The SIDE_TRACE keywords

MODE
DOCK Will ignore residue types and try to fit main chain fragments to sequence.
FIT Will keep types and try to build corresponding side chains.
SYMMetry
Make a guess ...
RESIdues
Defines which residue numbers will be considered (from to). Alternative is CHAIns
CHAIns
Defines which chains will be considered. Alternative is RESIdues
RSFIt
none builds proper side chain atoms but ignores density.
rotamer builds the best rotamers from the torsion angle data base.
torsion does real space torsional refinement
all first builds the best rotamers from the data base and then performs real space torsional refinement.
RSCYcles
Defines the number of real space refinement cycles to be performed.
RESHuffle
yes or no dictates if the program will try to assemble a spherical molecule from the chain or not.
CONFIdence
The first number sets the 'confidence' level for accepting the docking of a side chain. the confidence level shows how much bigger the score of the first choice is in comparison with the next available choice. Maximum is limited to 100, for simplicity. Values between 10 - 15 seem to be resonable. The second number is the step with which confidence is gradually decreased to accept more fragments docked into sequence. Sometimes it helps to do that slowly (1) but most times 10 is faster and makes no trouble !
END
Its guessing time again ...