============================================================================= Reading config file: /home/ubuntu/rna-tools/rna_tools/tools/webserver-engine/media/jobs/6b8f1efc/tmp/mir222m2ref_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/6b8f1efc/tmp/mir222m2ref_refx/mir222m2ref.pdb ============================================================================= Atom's 3506 H3' residue renamed to RU3 Atom's 3505 HO'2 residue renamed to RU3 Atom's 3504 H2' residue renamed to RU3 Atom's 3503 H5 residue renamed to RU3 Atom's 3502 H3 residue renamed to RU3 Atom's 3501 H6 residue renamed to RU3 Atom's 3500 H1' residue renamed to RU3 Atom's 3499 H4' residue renamed to RU3 Atom's 3498 H5'2 residue renamed to RU3 Atom's 3497 H5'1 residue renamed to RU3 Atom's 3496 C6 residue renamed to RU3 Atom's 3495 C5 residue renamed to RU3 Atom's 3494 O4 residue renamed to RU3 Atom's 3493 C4 residue renamed to RU3 Atom's 3492 N3 residue renamed to RU3 Atom's 3491 O2 residue renamed to RU3 Atom's 3490 C2 residue renamed to RU3 Atom's 3489 N1 residue renamed to RU3 Atom's 3488 O2' residue renamed to RU3 Atom's 3487 C2' residue renamed to RU3 Atom's 3486 C1' residue renamed to RU3 Atom's 3485 O4' residue renamed to RU3 Atom's 3484 P residue renamed to RU3 Atom's 3483 OP2 residue renamed to RU3 Atom's 3482 OP1 residue renamed to RU3 Atom's 3481 O3' residue renamed to RU3 Atom's 3480 C3' residue renamed to RU3 Atom's 3479 C4' residue renamed to RU3 Atom's 3478 C5' residue renamed to RU3 Atom's 3477 O5' residue renamed to RU3 Missing atom added: ATOM 31 H3T RU3 A 110 -16.119 -48.734 -46.202 1.00 0.00 H Missing atom added: ATOM 7 OP3 G A 1 -8.849 -36.040 -54.390 1.00 0.00 Number of atoms: 3508 Number of residues: 110 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: 3777 Number of angles built: 6765 Number of dihedrals built: 10303 Number of impropers built: 739 ----------------------------------------------------------------------------- End of molecule (chain) ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Building interresidual nonbonded pairs & H-bonds (it may take a while)... Number of electrostatic pairs: 6140736 Number of van der Waals pairs: 424299 Number of H-bonds built: 117 Number of spring restraints: 0 Number of positional restraints: 0 Number of base pairs built: 34 Number of molecules (chains) read: 1 ----------------------------------------------------------------------------- Performing minimization step: 1. Total energy = 112621.6843 kcal/mol (112580.9066 without restraints) Performing minimization step: 2. Total energy = 112526.6201 kcal/mol (112485.8536 without restraints) Performing minimization step: 3. Total energy = 112431.6253 kcal/mol (112390.8701 without restraints) Performing minimization step: 4. Total energy = 112336.7002 kcal/mol (112295.9564 without restraints) Performing minimization step: 5. Total energy = 112241.8439 kcal/mol (112201.1113 without restraints) Performing minimization step: 6. Total energy = 112147.0572 kcal/mol (112106.3360 without restraints) Performing minimization step: 7. Total energy = 112052.3399 kcal/mol (112011.6299 without restraints) Performing minimization step: 8. Total energy = 111957.6912 kcal/mol (111916.9924 without restraints) Performing minimization step: 9. Total energy = 111863.1122 kcal/mol (111822.4248 without restraints) Performing minimization step: 10. Total energy = 111768.6030 kcal/mol (111727.9269 without restraints) Performing minimization step: 11. Total energy = 111674.1627 kcal/mol (111633.4979 without restraints) Performing minimization step: 12. Total energy = 111579.7919 kcal/mol (111539.1382 without restraints) Performing minimization step: 13. Total energy = 111485.4899 kcal/mol (111444.8476 without restraints) Performing minimization step: 14. Total energy = 111391.2572 kcal/mol (111350.6261 without restraints) Performing minimization step: 15. Total energy = 111297.0937 kcal/mol (111256.4738 without restraints) Performing minimization step: 16. Total energy = 111202.9989 kcal/mol (111162.3902 without restraints) Performing minimization step: 17. Total energy = 111108.9734 kcal/mol (111068.3762 without restraints) Performing minimization step: 18. Total energy = 111015.0171 kcal/mol (110974.4310 without restraints) Performing minimization step: 19. Total energy = 110921.1300 kcal/mol (110880.5552 without restraints) Performing minimization step: 20. Total energy = 110827.3122 kcal/mol (110786.7486 without restraints) Performing minimization step: 21. Total energy = 110733.5629 kcal/mol (110693.0106 without restraints) Performing