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shuffle_nstruct should only take effect if you also pass the shuffle flag – this is used for certain modes to randomize the order that jobs are processed (specifically, it’s used on BOINC in the Rosetta@home project).
You’re welcome to try shuffle_nstruct but I don’t think it will help.
There are two option system commands that may help track this error down. First, -options::user will repeat the loaded options at the beginning of the run. This is useful for making sure Rosetta read your options file properly. Second, -show_accessed_options will print at the end of the run all the options whose value was checked – this will tell you if you’ve specified options that didn’t do anything. (You can’t use both these options in the same run – checking which ones are specified on command line for options::user will screw up the latter flag by marking all of the as used).