For each bond length measure its Z-score (that is the number of standard deviationss it
deviates from the ideal value). The average Z sum, (or
better the RMS-Z score) is measure for bond length quality.
The second answer to the same question is a lot more difficult..., But, in 1PPT you also see
Warning: Possible cell scaling problem
What happens here? Well, if the crystallographer has, for example, the A-axis of the cell too long,
then all bond lengths of bonds that fall parallel, or 'a bit parallel', to the A-axis will
get streched out a bit. WHAT_CHECK checks those things and provides advise on how to correct
the cell-dimensions. I guess this bit goes way beyond what I expect you to understand especially
since it is a fact and not a concept...