[phenixbb] Problem with rotamer refinement

Renato Ferras renatoferras.p at gmail.com
Tue Jul 11 10:06:05 PDT 2017

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.

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