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Probably, you have built water molecules that are associated with symmetry-related macromolecules rather than the host molecule. Turn symmetry on, check the nearest neighbors of the offending waters, and move the waters close to the host molecule if appropriate. I believe you can do this with the CCP4 program watertidy. kmj On Thu, Mar 11, 2010 at 12:15 PM, Azadeh Shahsavar < [log in to unmask]> wrote: > Dear All, > > In depositing a pdb file, after validation step, an error comes up: > *Solvent Atoms* The following solvent molecules lie farther than expected > from the protein. > > Can any one give me some advice about it? > deleting these water molecules results in a large increase of R factor, by > the way. > > Thank you in advance, > > A >