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Sir, I have examined the density. Its extremely clear. I am attaching the 2FoFc map map of this residue. As I mentioned previously, The side chain density was conformed by deleting it and refining. Thank you Regards Kavya > Dear Kavya, > > I would examine the electron density of your Arginine. It may be present > in two alternative conformations and you may have fitted the Arginine in > the middle, e.g. with the NH1 in one conformation and the NH2 in the > other. > > The Arginine may also just be incorrectly fitted. Using Coot with "Auto > Fit Rotatmer" and "Real Space Refine Zone" you might be able to correct > it. Just using "Regularize Zone" on the Arginine might give hints how the > Arginine got distorted. However, before running another round of > refinement, it needs to be fitted back in electron density. > > Best, > Herman > > -----Original Message----- > From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of > Kavyashree Manjunath > Sent: Monday, April 15, 2013 9:41 AM > To: [log in to unmask] > Subject: Re: [ccp4bb] Angle restraints > > Sir, > > I used RCSB validation server. Deviations are as given below - > Deviation Resi AT1 - AT2 - AT3 Bond Dict Std > Angle Value Dev > -------------------------------------------------------------- > 3.2 ARG NE - CZ - NH1 123.5 120.3 0.5 > -3.4 ARG NE - CZ - NH2 116.9 120.3 0.5 > > > Thus its more than 6 sigmas in both the cases. Its not an outlier. > zANGL is 0.628 and Rms BondAngle is 1.4077. > would you suggest me to ignore this deviation? But will it not be a > problem during PDB submission? > What is the reason I am getting a deviation like this? Should I reduce the > weighing term further down? > > Thanking you > Regards > Kavya >> 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: [log in to unmask] >> 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. >> >> -- >> This message has been scanned for viruses and dangerous content by >> MailScanner, and is believed to be clean. >> >> > > > > -- > This message has been scanned for viruses and dangerous content by > MailScanner, and is believed to be clean. > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.