Hi Kavya, Which validation program did you use? How big is the deviation (in sigma values)? Is it the only outlier? What is your overall bond angle rmsZ?
Using external restraints is a bit over the top here, especially if it is the only outlier. If your rmsZ is high (close to or over 1) then you may want to try tighter geometric restraints overall. In a normal distribution it is not surprising to find a 'true' outlier, so if your structure is large you need to worry less. Cheers, Robbie Sent from my Windows Phone ________________________________ From: Kavyashree Manjunath Sent: 2013-04-15 07:13 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Angle restraints Dear users, Validation of a structure showed a deviation in the angle between atoms NH1-CZ-NE and NH2-CZ-NE in the arginine residue. Several trials of modification of the orientation failed to solve this problem. I also confirmed by deleting the side chain and refining, it confirmed the presence of complete side chain. So I proceeded to use external restraints for these two angles in refmac5 (version 5.6.0117). The keyword was as follows - external angle first chain A residue 93 atom NE next chain A residue 93 atom CZ next chain A residue 93 atom NH1 value 120.3 sigma 0.5 external angle first chain A residue 93 atom NH2 next chain A residue 93 atom CZ next chain A residue 93 atom NE value 120.3 sigma 0.5 Still there is no change in the angle, it continues to have the same deviation. So kindly suggest whether there is any error in the keyword provided or other way to handle this problem. Thanking you Regards Kavya -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