minimization step: 22. Total energy = 110639.8830 kcal/mol (110599.3419 without restraints) Performing minimization step: 23. Total energy = 110546.2722 kcal/mol (110505.7424 without restraints) Performing minimization step: 24. Total energy = 110452.7302 kcal/mol (110412.2116 without restraints) Performing minimization step: 25. Total energy = 110359.2575 kcal/mol (110318.7500 without restraints) Performing minimization step: 26. Total energy = 110265.8529 kcal/mol (110225.3567 without restraints) Performing minimization step: 27. Total energy = 110172.5180 kcal/mol (110132.0330 without restraints) Performing minimization step: 28. Total energy = 110079.2517 kcal/mol (110038.7779 without restraints) Performing minimization step: 29. Total energy = 109986.0547 kcal/mol (109945.5921 without restraints) Performing minimization step: 30. Total energy = 109892.9261 kcal/mol (109852.4747 without restraints) Performing minimization step: 31. Total energy = 109799.8665 kcal/mol (109759.4263 without restraints) Performing minimization step: 32. Total energy = 109706.8759 kcal/mol (109666.4469 without restraints) Performing minimization step: 33. Total energy = 109613.9538 kcal/mol (109573.5360 without restraints) Performing minimization step: 34. Total energy = 109521.1007 kcal/mol (109480.6941 without restraints) Performing minimization step: 35. Total energy = 109428.3166 kcal/mol (109387.9210 without restraints) Performing minimization step: 36. Total energy = 109335.6007 kcal/mol (109295.2165 without restraints) Performing minimization step: 37. Total energy = 109242.9537 kcal/mol (109202.5806 without restraints) Performing minimization step: 38. Total energy = 109150.3753 kcal/mol (109110.0135 without restraints) Performing minimization step: 39. Total energy = 109057.8656 kcal/mol (109017.5150 without restraints) Performing minimization step: 40. Total energy = 108965.4252 kcal/mol (108925.0857 without restraints) Performing minimization step: 41. Total energy = 108873.0532 kcal/mol (108832.7249 without restraints) Performing minimization step: 42. Total energy = 108780.7492 kcal/mol (108740.4320 without restraints) Performing minimization step: 43. Total energy = 108688.5141 kcal/mol (108648.2081 without restraints) Performing minimization step: 44. Total energy = 108596.3474 kcal/mol (108556.0524 without restraints) Performing minimization step: 45. Total energy = 108504.2493 kcal/mol (108463.9656 without restraints) Performing minimization step: 46. Total energy = 108412.2198 kcal/mol (108371.9472 without restraints) Performing minimization step: 47. Total energy = 108320.2590 kcal/mol (108279.9977 without restraints) Performing minimization step: 48. Total energy = 108228.3667 kcal/mol (108188.1164 without restraints) Performing minimization step: 49. Total energy = 108136.5418 kcal/mol (108096.3027 without restraints) Performing minimization step: 50. Total energy = 108044.7866 kcal/mol (108004.5586 without restraints) Performing minimization step: 51. Total energy = 107953.0995 kcal/mol (107912.8826 without restraints) Performing minimization step: 52. Total energy = 107861.4808 kcal/mol (107821.2751 without restraints) Performing minimization step: 53. Total energy = 107769.9305 kcal/mol (107729.7359 without restraints) Performing minimization step: 54. Total energy = 107678.4486 kcal/mol (107638.2651 without restraints) Performing minimization step: 55. Total energy = 107587.0351 kcal/mol (107546.8628 without restraints) Performing minimization step: 56. Total energy = 107495.6900 kcal/mol (107455.5288 without restraints) Performing minimization step: 57. Total energy = 107404.4129 kcal/mol (107364.2627 without restraints) Performing minimization step: 58. Total energy = 107313.2038 kcal/mol (107273.0648 without restraints) Performing minimization step: 59. Total energy = 107222.0634 kcal/mol (107181.9355 without restraints) Performing minimization step: 60. Total energy = 107130.9910 kcal/mol (107090.8741 without restraints) Performing minimization step: 61. Total energy = 107039.9871 kcal/mol (106999.8814 without restraints) Performing minimization step: 62. Total energy = 106949.0513 kcal/mol (106908.9565 without restraints) Performing minimization step: 63. Total energy = 106858.1837 kcal/mol (106818.1003 without restraints) Performing minimization step: 64. Total energy = 106767.3845 kcal/mol (106727.3121 without restraints) Performing minimization step: 65. Total energy = 106676.6535 kcal/mol (106636.5921 without restraints) Performing minimization step: 66. Total energy = 106585.9904 kcal/mol (106545.9401 without restraints) Performing minimization step: 67. Total energy = 106495.3953 kcal/mol (106455.3561 without restraints) Performing minimization step: 68. Total energy = 106404.8681 kcal/mol (106364.8398 without restraints) Performing minimization step: 69. Total energy = 106314.4089 kcal/mol (106274.3918 without restraints) Performing minimization step: 70. Total energy = 106224.0180 kcal/mol (106184.0120 without restraints) Performing minimization step: 71. Total energy = 106133.6950 kcal/mol (106093.7000 without restraints) Performing minimization step: 72. Total energy = 106043.4401 kcal/mol (106003.4562 without restraints) Performing minimization step: 73. Total energy = 105953.2530 kcal/mol (105913.2801 without restraints) Performing minimization step: 74. Total energy = 105863.1340 kcal/mol (105823.1722 without restraints) Performing minimization step: 75. Total energy = 105773.0832 kcal/mol (105733.1325 without restraints) Performing minimization step: 76. Total energy = 105683.1002 kcal/mol (105643.1606 without restraints) Performing minimization step: 77. Total energy = 105593.1852 kcal/mol (105553.2565 without restraints) Performing minimization step: 78. Total energy = 105503.3378 kcal/mol (105463.4202 without restraints) Performing minimization step: 79. Total energy = 105413.5583 kcal/mol (105373.6517 without restraints) Performing minimization step: 80. Total energy = 105323.8471 kcal/mol (105283.9517 without restraints) Performing minimization step: 81. Total energy = 105234.2034 kcal/mol (105194.3188 without restraints) Performing minimization step: 82. Total energy = 105144.6273 kcal/mol (105104.7538 without restraints) Performing minimization step: 83. Total energy = 105055.1189 kcal/mol (105015.2564 without restraints) Performing minimization step: 84. Total energy = 104965.6782 kcal/mol (104925.8267 without restraints) Performing minimization step: 85. Total energy = 104876.3049 kcal/mol (104836.4644 without restraints) Performing minimization step: 86. Total energy = 104786.9996 kcal/mol (104747.1701 without restraints) Performing minimization step: 87. Total energy = 104697.7617 kcal/mol (104657.9432 without restraints) Performing minimization step: 88. Total energy = 104608.5919 kcal/mol (104568.7844 without restraints) Performing minimization step: 89. Total energy = 104519.4893 kcal/mol (104479.6928 without restraints) Performing minimization step: 90. Total energy = 104430.4544 kcal/mol (104390.6689 without restraints) Performing minimization step: 91. Total energy = 104341.4873 kcal/mol (104301.7128 without restraints) Performing minimization step: 92. Total energy = 104252.5876 kcal/mol (104212.8240 without restraints) Performing minimization step: 93. Total energy = 104163.7556 kcal/mol (104124.0030 without restraints) Performing minimization step: 94. Total energy = 104074.9912 kcal/mol (104035.2496 without restraints) Performing minimization step: 95. Total energy = 103986.2940 kcal/mol (103946.5634 without restraints) Performing minimization step: 96. Total energy = 103897.6643 kcal/mol (103857.9445 without restraints) Performing minimization step: 97. Total energy = 103809.1019 kcal/mol (103769.3931 without restraints) Performing minimization step: 98. Total energy = 103720.6071 kcal/mol (103680.9094 without restraints) Performing minimization step: 99. Total energy = 103632.1798 kcal/mol (103592.4930 without restraints) Performing minimization step: 100. Total energy = 103543.8199 kcal/mol (103504.1441 without restraints) Writing PDB file: /home/ubuntu/rna-tools/rna_tools/tools/webserver-engine/media/jobs/6b8f1efc/tmp/mir222m2ref_refx/mir222m2ref_refx.pdb ...Done. Performing minimization step: 101. Total energy = 103455.5273 kcal/mol (103415.8624 without restraints) Performing minimization step: 102. Total energy = 103367.3021 kcal/mol (103327.6482 without restraints) Performing minimization step: 103. Total energy = 103279.1445 kcal/mol (103239.5015 without restraints) Performing minimization step: 104. Total energy = 103191.0539 kcal/mol (103151.4219 without restraints) Performing minimization step: 105. Total energy = 103103.0309 kcal/mol (103063.4100 without restraints) Performing minimization step: 106. Total energy = 103015.0753 kcal/mol (102975.4651 without restraints) Performing minimization step: 107. Total energy = 102927.1863 kcal/mol (102887.5871 without restraints) Performing minimization step: 108. Total energy = 102839.3647 kcal/mol (102799.7761 without restraints) Performing minimization step: 109. Total energy = 102751.6099 kcal/mol (102712.0325 without restraints) Performing minimization step: 110. Total energy = 102663.9229 kcal/mol (102624.3565 without restraints) Performing minimization step: 111. Total energy = 102576.3031 kcal/mol (102536.7476 without restraints) Performing minimization step: 112. Total energy = 102488.7502 kcal/mol (102449.2055 without restraints) Performing minimization step: 113. Total energy = 102401.2645 kcal/mol (102361.7308 without restraints) Performing minimization step: 114. Total energy = 102313.8457 kcal/mol (102274.3229 without restraints) Performing minimization step: 115. Total energy = 102226.4938 kcal/mol (102186.9819 without restraints) Performing minimization step: 116. Total energy = 102139.2090 kcal/mol (102099.7079 without restraints) Performing minimization step: 117. Total energy = 102051.9915 kcal/mol (102012.5013 without restraints) Performing minimization step: 118. Total energy = 101964.8410 kcal/mol (101925.3617 without restraints) Performing minimization step: 119. Total energy = 101877.7578 kcal/mol (101838.2894 without restraints) Performing minimization step: 120. Total energy = 101790.7411 kcal/mol (101751.2836 without restraints) Performing minimization step: 121. Total energy = 101703.7910 kcal/mol (101664.3444 without restraints) Performing minimization step: 122. Total energy = 101616.9078 kcal/mol (101577.4720 without restraints) Performing minimization step: 123. Total energy = 101530.0920 kcal/mol (101490.6674 without restraints) Performing minimization step: 124. Total energy = 101443.3431 kcal/mol (101403.9290 without restraints) Performing minimization step: 125. Total energy = 101356.6607 kcal/mol (101317.2575 without restraints) Performing minimization step: 126. Total energy = 101270.0451 kcal/mol (101230.6527 without restraints) Performing minimization step: 127. Total energy = 101183.4962 kcal/mol (101144.1146 without restraints) Performing minimization step: 128. Total energy = 101097.0141 kcal/mol (101057.6435 without restraints) Performing minimization step: 129. Total energy = 101010.5986 kcal/mol (100971.2388 without restraints) Performing minimization step: 130. Total energy = 100924.2500 kcal/mol (100884.9010 without restraints) Performing minimization step: 131. Total energy = 100837.9683 kcal/mol (100798.6301 without restraints) Performing minimization step: 132. Total energy = 100751.7528 kcal/mol (100712.4256 without restraints) Performing minimization step: 133. Total energy = 100665.6042 kcal/mol (100626.2878 without restraints) Performing minimization step: 134. Total energy = 100579.5220 kcal/mol (100540.2164 without restraints) Performing minimization step: 135. Total energy = 100493.5066 kcal/mol (100454.2118 without restraints) Performing minimization step: 136. Total energy = 100407.5578 kcal/mol (100368.2738 without restraints) Performing minimization step: 137. Total energy = 100321.6753 kcal/mol (100282.4021 without restraints) Performing minimization step: 138. Total energy = 100235.8588 kcal/mol (100196.5965 without restraints) Performing minimization step: 139. Total energy = 100150.1096 kcal/mol (100110.8580 without restraints) Performing minimization step: 140. Total energy = 100064.4269 kcal/mol (100025.1861 without restraints) Performing minimization step: 141. Total energy = 99978.8104 kcal/mol (99939.5804 without restraints) Performing minimization step: 142. Total energy = 99893.2604 kcal/mol (99854.0411 without restraints) Performing minimization step: 143. Total energy = 99807.7768 kcal/mol (99768.5684 without restraints) Performing minimization step: 144. Total energy = 99722.3600 kcal/mol (99683.1624 without restraints) Performing minimization step: 145. Total energy = 99637.0098 kcal/mol (99597.8229 without restraints) Performing minimization step: 146. Total energy = 99551.7252 kcal/mol (99512.5492 without restraints) Performing minimization step: 147. Total energy = 99466.5069 kcal/mol (99427.3416 without restraints) Performing minimization step: 148. Total energy = 99381.3552 kcal/mol (99342.2007 without restraints) Performing minimization step: 149. Total energy = 99296.2695 kcal/mol (99257.1258 without restraints) Performing minimization step: 150. Total energy = 99211.2507 kcal/mol (99172.1177 without restraints) Performing minimization step: 151. Total energy = 99126.2974 kcal/mol (99087.1752 without restraints) Performing minimization step: 152. Total energy = 99041.4106 kcal/mol (99002.2991 without restraints) Performing minimization step: 153. Killed /home/ubuntu/rna-tools//opt/qrnas/ Save to mir222m2ref_refx.pdb DONE!