[phenixbb] Low resolution refinement

Pavel Afonine pafonine at lbl.gov
Tue Nov 16 12:58:00 PST 2021

Hi Armando,

> I have got a very promising MR solution at 5A resolution. Can I refine this structure? Any hint would be very much appreciated

this is a low resolution indeed, so modeling and refinement is likely to 
be challenging. All the standard 'low-resolution refinement' advises 
apply here. Since there are few data (low-res) you need to employ as 
much 'a priori' known information as possible, in form of restraints 
or/and constraints. Those typically include:

- If NCS is present, use NCS constraints (yes, constraints, not 
restraints, as at this resolution you are highly unlikely to see 
data-supported genuine differences between NCS copies!);

- if similar homologous models obtained at higher resolution are 
available -- try using them as reference models;

- Use secondary structure restraints. Important: make sure to obtain 
secondary structure annotation as accurately as possible.

- Use Ramachandran plot restraints (to avoid appearing outliers during 
refinement, not to fix existing ones!);

- Avoid stretching your imagination by adding model in the absence of 

- At this resolution refining group B factors (two B per residue) may be 
a good idea.

Let me know if you have any more specific questions!

Good luck!

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