Distance dependence of correctly aligned residue fractions. The structure pairs were superposed using the reference alignments to calculate the distance between the C
atoms of all aligned residue pairs. The residue pairs were then grouped into distance bins of size 0.5 Å. The residue pairs that were 10 Å or more apart were collected in the last bin. For each test alignment, the fraction of correctly aligned residues were calculated (scale on the left y-axis) in each distance bin with (dotted lines with open symbols) or without (solid lines with closed symbols) shift error. The symbols and colors for the methods are the same as in the Figure 7. The solid grey circles and grey lines give the total number of residue pairs in each bin (scale on the right y-axis).