Hi Bruce,
It seems to me that if you use the absolute value to force the difference to be a positive number, then set the scale to a negative number, that would *reward* a large difference rather than *penalize* it.
Nope, the idea is to make the value of the restraint 0. Negative and positive errors in the value are penalized equally.
But perhaps I am confused in how the restraints are added to chi-square. I am under the impression that restraints are added as written to chi-square. This seems consistent with the language in section 7.9 of the reference manual. However, if the restraint is squared before adding to chi-square then what I said about the negative value of the scaling term is clearly wrong.
A restraint is an additional element in the vector to be minimized. chi-square is the sum of squares of the elements of this vector. I guess I should fix the document! --Matt