============================================================================= Reading config file: /home/ubuntu/rna-tools/rna_tools/tools/webserver-engine/media/jobs/a701fc9b/tmp/example1_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/a701fc9b/tmp/example1_refx/example1.pdb ============================================================================= Atom's 1 H5T residue renamed to RA5 Atom's 2 O5' residue renamed to RA5 Atom's 3 C5' residue renamed to RA5 Atom's 4 H5'1 residue renamed to RA5 Atom's 5 H5'2 residue renamed to RA5 Atom's 6 C4' residue renamed to RA5 Atom's 7 H4' residue renamed to RA5 Atom's 8 O4' residue renamed to RA5 Atom's 9 C1' residue renamed to RA5 Atom's 10 H1' residue renamed to RA5 Atom's 11 N9 residue renamed to RA5 Atom's 12 C4 residue renamed to RA5 Atom's 13 N3 residue renamed to RA5 Atom's 14 C2 residue renamed to RA5 Atom's 15 H2 residue renamed to RA5 Atom's 16 N1 residue renamed to RA5 Atom's 17 C6 residue renamed to RA5 Atom's 18 N6 residue renamed to RA5 Atom's 19 H61 residue renamed to RA5 Atom's 20 H62 residue renamed to RA5 Atom's 21 C5 residue renamed to RA5 Atom's 22 N7 residue renamed to RA5 Atom's 23 C8 residue renamed to RA5 Atom's 24 H8 residue renamed to RA5 Atom's 25 C2' residue renamed to RA5 Atom's 26 H2' residue renamed to RA5 Atom's 27 O2' residue renamed to RA5 Atom's 28 HO'2 residue renamed to RA5 Atom's 29 C3' residue renamed to RA5 Atom's 30 H3' residue renamed to RA5 Atom's 31 O3' residue renamed to RA5 Atom's 3462 H3T residue renamed to RG3 Atom's 3461 O3' residue renamed to RG3 Atom's 3460 C3' residue renamed to RG3 Atom's 3459 H3' residue renamed to RG3 Atom's 3458 HO'2 residue renamed to RG3 Atom's 3457 O2' residue renamed to RG3 Atom's 3456 H2' residue renamed to RG3 Atom's 3455 C2' residue renamed to RG3 Atom's 3454 H8 residue renamed to RG3 Atom's 3453 C8 residue renamed to RG3 Atom's 3452 N7 residue renamed to RG3 Atom's 3451 C5 residue renamed to RG3 Atom's 3450 O6 residue renamed to RG3 Atom's 3449 C6 residue renamed to RG3 Atom's 3448 H1 residue renamed to RG3 Atom's 3447 N1 residue renamed to RG3 Atom's 3446 H22 residue renamed to RG3 Atom's 3445 H21 residue renamed to RG3 Atom's 3444 N2 residue renamed to RG3 Atom's 3443 C2 residue renamed to RG3 Atom's 3442 N3 residue renamed to RG3 Atom's 3441 C4 residue renamed to RG3 Atom's 3440 N9 residue renamed to RG3 Atom's 3439 H1' residue renamed to RG3 Atom's 3438 C1' residue renamed to RG3 Atom's 3437 O4' residue renamed to RG3 Atom's 3436 H4' residue renamed to RG3 Atom's 3435 C4' residue renamed to RG3 Atom's 3434 H5'2 residue renamed to RG3 Atom's 3433 H5'1 residue renamed to RG3 Atom's 3432 C5' residue renamed to RG3 Atom's 3431 O5' residue renamed to RG3 Atom's 3430 OP2 residue renamed to RG3 Atom's 3429 OP1 residue renamed to RG3 Atom's 3428 P residue renamed to RG3 Number of atoms: 3462 Number of residues: 108 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: 3732 Number of angles built: 6678 Number of dihedrals built: 10174 Number of impropers built: 735 ----------------------------------------------------------------------------- End of molecule (chain) ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Building interresidual nonbonded pairs & H-bonds (it may take a while)... Number of electrostatic pairs: 5980581 Number of van der Waals pairs: 433399 Number of H-bonds built: 93 Number of spring restraints: 0 Number of positional restraints: 0 Number of base pairs built: 28 Number of molecules (chains) read: 1 ----------------------------------------------------------------------------- Performing minimization step: 1. Total energy = 6195 kcal/mol (6189 without restraints) Performing minimization step: 2. Total energy = 6183 kcal/mol (6177 without restraints) Performing minimization step: 3. Total energy = 6172 kcal/mol (6166 without restraints) Performing minimization step: 4. Total energy = 6160 kcal/mol (6154 without restraints) Performing minimization step: 5. Total energy = 6149 kcal/mol (6143 without restraints) Performing minimization step: 6. Total energy = 6137 kcal/mol (6131 without restraints) Performing minimization step: 7. Total energy = 6126 kcal/mol (6120 without restraints) Performing minimization step: 8. Total energy = 6115 kcal/mol (6109 without restraints) Performing minimization step: 9. Total energy = 6104 kcal/mol (6098 without restraints) Performing minimization step: 10. Total energy = 6093 kcal/mol (6087 without restraints) Performing minimization step: 11. Total energy = 6082 kcal/mol (6076 without restraints) Performing minimization step: 12. Total energy = 6072 kcal/mol (6065 without restraints) Performing minimization step: 13. Total energy = 6061 kcal/mol (6055 without restraints) Performing minimization step: 14. Total energy = 6050 kcal/mol (6044 without restraints) Performing minimization step: 15. Total energy = 6040 kcal/mol (6034 without restraints) Performing minimization step: 16. Total energy = 6029 kcal/mol (6023 without restraints) Performing minimization step: 17. Total energy = 6019 kcal/mol (6013 without restraints) Performing minimization step: 18. Total energy = 6009 kcal/mol (6003 without restraints) Performing minimization step: 19. Total energy = 5999 kcal/mol (5993 without restraints) Performing minimization step: 20. Total energy = 5989 kcal/mol (5983 without restraints) Performing minimization step: 21. Total energy = 5979 kcal/mol (5973 without restraints) Performing minimization step: 22. Total energy = 5969 kcal/mol (5963 without restraints) Performing minimization step: 23. Total energy = 5959 kcal/mol (5953 without restraints) Performing minimization step: 24. Total energy = 5949 kcal/mol (5943 without restraints) Performing minimization step: 25. Total energy = 5940 kcal/mol (5934 without restraints) Performing minimization step: 26. Total energy = 5930 kcal/mol (5924 without restraints) Performing minimization step: 27. Total energy = 5921 kcal/mol (5915 without restraints) Performing minimization step: 28. Total energy = 5911 kcal/mol (5905 without restraints) Performing minimization step: 29. Total energy = 5902 kcal/mol (5896 without restraints) Performing minimization step: 30. Total energy = 5893 kcal/mol (5887 without restraints) Performing minimization step: 31. Total energy = 5883 kcal/mol (5878 without restraints) Performing minimization step: 32. Total energy = 5874 kcal/mol (5868 without restraints) Performing minimization step: 33. Total energy = 5865 kcal/mol (5859 without restraints) Performing minimization step: 34. Total energy = 5856 kcal/mol (5850 without restraints) Performing minimization step: 35. Total energy = 5847 kcal/mol (5842 without restraints) Performing minimization step: 36. Total energy = 5839 kcal/mol (5833 without restraints) Performing minimization step: 37. Total energy = 5830 kcal/mol (5824 without restraints) Performing minimization step: 38. Total energy = 5821 kcal/mol (5815 without restraints) Performing minimization step: 39. Total energy = 5812 kcal/mol (5807 without restraints) Performing minimization step: 40. Total energy = 5804 kcal/mol (5798 without restraints) Performing minimization step: 41. Total energy = 5795 kcal/mol (5790 without restraints) Performing minimization step: 42. Total energy = 5787 kcal/mol (5781 without restraints) Performing minimization step: 43. Total energy = 5779 kcal/mol (5773 without restraints) Performing minimization step: 44. Total energy = 5770 kcal/mol (5765 without restraints) Performing minimization step: 45. Total energy = 5762 kcal/mol (5756 without restraints) Performing minimization step: 46. Total energy = 5754 kcal/mol (5748 without restraints) Performing minimization step: 47. Total energy = 5746 kcal/mol (5740 without restraints) Performing minimization step: 48. Total energy = 5738 kcal/mol (5732 without restraints) Performing minimization step: 49. Total energy = 5730 kcal/mol (5724 without restraints) Performing minimization step: 50. Total energy = 5722 kcal/mol (5716 without restraints) Performing minimization step: 51. Total energy = 5714 kcal/mol (5708 without restraints) Performing minimization step: 52. Total energy = 5706 kcal/mol (5701 without restraints) Performing minimization step: 53. Total energy = 5699 kcal/mol (5693 without restraints) Performing minimization step: 54. Total energy = 5691 kcal/mol (5685 without restraints) Performing minimization step: 55. Total energy = 5683 kcal/mol (5678 without restraints) Performing minimization step: 56. Total energy = 5676 kcal/mol (5670 without restraints) Performing minimization step: 57. Total energy = 5668 kcal/mol (5663 without restraints) Performing minimization step: 58. Total energy = 5661 kcal/mol (5655 without restraints) Performing minimization step: 59. Total energy = 5653 kcal/mol (5648 without restraints) Performing minimization step: 60. Total energy = 5646 kcal/mol (5640 without restraints) Performing minimization step: 61. Total energy = 5639 kcal/mol (5633 without restraints) Performing minimization step: 62. Total energy = 5632 kcal/mol (5626 without restraints) Performing minimization step: 63. Total energy = 5624 kcal/mol (5619 without restraints) Performing minimization step: 64. Total energy = 5617 kcal/mol (5612 without restraints) Performing minimization step: 65. Total energy = 5610 kcal/mol (5605 without restraints) Performing minimization step: 66. Total energy = 5603 kcal/mol (5598 without restraints) Performing minimization step: 67. Total energy = 5596 kcal/mol (5591 without restraints) Performing minimization step: 68. Total energy = 5589 kcal/mol (5584 without restraints) Performing minimization step: 69. Total energy = 5583 kcal/mol (5577 without restraints) Performing minimization step: 70. Total energy = 5576 kcal/mol (5570 without restraints) Performing minimization step: 71. Total energy = 5569 kcal/mol (5563 without restraints) Performing minimization step: 72. Total energy = 5562 kcal/mol (5557 without restraints) Performing minimization step: 73. Total energy = 5556 kcal/mol (5550 without restraints) Performing minimization step: 74. Total energy = 5549 kcal/mol (5544 without restraints) Performing minimization step: 75. Total energy = 5543 kcal/mol (5537 without restraints) Performing minimization step: 76. Total energy = 5536 kcal/mol (5531 without restraints) Performing minimization step: 77. Total energy = 5530 kcal/mol (5524 without restraints) Performing minimization step: 78. Total energy = 5523 kcal/mol (5518 without restraints) Performing minimization step: 79. Total energy = 5517 kcal/mol (5511 without restraints) Performing minimization step: 80. Killed /home/ubuntu/rna-tools//opt/qrnas/ Save to example1_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/a701fc9b/tmp/example1_refx/example1_refx.pdb' DONE!