[phenixbb] Problem with rotamer refinement

Pavel Afonine pafonine at lbl.gov
Tue Jul 11 10:10:34 PDT 2017

Hi Renato,

could you please send me files that are sufficient to reproduce this?


On 7/11/17 10:06, Renato Ferras wrote:
> Dear all,
> I am refining a protein structure at 1.74 A resolution with 
> phenix.refine (version 1.10.1_2155) and I have noticed that some side 
> chains don't remain in the electronic density even after careful hand 
> adjustment in which they are almost perfect. It seems pretty clear 
> where the side chain should (must) be located, moreover it is 
> consistent with two rotamers (either rotamer tp60 - #4 in coot - or 
> rotamer tp-100 - #9 in coot -, which are approx. at 180 deg for chi3). 
> In spite of that, after reciprocal space refinement, I observe that 
> the end of side chain rotates chi3 angle and both N and O gets far 
> from where they started (there is this difference in the chi3 angle).
> My concerns are about the proper interpretation of geometrical 
> restraints listed in .geo file, specially what the ideal value is, how 
> weights are applied to ideal value and why phenix doesn't reach 
> convergence in reciprocal space refinement. Below are the values from 
> .geo for the referred Gln:
> dihedral pdb=" CB  GLN B  21 "
>             pdb=" CG  GLN B  21 "
>             pdb=" CD  GLN B  21 "
>             pdb=" OE1 GLN B  21 "
>     ideal   model   delta    sinusoidal    sigma weight residual
>     0.00   23.41    -23.41       2            3.00e+01 1.11e-03   8.42e-01
> is there a description for us to interpret what these numbers are? To 
> my understanding, the ideal values are established as being either 0 
> or 180 degrees (yet sinusoidal 2). I cannot say about how heavy the 
> weights are on these (in fact, I left my refinement to optimize 
> weights), but anyway, if I understand correctly, the ideal value (for 
> chi3) should be rotamer dependent. Taking Gln as an example, I see 
> several rotamers do have values close to either 0 or 180 degree, but 
> what about rotamers 4 and 9? I might imagine a similar situation for 
> residues like Asn and His, though I have not searched deep for these yet.
>     Thanks,
> Renato
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