(color online) The intermediate conformation derived from the post-translocation state. (a) Distribution of the displacement of -end of DNA–RNA hybrid (). Yellow and green lines represent Gaussian fits; the blue line represents the sum of two Gaussians. (b) Distribution of displacements of CA atom of residue Y639. Yellow and green lines represent Gaussian fits; the blue line represents the sum of two Gaussians. (c) A 2D sampling map along the displacement of CA atom of Y639 and the displacement of CA atom of R627. Color-coding represents relative free energies (−ln P) as indicated with color bar. (d) A snapshot of the intermediate state where the side chain of the template DNA nucleotide has moved into the active site. Components near the active site of pre- and post-translocation conformations are shown in green and yellow, respectively. The red one is the snapshot derived from our MD trajectories.