Z-scores from alignment scans of 6 sample domains. The Z-score vs. rotation angle scatter plot for all alignments from the alignment scan for (a) d1s99a_, (b) d1wd3a2, (c) d1jofc_, (d) d1vzwa1, and (f) d2j8ka1. The red points are those whose rotation axis is within about 20° (cosθ > 0.95) of that of the point with the highest Z-score. Others are in black. Panel (e) for d1bk5a_, is an exception; here the Z-scores are plotted against the average alignment shift (average of the residue serial number differences between aligned residues). Note that points with negative Z-scores are not shown. Note also that the self-alignment peak, which would occur at angle 0° or zero average shift, is not visible in these plots. This is because the aligned pairs between residues whose serial numbers differ by 3 or fewer residues were not included in the T-score calculation (see Methods).