It may be helpful to include the coordinate file for inspection. With just what you've said, ensure you don't have alternative conformations on the residue to which atom 3662 belongs. Some crystallographic refinement programs will output just hydrogens in alternative positions, so e.g. there may be 2 HD1 hydrogens on that residue and HD1 in A conformation is involved in an H-bond and HD1 in B conformation involved in a different H-bond, giving you a bad group size.

thanks, Dr.coban,

I have solved this problem.