Dear Kavya,
First try Herman's suggestions. You can try changing the restraint weight but it will probably not solve the problem; it may hide it. If you cannot solve the problem and you did the best you can do, you can deposit the model with the outlier. The PDB does not reject models with (minor) issues.
Future users will be warned by REMARK 500 if they want to use that specific arginine for further research.
Cheers,
Robbie
Sent from my Windows Phone
________________________________
From: Kavyashree Manjunath
Sent: 2013-04-15 09:35
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
>
>
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