============================================================================= Reading config file: /home/ubuntu/rna-tools/rna_tools/tools/webserver-engine/media/jobs/e5991eff/tmp/seq2_konsensus_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/e5991eff/tmp/seq2_konsensus_refx/seq2_konsensus.pdb ============================================================================= Atom's 1 H5T residue renamed to RG5 Atom's 2 O5' residue renamed to RG5 Atom's 3 C5' residue renamed to RG5 Atom's 4 H5'1 residue renamed to RG5 Atom's 5 H5'2 residue renamed to RG5 Atom's 6 C4' residue renamed to RG5 Atom's 7 H4' residue renamed to RG5 Atom's 8 O4' residue renamed to RG5 Atom's 9 C1' residue renamed to RG5 Atom's 10 H1' residue renamed to RG5 Atom's 11 N9 residue renamed to RG5 Atom's 12 C4 residue renamed to RG5 Atom's 13 N3 residue renamed to RG5 Atom's 14 C2 residue renamed to RG5 Atom's 15 N2 residue renamed to RG5 Atom's 16 H21 residue renamed to RG5 Atom's 17 H22 residue renamed to RG5 Atom's 18 N1 residue renamed to RG5 Atom's 19 H1 residue renamed to RG5 Atom's 20 C6 residue renamed to RG5 Atom's 21 O6 residue renamed to RG5 Atom's 22 C5 residue renamed to RG5 Atom's 23 N7 residue renamed to RG5 Atom's 24 C8 residue renamed to RG5 Atom's 25 H8 residue renamed to RG5 Atom's 26 C2' residue renamed to RG5 Atom's 27 H2' residue renamed to RG5 Atom's 28 O2' residue renamed to RG5 Atom's 29 HO'2 residue renamed to RG5 Atom's 30 C3' residue renamed to RG5 Atom's 31 H3' residue renamed to RG5 Atom's 32 O3' residue renamed to RG5 Atom's 4883 H3T residue renamed to RA3 Atom's 4882 O3' residue renamed to RA3 Atom's 4881 C3' residue renamed to RA3 Atom's 4880 H3' residue renamed to RA3 Atom's 4879 HO'2 residue renamed to RA3 Atom's 4878 O2' residue renamed to RA3 Atom's 4877 H2' residue renamed to RA3 Atom's 4876 C2' residue renamed to RA3 Atom's 4875 H8 residue renamed to RA3 Atom's 4874 C8 residue renamed to RA3 Atom's 4873 N7 residue renamed to RA3 Atom's 4872 C5 residue renamed to RA3 Atom's 4871 H62 residue renamed to RA3 Atom's 4870 H61 residue renamed to RA3 Atom's 4869 N6 residue renamed to RA3 Atom's 4868 C6 residue renamed to RA3 Atom's 4867 N1 residue renamed to RA3 Atom's 4866 H2 residue renamed to RA3 Atom's 4865 C2 residue renamed to RA3 Atom's 4864 N3 residue renamed to RA3 Atom's 4863 C4 residue renamed to RA3 Atom's 4862 N9 residue renamed to RA3 Atom's 4861 H1' residue renamed to RA3 Atom's 4860 C1' residue renamed to RA3 Atom's 4859 O4' residue renamed to RA3 Atom's 4858 H4' residue renamed to RA3 Atom's 4857 C4' residue renamed to RA3 Atom's 4856 H5'2 residue renamed to RA3 Atom's 4855 H5'1 residue renamed to RA3 Atom's 4854 C5' residue renamed to RA3 Atom's 4853 O5' residue renamed to RA3 Atom's 4852 OP2 residue renamed to RA3 Atom's 4851 OP1 residue renamed to RA3 Atom's 4850 P residue renamed to RA3 Number of atoms: 4883 Number of residues: 152 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: 5264 Number of angles built: 9417 Number of dihedrals built: 14342 Number of impropers built: 1039 ----------------------------------------------------------------------------- End of molecule (chain) ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Building interresidual nonbonded pairs & H-bonds (it may take a while)... Killed /home/ubuntu/rna-tools//opt/qrnas/ Save to seq2_konsensus_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/e5991eff/tmp/seq2_konsensus_refx/seq2_konsensus_refx.pdb' DONE!