I build a homology model for a protein which show 44% sequence identity with its template and molprobity score is 1.59
"[The MolProbity score] is a log-weighted combination of the clashscore, percentage Ramachandran not favored and percentage bad side-chain rotamers, giving one number that reflects the crystallographic resolution at which those values would be expected. Therefore, a structure with a numerically lower MolProbity score than its actual crystallographic resolution is, quality-wise, better than the average structure at that resolution."
Article MolProbity: All-Atom Structure Validation for Macromolecular...
The score is supposed to reflect crystallographic resolution, but in the end it is just a number. Taking the MolProbity of the template and comparing them together will tell you which residues have new critical errors. They're mostly around prolines and glycines. Even if you have score in the green from first trial, it is still advisable to correct the errors before proceeding. Easiest way to do refinement is by "selecting" the residues with errors and minimizing their energy specifically. Even before you minimize the whole system.
Hi Nikunj,
I agree with Yazad, rather than paying attention to the molprobity score you have to check that the conformational and geometric criteria have acceptable values, and if it is not the case to make more refinements of your model using some online server such as MODREFINER SERVER or MD simulations to improve the geometric and conformational criteria.
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