints) Performing minimization step: 429. Total energy = 1846.1704 kcal/mol (1845.8303 without restraints) Performing minimization step: 430. Total energy = 1843.2933 kcal/mol (1842.9542 without restraints) Performing minimization step: 431. Total energy = 1840.4240 kcal/mol (1840.0858 without restraints) Performing minimization step: 432. Total energy = 1837.5625 kcal/mol (1837.2252 without restraints) Performing minimization step: 433. Total energy = 1834.7085 kcal/mol (1834.3721 without restraints) Performing minimization step: 434. Total energy = 1831.8621 kcal/mol (1831.5266 without restraints) Performing minimization step: 435. Total energy = 1829.0234 kcal/mol (1828.6888 without restraints) Performing minimization step: 436. Total energy = 1826.1922 kcal/mol (1825.8585 without restraints) Performing minimization step: 437. Total energy = 1823.3684 kcal/mol (1823.0355 without restraints) Performing minimization step: 438. Total energy = 1820.5524 kcal/mol (1820.2204 without restraints) Performing minimization step: 439. Total energy = 1817.7439 kcal/mol (1817.4128 without restraints) Performing minimization step: 440. Total energy = 1814.9429 kcal/mol (1814.6128 without restraints) Performing minimization step: 441. Total energy = 1812.1495 kcal/mol (1811.8202 without restraints) Performing minimization step: 442. Total energy = 1809.3633 kcal/mol (1809.0349 without restraints) Performing minimization step: 443. Total energy = 1806.5848 kcal/mol (1806.2573 without restraints) Performing minimization step: 444. Total energy = 1803.8137 kcal/mol (1803.4871 without restraints) Performing minimization step: 445. Total energy = 1801.0500 kcal/mol (1800.7243 without restraints) Performing minimization step: 446. Total energy = 1798.2938 kcal/mol (1797.9689 without restraints) Performing minimization step: 447. Total energy = 1795.5449 kcal/mol (1795.2209 without restraints) Performing minimization step: 448. Total energy = 1792.8034 kcal/mol (1792.4802 without restraints) Performing minimization step: 449. Total energy = 1790.0692 kcal/mol (1789.7469 without restraints) Performing minimization step: 450. Total energy = 1787.3423 kcal/mol (1787.0209 without restraints) Performing minimization step: 451. Total energy = 1784.6227 kcal/mol (1784.3022 without restraints) Performing minimization step: 452. Total energy = 1781.9104 kcal/mol (1781.5907 without restraints) Performing minimization step: 453. Total energy = 1779.2054 kcal/mol (1778.8865 without restraints) Performing minimization step: 454. Total energy = 1776.5076 kcal/mol (1776.1895 without restraints) Performing minimization step: 455. Total energy = 1773.8170 kcal/mol (1773.4998 without restraints) Performing minimization step: 456. Total energy = 1771.1336 kcal/mol (1770.8173 without restraints) Performing minimization step: 457. Total energy = 1768.4573 kcal/mol (1768.1419 without restraints) Performing minimization step: 458. Total energy = 1765.7880 kcal/mol (1765.4734 without restraints) Performing minimization step: 459. Total energy = 1763.1260 kcal/mol (1762.8122 without restraints) Performing minimization step: 460. Total energy = 1760.4712 kcal/mol (1760.1582 without restraints) Performing minimization step: 461. Total energy = 1757.8235 kcal/mol (1757.5114 without restraints) Performing minimization step: 462. Total energy = 1755.1828 kcal/mol (1754.8715 without restraints) Performing minimization step: 463. Total energy = 1752.5491 kcal/mol (1752.2387 without restraints) Performing minimization step: 464. Total energy = 1749.9226 kcal/mol (1749.6130 without restraints) Performing minimization step: 465. Total energy = 1747.3030 kcal/mol (1746.9942 without restraints) Performing minimization step: 466. Total energy = 1744.6904 kcal/mol (1744.3824 without restraints) Performing minimization step: 467. Total energy = 1742.0847 kcal/mol (1741.7776 without restraints) Performing minimization step: 468. Total energy = 1739.4860 kcal/mol (1739.1797 without restraints) Performing minimization step: 469. Total energy = 1736.8942 kcal/mol (1736.5887 without restraints) Performing minimization step: 470. Total energy = 1734.3094 kcal/mol (1734.0047 without restraints) Performing minimization step: 471. Total energy = 1731.7314 kcal/mol (1731.4275 without restraints) Performing minimization step: 472. Total energy = 1729.1603 kcal/mol (1728.8572 without restraints) Performing minimization step: 473. Total energy = 1726.5960 kcal/mol (1726.2937 without restraints) Performing minimization step: 474. Total energy = 1724.0385 kcal/mol (1723.7371 without restraints) Performing minimization step: 475. Total energy = 1721.4879 kcal/mol (1721.1872 without restraints) Performing minimization step: 476. Total energy = 1718.9440 kcal/mol (1718.6441 without restraints) Performing minimization step: 477. Total energy = 1716.4069 kcal/mol (1716.1078 without restraints) Performing minimization step: 478. Total energy = 1713.8765 kcal/mol (1713.5782 without restraints) Performing minimization step: 479. Total energy = 1711.3528 kcal/mol (1711.0554 without