<div dir="ltr">Dear all,<br><br>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).<br>
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:<br><br><span class="gmail-im">dihedral pdb=" CB GLN B 21 "<br>
pdb=" CG GLN B 21 "<br>
pdb=" CD GLN B 21 "<br>
pdb=" OE1 GLN B 21 "<br>
ideal model delta sinusoidal sigma weight residual<br>
0.00 23.41 -23.41 2 3.00e+01 1.11e-03 8.42e-01<br><br></span><br>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.<br>
Thanks,<br>
<br>
<br>
Renato<span class="gmail-im"></span></div>