There are many reasons why this could have ocurred.
One is that your NCS operator is very close to being a crystallographic one.

But you need to give more details of the problem before I can comment sensibly
Eleanor

Sun Tang wrote:
Dear All,

In refining my structure (two molecules in au) that was solved with molecular 
replacement,  refinement starting with restrained lowered the R-free to about 
0.35 while with NCS increased the R-free to 0.55. Does it imply that two 
molecules are quite different or something wrong with the refinement?

Thank you very much for your suggestions?

Best wishes,

Sun Tang



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