I'd tried to analyse my silent file that came from other concatenated silent files (cat *.out > 5novo.out) running the scoring application through my command line  but the program gave me this message:
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 420 in file 1IYT.pdb. Best match rsd_type: ALA_p:CtermProteinFull
core.pack.task: Packer task: initialize from command line()
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.jobdist.JobDistributors: Looking for an available job: 1 1 S_00000001 1
Starting work on structure: S_00000001_0001 <--- S_00000001
protocols.jobdist.main: Working on: S_00000001
ERROR: Illegal attempt to score with non-identical atom set between pose and etable
ERROR:: Exit from: src/core/scoring/etable/EtableEnergy.cc line: 104
I'd searched throughout this forum and I only find this post with similar (unsolved) problem (https://www.rosettacommons.org/node/2335). I know that my reference structure (1IYT) and my predicted structure (5novo.out) aren't identical (i.e. hasn't the same aminoacid sequences) and thus I decided to use the in:file:centroid option but the problem persists. I wonder to know if somebody could help me to circunvemt this error message.
 Command line
/home/guest/Downloads/rosetta3.5/rosetta_source/bin/score.linuxgccrelease -database /home/guest/Downloads/rosetta3.5/rosetta_database in:file:fullatom -in:file:silent 5novo.out -out:pdb -out:file:silent 5novo.1iyt.out -relax:fast -out:output -out:file:scorefile 5novo.1iyt.data -in:file:native 1IYT.pdb -silent_read_through_errors