restraints) Performing minimization step: 480. Total energy = 1708.8359 kcal/mol (1708.5392 without restraints) Performing minimization step: 481. Total energy = 1706.3256 kcal/mol (1706.0297 without restraints) Performing minimization step: 482. Total energy = 1703.8220 kcal/mol (1703.5268 without restraints) Performing minimization step: 483. Total energy = 1701.3250 kcal/mol (1701.0306 without restraints) Performing minimization step: 484. Total energy = 1698.8348 kcal/mol (1698.5413 without restraints) Performing minimization step: 485. Total energy = 1696.3510 kcal/mol (1696.0582 without restraints) Performing minimization step: 486. Total energy = 1693.8738 kcal/mol (1693.5818 without restraints) Performing minimization step: 487. Total energy = 1691.4032 kcal/mol (1691.1119 without restraints) Performing minimization step: 488. Total energy = 1688.9390 kcal/mol (1688.6486 without restraints) Performing minimization step: 489. Total energy = 1686.4814 kcal/mol (1686.1917 without restraints) Performing minimization step: 490. Total energy = 1684.0303 kcal/mol (1683.7414 without restraints) Performing minimization step: 491. Total energy = 1681.5856 kcal/mol (1681.2975 without restraints) Performing minimization step: 492. Total energy = 1679.1474 kcal/mol (1678.8600 without restraints) Performing minimization step: 493. Total energy = 1676.7157 kcal/mol (1676.4290 without restraints) Performing minimization step: 494. Total energy = 1674.2905 kcal/mol (1674.0046 without restraints) Performing minimization step: 495. Total energy = 1671.8715 kcal/mol (1671.5864 without restraints) Performing minimization step: 496. Total energy = 1669.4589 kcal/mol (1669.1745 without restraints) Performing minimization step: 497. Total energy = 1667.0526 kcal/mol (1666.7690 without restraints) Performing minimization step: 498. Total energy = 1664.6527 kcal/mol (1664.3698 without restraints) Performing minimization step: 499. Total energy = 1662.2591 kcal/mol (1661.9769 without restraints) Performing minimization step: 500. Total energy = 1659.8717 kcal/mol (1659.5903 without restraints) Writing PDB file: /home/ubuntu/rna-tools/rna_tools/tools/webserver-engine/media/jobs/a01028d0/tmp/C11_refx/C11_refx.pdb ...Done. Performing minimization step: 501. Total energy = 1657.4906 kcal/mol (1657.2100 without restraints) Performing minimization step: 502. Total energy = 1655.1158 kcal/mol (1654.8359 without restraints) Performing minimization step: 503. Total energy = 1652.7472 kcal/mol (1652.4680 without restraints) Performing minimization step: 504. Total energy = 1650.3848 kcal/mol (1650.1063 without restraints) Performing minimization step: 505. Total energy = 1648.0287 kcal/mol (1647.7510 without restraints) Performing minimization step: 506. Total energy = 1645.6787 kcal/mol (1645.4017 without restraints) Performing minimization step: 507. Total energy = 1643.3348 kcal/mol (1643.0585 without restraints) Performing minimization step: 508. Total energy = 1640.9970 kcal/mol (1640.7214 without restraints) Performing minimization step: 509. Total energy = 1638.6652 kcal/mol (1638.3904 without restraints) Performing minimization step: 510. Total energy = 1636.3396 kcal/mol (1636.0655 without restraints) Performing minimization step: 511. Total energy = 1634.0200 kcal/mol (1633.7466 without restraints) Performing minimization step: 512. Total energy = 1631.7065 kcal/mol (1631.4338 without restraints) Performing minimization step: 513. Total energy = 1629.3990 kcal/mol (1629.1270 without restraints) Performing minimization step: 514. Total energy = 1627.0975 kcal/mol (1626.8262 without restraints) Performing minimization step: 515. Total energy = 1624.8024 kcal/mol (1624.5318 without restraints) Performing minimization step: 516. Total energy = 1622.5128 kcal/mol (1622.2429 without restraints) Performing minimization step: 517. Total energy = 1620.2292 kcal/mol (1619.9600 without restraints) Performing minimization step: 518. Total energy = 1617.9514 kcal/mol (1617.6829 without restraints) Performing minimization step: 519. Total energy = 1615.6796 kcal/mol (1615.4118 without restraints) Performing minimization step: 520. Total energy = 1613.4136 kcal/mol (1613.1465 without restraints) Performing minimization step: 521. Total energy = 1611.1535 kcal/mol (1610.8871 without restraints) Performing minimization step: 522. Total energy = 1608.8993 kcal/mol (1608.6335 without restraints) Performing minimization step: 523. Total energy = 1606.6508 kcal/mol (1606.3858 without restraints) Performing minimization step: 524. Total energy = 1604.4081 kcal/mol (1604.1438 without restraints) Performing minimization step: 525. Total energy = 1602.1710 kcal/mol (1601.9073 without restraints) Performing minimization step: 526. Total energy = 1599.9399 kcal/mol (1599.6769 without restraints) Performing minimization step: 527. Total energy = 1597.7145 kcal/mol (1597.4522 without restraints) Performing minimization step: 528. Total energy = 1595.4948 kcal/mol (1595.2331 without restraints) Killed /home/ubuntu/rna-tools//opt/qrnas/ Save to C11_refx.pdb DONE!