=============================================================================
Reading config file: /home/ubuntu/rna-tools/rna_tools/tools/webserver-engine/media/jobs/c2f2c7f1/tmp/4way-GCGA_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
Killed
/home/ubuntu/rna-tools//opt/qrnas/
Save to 4way-GCGA_refx.pdb
Traceback (most recent call last):
  File "/home/ubuntu/miniconda3/bin/rna_refinement.py", line 7, in <module>
    exec(compile(f.read(), __file__, 'exec'))
  File "/home/ubuntu/rna-tools/rna_tools/tools/rna_refinement/rna_refinement.py", line 181, in <module>
    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/c2f2c7f1/tmp/4way-GCGA_refx/4way-GCGA_refx.pdb'
DONE!