I have finally run Rosetta Holes successfully, however since there is no documentation of any kind for Holes, I don’t know how to interpret the output:
RosettaHoles: HEADER File/Tag RosHol resl dec25 dec15 AAresl AAdec25 AAdec15 RosScore
RosettaHoles: RMS 1UBQ.pdb 1.7825 1.7813 -1.9173 -0.6209 1072.32 -1154.23 -373.78 -16.036 0.0000
Can anyone tell me the meaning of the abbreviations in the header? (at least the non-obvious ones)
Why is there a 0.000 at the end of the score list?
You probably only care about the first 3 numbers, which are the scores referred to in the paper. The first is the combined score, which can be interpreted roughly by comparing to the resolution of the structure… the rosettaholes score should be lower than the resolution in almost all cases. The second score assess minor packing defects and the third major ones. The combined score is the resl score plus 3 * sigmoid( dec25 ).