Look at http://swift.cmbi.ru.nl/servers/html/index.html under "structure validation" you will find a server that predicts which peptide planes most likely need to be flipped. This server is the implementation of:

Detection of trans-cis flips and peptide-plane flips in protein structures.

Touw WG, Joosten RP, Vriend G.

Acta Crystallogr D Biol Crystallogr. 2015 Aug;71(Pt 8):1604-14. doi: 10.1107/S1399004715008263. Epub 2015 Jul 28.

Good luck,

Gert

On 10-10-2017 15:28, Yang Shi wrote:

Hi, Tristan Croll,

Thanks for your suggestion.I will consider to rebuild these first.

Yang

在 2017年10月10日，下午9:18，Tristan Croll <[log in to unmask]> 写道：

Relying on refinement to fix cis peptide bonds for you is unlikely to end well. It looks to me like you really need to spend some time investigating and manually rebuilding these first.

On 2017-10-10 13:52, 师扬 wrote:

Dear all,
I am refining a model based on a 4.3A EM density map,and there are
some cis-peptides in the beginning model.
By using phenix.real_space_refine with a very low cis-peptide
threshold (0), all the cis-peptide become to the twisted.
The start Omega angle:
cis-proline: 31.63 %
twisted proline: 0.00 %
cis-general: 11.11 %
twisted-general: 0.05 %
The final Omega angle:
cis-proline: 0.00 %
twisted proline: 27.55 %
cis-general: 0.00 %
twisted-general: 6.04 %
My questions are:
1) What is the twisted peptide?
2) Is the amount acceptable at the current resolution?
2) How to refine it?
Thanks in advance!
Yang Shi
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