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: 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
>
>
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