============================================================================= Reading config file: /home/ubuntu/rna-tools/rna_tools/tools/webserver-engine/media/jobs/c65ee316/tmp/S_000001_012_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/c65ee316/tmp/S_000001_012_refx/S_000001_012.pdb ============================================================================= Atom's 1 C5' residue renamed to RA5 Atom's 2 C4' residue renamed to RA5 Atom's 3 O4' residue renamed to RA5 Atom's 4 C3' residue renamed to RA5 Atom's 5 O3' residue renamed to RA5 Atom's 6 C1' residue renamed to RA5 Atom's 7 C2' residue renamed to RA5 Atom's 8 O2' residue renamed to RA5 Atom's 9 N1 residue renamed to RA5 Atom's 10 C2 residue renamed to RA5 Atom's 11 N3 residue renamed to RA5 Atom's 12 C4 residue renamed to RA5 Atom's 13 C5 residue renamed to RA5 Atom's 14 C6 residue renamed to RA5 Atom's 15 N6 residue renamed to RA5 Atom's 16 N7 residue renamed to RA5 Atom's 17 C8 residue renamed to RA5 Atom's 18 N9 residue renamed to RA5 Atom's 19 H4' residue renamed to RA5 Atom's 20 H3' residue renamed to RA5 Atom's 21 H1' residue renamed to RA5 Atom's 22 H2' residue renamed to RA5 Atom's 23 HO'2 residue renamed to RA5 Atom's 24 H2 residue renamed to RA5 Atom's 25 H61 residue renamed to RA5 Atom's 26 H62 residue renamed to RA5 Atom's 27 H8 residue renamed to RA5 Atom's 6001 H6 residue renamed to RU3 Atom's 6000 H5 residue renamed to RU3 Atom's 5999 H3 residue renamed to RU3 Atom's 5998 HO'2 residue renamed to RU3 Atom's 5997 H2' residue renamed to RU3 Atom's 5996 H1' residue renamed to RU3 Atom's 5995 H3' residue renamed to RU3 Atom's 5994 H4' residue renamed to RU3 Atom's 5993 H5'2 residue renamed to RU3 Atom's 5992 H5'1 residue renamed to RU3 Atom's 5991 C6 residue renamed to RU3 Atom's 5990 C5 residue renamed to RU3 Atom's 5989 O4 residue renamed to RU3 Atom's 5988 C4 residue renamed to RU3 Atom's 5987 N3 residue renamed to RU3 Atom's 5986 O2 residue renamed to RU3 Atom's 5985 C2 residue renamed to RU3 Atom's 5984 N1 residue renamed to RU3 Atom's 5983 O2' residue renamed to RU3 Atom's 5982 C2' residue renamed to RU3 Atom's 5981 C1' residue renamed to RU3 Atom's 5980 O3' residue renamed to RU3 Atom's 5979 C3' residue renamed to RU3 Atom's 5978 O4' residue renamed to RU3 Atom's 5977 C4' residue renamed to RU3 Atom's 5976 C5' residue renamed to RU3 Atom's 5975 O5' residue renamed to RU3 Atom's 5974 OP1 residue renamed to RU3 Atom's 5973 OP2 residue renamed to RU3 Atom's 5972 P residue renamed to RU3 Missing atom added: ATOM 2 O5' RA5 A 1 1.576 -0.160 0.204 1.00 0.00 O Missing atom added: ATOM 21 H5'1 RA5 A 1 1.885 1.708 0.936 1.00 0.00 H Missing atom added: ATOM 22 H5'2 RA5 A 1 2.087 1.471 -0.892 1.00 0.00 H Missing atom added: ATOM 31 H3T RU3 A 190 13.605 -10.612 6.444 1.00 0.00 H Number of atoms: 6005 Number of residues: 190 Building intraresidual bonds... Warning: Bond expected, but some of the atoms are missing: H5T O5', residue No. A 1 Building intraresidual angles... Warning: Angle expected, but some of the atoms are missing: C5' O5' H5T, residue No. A 1 Building intraresidual dihedrals... Warning: Dihedral expected, but some of the atoms are missing: H5T O5' C5' C4', residue No. A 1 Warning: Dihedral expected, but some of the atoms are missing: H5T O5' C5' H5'1, residue No. A 1 Warning: Dihedral expected, but some of the atoms are missing: H5T O5' C5' H5'2, residue No. A 1 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: 6473 Number of angles built: 11606 Number of dihedrals built: 17689 Number of impropers built: 1248 ----------------------------------------------------------------------------- End of molecule (chain) ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Building interresidual nonbonded pairs & H-bonds (it may take a while)... Killed /home/ubuntu/rna-tools//opt/qrnas/ Save to S_000001_012_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/c65ee316/tmp/S_000001_012_refx/S_000001_012_refx.pdb' DONE!