============================================================================= Reading config file: /home/ubuntu/rna-tools/rna_tools/tools/webserver-engine/media/jobs/4fa7e965/tmp/mir222m3ref_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/4fa7e965/tmp/mir222m3ref_refx/mir222m3ref.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 47.934 28.042 25.934 1.00 0.00 H Missing atom added: ATOM 7 OP3 G A 1 38.247 41.301 21.865 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: 424298 Number of H-bonds built: 116 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 = 112409.9735 kcal/mol (112368.6686 without restraints) Performing minimization step: 2. Total energy = 112315.0379 kcal/mol (112273.7444 without restraints) Performing minimization step: 3. Total energy = 112220.1716 kcal/mol (112178.8895 without restraints) Performing minimization step: 4. Total energy = 112125.3747 kcal/mol (112084.1039 without restraints) Performing minimization step: 5. Total energy = 112030.6467 kcal/mol (111989.3871 without restraints) Performing minimization step: 6. Total energy = 111935.9880 kcal/mol (111894.7399 without restraints) Performing minimization step: 7. Total energy = 111841.3989 kcal/mol (111800.1622 without restraints) Performing minimization step: 8. Total energy = 111746.8788 kcal/mol (111705.6536 without restraints) Performing minimization step: 9. Total energy = 111652.4279 kcal/mol (111611.2140 without restraints) Performing minimization step: 10. Total energy = 111558.0466 kcal/mol (111516.8441 without restraints) Performing minimization step: 11. Total energy = 111463.7344 kcal/mol (111422.5432 without restraints) Performing minimization step: 12. Total energy = 111369.4915 kcal/mol (111328.3117 without restraints) Performing minimization step: 13. Total energy = 111275.3177 kcal/mol (111234.1492 without restraints) Performing minimization step: 14. Total energy = 111181.2129 kcal/mol (111140.0558 without restraints) Performing minimization step: 15. Total energy = 111087.1776 kcal/mol (111046.0318 without restraints) Performing minimization step: 16. Total energy = 110993.2114 kcal/mol (110952.0769 without restraints) Performing minimization step: 17. Total energy = 110899.3140 kcal/mol (110858.1908 without restraints) Performing minimization step: 18. Total energy = 110805.4857 kcal/mol (110764.3740 without restraints) Performing minimization step: 19. Total energy = 110711.7260 kcal/mol (110670.6256 without restraints) Performing minimization step: 20. Total energy = 110618.0360 kcal/mol (110576.9471 without restraints) Performing minimization step: 21. Total energy = 110524.4149 kcal/mol (110483.3372 without restraints) Performing minimization step: 22. Total energy = 110430.8629 kcal/mol (110389.7965 without restraints) Performing minimization step: 23. Total energy = 110337.3801 kcal/mol (110296.3250 without restraints) Performing minimization step: 24. Total energy = 110243.9662 kcal/mol (110202.9224 without restraints) Performing minimization step: 25. Total energy = 110150.6213 kcal/mol (110109.5888 without restraints) Performing minimization step: 26. Total energy = 110057.3449 kcal/mol (110016.3237 without restraints) Performing minimization step: 27. Total energy = 109964.1374 kcal/mol (109923.1277 without restraints) Performing minimization step: 28. Total energy = 109870.9988 kcal/mol (109830.0002 without restraints) Performing minimization step: 29. Total energy = 109777.9292 kcal/mol (109736.9419 without restraints) Performing minimization step: 30. Total energy = 109684.9282 kcal/mol (109643.9521 without restraints) Performing minimization step: 31. Total energy = 109591.9961 kcal/mol (109551.0314 without restraints) Performing minimization step: 32. Total energy = 109499.1329 kcal/mol (109458.1796 without restraints) Performing minimization step: 33. Total energy = 109406.3386 kcal/mol (109365.3965 without restraints) Performing minimization step: 34. Total energy = 109313.6129 kcal/mol (109272.6821 without restraints) Performing minimization step: 35. Total energy = 109220.9561 kcal/mol (109180.0365 without restraints) Performing minimization step: 36. Total energy = 109128.3675 kcal/mol (109087.4592 without restraints) Performing minimization step: 37. Total energy = 109035.8482 kcal/mol (108994.9513 without restraints) Performing minimization step: 38. Total energy = 108943.3975 kcal/mol (108902.5118 without restraints) Performing minimization step: 39. Total energy = 108851.0155 kcal/mol (108810.1411 without restraints) Performing minimization step: 40. Total energy = 108758.7016 kcal/mol (108717.8384 without restraints) Performing minimization step: 41. Total energy = 108666.4565 kcal/mol (108625.6044 without restraints) Performing minimization step: 42. Total energy = 108574.2803 kcal/mol (108533.4396 without restraints) Performing minimization step: 43. Total energy = 108482.1726 kcal/mol (108441.3432 without restraints) Performing minimization step: 44. Total energy = 108390.1334 kcal/mol (108349.3152 without restraints) Performing minimization step: 45. Total energy = 108298.1624 kcal/mol (108257.3554 without restraints) Performing minimization step: 46. Total energy = 108206.2605 kcal/mol (108165.4648 without restraints) Performing minimization step: 47. Total energy = 108114.4269 kcal/mol (108073.6425 without restraints) Performing minimization step: 48. Total energy = 108022.6618 kcal/mol (107981.8886 without restraints) Performing minimization step: 49. Total energy = 107930.9653 kcal/mol (107890.2033 without restraints) Performing minimization step: 50. Total energy = 107839.3369 kcal/mol (107798.5860 without restraints) Performing minimization step: 51. Total energy = 107747.7767 kcal/mol (107707.0371 without restraints) Performing minimization step: 52. Total energy = 107656.2851 kcal/mol (107615.5568 without restraints) Performing minimization step: 53. Total energy = 107564.8616 kcal/mol (107524.1444 without restraints) Performing minimization step: 54. Killed /home/ubuntu/rna-tools//opt/qrnas/ Save to mir222m3ref_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/4fa7e965/tmp/mir222m3ref_refx/mir222m3ref_refx.pdb' DONE!