There’s two things going into the highres filter, the total (fullatom) score and the interface score (I_sc). The cutoff for the first is controlled by the -cluster:output_score_filter option, and the second is hard coded at 0.
Recent versions of the SymDockProtocol (the weekly releases since mid 2014) will actually print out the two values that it encountered on the error line. Rosetta3.5 doesn’t have that, though.
The defaults for both of these are rather generous, though. By default the fullatom filter is set to 1000000.0, which means anything but the most massively broken structure is likely to pass. (Unless you’re doing something strange with structure scoring.) And if the interface score is greater than zero, that means that Rosetta doesn’t think things aren’t going to bind. If you’re not passing the default high res filter, things are probably going wrong with your docking job.
There is a very limited facility to turn off the filtering, though. If the -docking::dock_ppk flag is set, the high-res filter will be skipped – though that will also change how docking progresses, so I wouldn’t suggest it as a general solution.
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