I am trying to calculate real-space R-factors and correlation coefficients for an array of different ligand conformations to find out which fits best in experimental density. So far, I have been trying to use Overlapmap in CCP4 6.1.2 to do this, by correlating maps by residue and selecting the list a real-space R-factor option. I would like to compare a map with the ligand omitted to maps calculated with each ligand conformer.
I am supplying Overlapmap with a refmac mtz file calculated without ligand in the model for map 1 and a pdb file that contains both protein and ligand coordinates to calculate map 2. However, I’m confused about the output. For the protein, which I know is well-defined and modeled correctly in the density, I see mostly reasonable correlation coefficients, ~0.9, but the real-space R-factor values are all over the place and range from zero to hundreds. For example, for one residue the correlation coefficient is 0.8309 with an R-factor of 210.333. I am very confused about how to interpret these values. Has anyone else tried to use Overlap for a similar purpose and could give suggestions as to what I’m doing wrong? Thanks!