Use full backbone atoms (N, CA, C for peptide residues, O5', C5', C4', C3',
O3 for nucleotide residues) if number of mapped residues is below 3.
This has a direct impact on RMSD. The behaviour before was a random value
as the fallback transformation in these cases was an identity matrix.
While RMSD is still computed on CA/C3' only, we now apply the transformation
derived from all backbone atoms.