The latter category are the options required to generate and inspect the quality control boxes. The text of an article written on this subject is added to this writeup as an appendix. The deviation from the average quality value for all residues in this range will be shown. Depending on the parameter setting you will or will not see which atoms contributed in which way to the values per residue. Since this option needs the surface contact area to be known, you will be brought in the accessibility module if this has not been done prior to calculating quality values.
Quality control is a time consuming option.
In an individual residue has a quality control value of -5.0 or worse, you should take a look at it. The deviation from the average quality value for all residues in this range will be shown. Depending on the parameter setting you will or will not see which atoms contributed in which way to the values per residue. Since this option needs the surface contact area to be known, you will be brought in the accessibility module if this has not been done prior to calculating quality values. In an individual residue has a quality control value of -2.5 or worse, you should take a look at it.