[phenixbb] Error message on minimization global

Phil Jeffrey pjeffrey at princeton.edu
Tue Mar 8 11:53:08 PST 2022

I'm not sure how you ended up with all those Mets labeled like this, but 
the sulfur in Methionine is SD, not S.

ATOM   2267  SD  MET A 289      -8.619   2.711 -11.138  1.00 81.12 

Fix the atom name (keep the S in the same column) and you should be OK.

Phil Jeffrey

On 3/8/22 2:37 PM, Abhipsa Shatarupa wrote:
> Hello,
> I am a beginner in phenix. Currently, I am running minimization global 
> under real-space refinement. The input files for this job are a .pdb 
> file generated from rigid-body refinement and a .ccp4 map. I end up 
> receiving the following error message (image attached -Error file). The 
> output log file gives me the description of the number of atoms and the 
> atoms responsible for generating the error (image attached – atoms file).
> I ended up finding a couple of Q/A on a similar error message, but I am 
> not sure how to generate the CIF file to overcome the problem using eLBOW?
> Could someone please help me resolve this issue?
> Thanks in advance,
> Abhipsa
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