Hi, I am getting two errors in pdb validation report as follows: I think I need to use B-DNA constraint in the refinement. This is a 2.4 A data. How can I do that in PHENIX in cammand line promt. Another thing is, I have a small molecule in the complex, which I called as BML. I think that's might be the problem. This is known as BML210. What I should call this compound? Should I also give a chain ID for this compound? See the errors given below. *** Covalent Angle Values: The overall RMS deviation for covalent angles relative to the standard dictionary is 1.4 degrees. The following table contains a list of the covalent bond angles greater than 6 times standard deviation. Deviation Residue Chain Sequence AT1 - AT2 - AT3 Bond Dictionary Standard Name ID Number Angle Value Deviation ------------------------------------------------------------------------------------------- -4.8 DA E 1 C1' - C2' - C3' 97.6 102.4 0.8 -5.8 DA E 2 C1' - C2' - C3' 96.6 102.4 0.8 3.3 DA E 2 N9 - C1' - O4' 111.6 108.3 0.3 -5.0 DC E 5 N1 - C1' - O4' 103.0 108.0 0.7 -5.1 DT E 6 C1' - C2' - C3' 97.3 102.4 0.8 -6.7 DT E 8 C1' - O4' - C4' 103.4 110.1 1.0 2.3 DT E 8 N1 - C1' - O4' 110.6 108.3 0.3 -4.5 DT E 11 N1 - C1' - O4' 103.5 108.0 0.7 -6.1 DA F 2 C1' - C2' - C3' 96.3 102.4 0.8 3.0 DA F 2 N9 - C1' - O4' 111.3 108.3 0.3 -5.3 DC F 5 N1 - C1' - O4' 102.7 108.0 0.7 -4.9 DT F 6 C1' - C2' - C3' 97.5 102.4 0.8 -4.5 DA F 10 N9 - C1' - O4' 103.5 108.0 0.7 -7.8 DA F 11 N9 - C1' - O4' 100.2 108.0 0.7 ==> The following residues have extra atoms: RES MOD#C SEQ ATOMS BML( 100) N1 C10 C11 C12 C13 C14 C15 C16 C17 C18 C19 O2 N2 C20 N3 C7 C8 C9 ERROR: dissociated residue(s): BML 100 Raja