RMSD dependence of F
in the root node set. The structure pairs were superposed using the reference alignments to calculate the RMSDs. The test alignments were grouped into RMSD bins of size 0.5 Å and then the alignments within each bin were grouped according to its CD name for averaging. The avearge Fcar values are shown with the scale on the left y-axis: open symbols, Fcar(8); closed symbols, Fcar(0). The x-axis shows the midpoint of each RMSD bin. All the structure pairs with RMSD greater than 4.0 Å were collected in the last bin. The histogram (grey bars) shows the number of superfamilies in each bin with the scale on the right y-axis.