============================================================================= Reading config file: /home/ubuntu/rna-tools/rna_tools/tools/webserver-engine/media/jobs/be483565/tmp/mir222m4ref_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/be483565/tmp/mir222m4ref_refx/mir222m4ref.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 8.254 45.764 48.764 1.00 0.00 H Missing atom added: ATOM 7 OP3 G A 1 -0.283 48.060 34.356 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: 423484 Number of H-bonds built: 114 Number of spring restraints: 0 Number of positional restraints: 0 Number of base pairs built: 38 Number of molecules (chains) read: 1 ----------------------------------------------------------------------------- Performing minimization step: 1. Total energy = 112432.6539 kcal/mol (112385.7807 without restraints) Performing minimization step: 2. Total energy = 112337.6491 kcal/mol (112290.7878 without restraints) Performing minimization step: 3. Total energy = 112242.7135 kcal/mol (112195.8642 without restraints) Performing minimization step: 4. Total energy = 112147.8476 kcal/mol (112101.0103 without restraints) Performing minimization step: 5. Total energy = 112053.0511 kcal/mol (112006.2257 without restraints) Performing minimization step: 6. Total energy = 111958.3241 kcal/mol (111911.5108 without restraints) Performing minimization step: 7. Total energy = 111863.6663 kcal/mol (111816.8647 without restraints) Performing minimization step: 8. Total energy = 111769.0771 kcal/mol (111722.2876 without restraints) Performing minimization step: 9. Total energy = 111674.5578 kcal/mol (111627.7803 without restraints) Performing minimization step: 10. Total energy = 111580.1076 kcal/mol (111533.3420 without restraints) Performing minimization step: 11. Total energy = 111485.7267 kcal/mol (111438.9730 without restraints) Performing minimization step: 12. Total energy = 111391.4152 kcal/mol (111344.6735 without restraints) Performing minimization step: 13. Total energy = 111297.1734 kcal/mol (111250.4437 without restraints) Performing minimization step: 14. Total energy = 111203.0011 kcal/mol (111156.2833 without restraints) Performing minimization step: 15. Total energy = 111108.8975 kcal/mol (111062.1915 without restraints) Performing minimization step: 16. Total energy = 111014.8631 kcal/mol (110968.1691 without restraints) Performing minimization step: 17. Total energy = 110920.8979 kcal/mol (110874.2158 without restraints) Performing minimization step: 18. Total energy = 110827.0014 kcal/mol (110780.3312 without restraints) Performing minimization step: 19. Total energy = 110733.1745 kcal/mol (110686.5162 without restraints) Performing minimization step: 20. Total energy = 110639.4166 kcal/mol (110592.7703 without restraints) Performing minimization step: 21. Total energy = 110545.7279 kcal/mol (110499.0934 without restraints) Performing minimization step: 22. Total energy = 110452.1082 kcal/mol (110405.4857 without restraints) Performing minimization step: 23. Total energy = 110358.5577 kcal/mol (110311.9470 without restraints) Performing minimization step: 24. Total energy = 110265.0758 kcal/mol (110218.4771 without restraints) Performing minimization step: 25. Total energy = 110171.6633 kcal/mol (110125.0764 without restraints) Performing minimization step: 26. Total energy = 110078.3199 kcal/mol (110031.7449 without restraints) Performing minimization step: 27. Total energy = 109985.0453 kcal/mol (109938.4823 without restraints) Performing minimization step: 28. Total energy = 109891.8395 kcal/mol (109845.2882 without restraints) Performing minimization step: 29. Total energy = 109798.7029 kcal/mol (109752.1635 without restraints) Performing minimization step: 30. Total energy = 109705.6352 kcal/mol (109659.1077 without restraints) Performing minimization step: 31. Total energy = 109612.6362 kcal/mol (109566.1205 without restraints) Performing minimization step: 32. Total energy = 109519.7060 kcal/mol (109473.2022 without restraints) Performing minimization step: 33. Total energy = 109426.8441 kcal/mol (109380.3521 without restraints) Performing minimization step: 34. Total energy = 109334.0514 kcal/mol (109287.5713 without restraints) Performing minimization step: 35. Total energy = 109241.3274 kcal/mol (109194.8592 