============================================================================= Reading config file: /home/ubuntu/rna-tools/rna_tools/tools/webserver-engine/media/jobs/8a3c001f/tmp/CPMA1_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/8a3c001f/tmp/CPMA1_refx/CPMA1.pdb ============================================================================= Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue: T Error: unknown residue(s). Molecule discarded. ----------------------------------------------------------------------------- Building interresidual nonbonded pairs & H-bonds (it may take a while)... Number of electrostatic pairs: 0 Number of van der Waals pairs: 0 Number of H-bonds built: 0 Number of spring restraints: 0 Number of positional restraints: 0 Number of base pairs built: 0 Number of molecules (chains) read: 0 ----------------------------------------------------------------------------- Warning: empty system, cannot proceed. /home/ubuntu/rna-tools//opt/qrnas/ Save to CPMA1_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/8a3c001f/tmp/CPMA1_refx/CPMA1_refx.pdb' DONE!