Dear Yangzhang,
I performed one refinement on your Modrefiner serve (https://zhanglab.ccmb.med.umich.edu/ModRefiner/). I could not understand the meaning of RMSD and TM-score values, and what is the acceptable range of these values. For one of my refinement at your server the RMSD value was as high as 14.5, what it indicates, is the model ok?
Do the server also perform refinement for protein models with gaps?
Many thanks for your suggestions and kind help.
Sincere regards,
Sukrit