without restraints) Performing minimization step: 36. Total energy = 109148.6728 kcal/mol (109102.2164 without restraints) Performing minimization step: 37. Total energy = 109056.0868 kcal/mol (109009.6423 without restraints) Performing minimization step: 38. Total energy = 108963.5692 kcal/mol (108917.1365 without restraints) Performing minimization step: 39. Total energy = 108871.1202 kcal/mol (108824.6991 without restraints) Performing minimization step: 40. Total energy = 108778.7397 kcal/mol (108732.3307 without restraints) Performing minimization step: 41. Total energy = 108686.4290 kcal/mol (108640.0318 without restraints) Performing minimization step: 42. Total energy = 108594.1865 kcal/mol (108547.8012 without restraints) Performing minimization step: 43. Total energy = 108502.0125 kcal/mol (108455.6389 without restraints) Performing minimization step: 44. Total energy = 108409.9068 kcal/mol (108363.5450 without restraints) Performing minimization step: 45. Total energy = 108317.8700 kcal/mol (108271.5202 without restraints) Performing minimization step: 46. Total energy = 108225.9022 kcal/mol (108179.5641 without restraints) Performing minimization step: 47. Total energy = 108134.0024 kcal/mol (108087.6761 without restraints) Performing minimization step: 48. Total energy = 108042.1711 kcal/mol (107995.8565 without restraints) Performing minimization step: 49. Total energy = 107950.4083 kcal/mol (107904.1056 without restraints) Performing minimization step: 50. Total energy = 107858.7137 kcal/mol (107812.4227 without restraints) Performing minimization step: 51. Total energy = 107767.0879 kcal/mol (107720.8088 without restraints) Performing minimization step: 52. Total energy = 107675.5306 kcal/mol (107629.2633 without restraints) Performing minimization step: 53. Total energy = 107584.0419 kcal/mol (107537.7862 without restraints) Performing minimization step: 54. Total energy = 107492.6208 kcal/mol (107446.3771 without restraints) Performing minimization step: 55. Total energy = 107401.2683 kcal/mol (107355.0364 without restraints) Performing minimization step: 56. Total energy = 107309.9845 kcal/mol (107263.7642 without restraints) Performing minimization step: 57. Total energy = 107218.7687 kcal/mol (107172.5603 without restraints) Performing minimization step: 58. Total energy = 107127.6216 kcal/mol (107081.4250 without restraints) Performing minimization step: 59. Total energy = 107036.5429 kcal/mol (106990.3580 without restraints) Performing minimization step: 60. Total energy = 106945.5326 kcal/mol (106899.3594 without restraints) Performing minimization step: 61. Total energy = 106854.5901 kcal/mol (106808.4287 without restraints) Performing minimization step: 62. Total energy = 106763.7161 kcal/mol (106717.5664 without restraints) Performing minimization step: 63. Total energy = 106672.9106 kcal/mol (106626.7730 without restraints) Performing minimization step: 64. Total energy = 106582.1731 kcal/mol (106536.0469 without restraints) Performing minimization step: 65. Total energy = 106491.5035 kcal/mol (106445.3890 without restraints) Performing minimization step: 66. Total energy = 106400.9023 kcal/mol (106354.7996 without restraints) Performing minimization step: 67. Total energy = 106310.3689 kcal/mol (106264.2780 without restraints) Performing minimization step: 68. Total energy = 106219.9039 kcal/mol (106173.8247 without restraints) Performing minimization step: 69. Killed /home/ubuntu/rna-tools//opt/qrnas/ Save to mir222m4ref_refx.pdb Traceback (most recent call last): File "/home/ubuntu/miniconda3/bin/rna_refinement.py", line 7, in exec(compile(f.read(), __file__, 'exec')) File "/home/ubuntu/rna-tools/rna_tools/tools/rna_refinement/rna_refinement.py", line 181, in q.run(args.fn, output_file, steps=args.steps, interactive=args.interactive, verbose=args.verbose) File "/home/ubuntu/rna-tools/rna_tools/tools/rna_refinement/rna_refinement.py", line 156, in run copyfile(qrnas_outputfile, outputfile) File "/home/ubuntu/miniconda3/lib/python3.8/shutil.py", line 264, in copyfile with open(src, 'rb') as fsrc, open(dst, 'wb') as fdst: FileNotFoundError: [Errno 2] No such file or directory: '/home/ubuntu/rna-tools/rna_tools/tools/webserver-engine/media/jobs/be483565/tmp/mir222m4ref_refx/mir222m4ref_refx.pdb' DONE!