Hi,

Am I missing a trick to get my Arginines planar?

I took a reasonably refined PDB (no non-planar arg) (coming out of PHENIX) and 
noticed a series of close contacts so did some limited  “sphere refine” against 
my 2.9A EM map and now I have fewer close contacts but gained 5 non-planar 
Arginines (sidechain) according to the PDB deposit review. I’ve seen this 
before. There is some problem in coot with the Arg refinement restraints.

Original is green and sphere refined is yellow – looking down the guanidinium 
group and the NE hydrogen is wonky.
[A close up of a network  Description automatically generated]

If I “send in the bond angles” then the NE hydrogen straightens out but the 
NH1/2 hydrogens go off axis.

Heidi


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