Dear Pavel,

On Oct 9, 2015 I have e-mailed to you my experience with 1.9-1692 and version 1.10 (and 1.10.1) on phenix.real_space_refine.

Today I just completed another protein phenix.real_space_refine. For the following comparison runs, the initial model same, the map same, all 5 macro_cycles default run.

For version 1.10.1, the results were as following,

Map CC (whole unit cell)： 0.672

Map CC （around atoms）： 0.761

rmsd （bonds): 0.01

rmsd (angles): 1.55

All-atom clahscore: 39.27

Ramachandran outlier: 0.98%

Ramachandran allowed: 12.71%

Ramachandran favoured: 86.31%

Rotamer outliers: 0.91%

C-beta deviations: 0

For version 1.9-1692, the results were as following,

Map CC (whole unit cell)： 0.645

Map CC （around atoms）： 0.687

rmsd （bonds): 0.0071

rmsd (angles): 1.15

All-atom clahscore:16.88

Ramachandran outlier: 2.00%

Ramachandran allowed: 6.23%

Ramachandran favoured: 91.77%

Rotamer outliers: 0.05%

C-beta deviations: 0

For the version 1.10.1 phenix.real_space_refine, the most unacceptable was on the clashscore, the whole refine process seems did not care on the clashcore refine at all.

I am looking forward to getting an explanation from you on the causes of the difference for phenix.real_space_refine for the 2 versions, and the possible strategy we can take to eliminate the difference to get the acceptable results.

Best regards.

Smith

On Friday, October 9, 2015 12:52 AM, Smith Lee <[email protected]> wrote:

Dear Pavel，

As I have told you, I have tried phenix.real_space_refine for 2 protein with version 1.9-1692 and version 1.10 (and 1.10.1) for many times, with cif or without cif, with or without annealing. The general feedback was that the version 1.9-1692 was much much better for the final analysis of the PDB given at the end of the run of the phenix.real_space_refine. Especially for clashing score, version 1.9-1692 can gave acceptable results (below 20 or around 20), but the clashing score given by the above 2 new versions of phenix.real_space_refine was very high (around 50 or 100). For C-beta deviations, the output by 1.9-1692 was also much better

Before I have tried the other nightly built versions of phenix.real_space_ refine between version 1.9-1692 and version 1.10 (and 1.10.1) , all I gave acceptable output analysis (something like the Molprobity analysis at the end of the run).

Thus may I ask the reason you have version 1.10 (and 1.10.1) phenix.real_space_refine was because you have realized that the result given by version 1.9-1692 was too satisfactory?

One direct concern of me was that you have recommended not to use the old version phenix. But I cannot get the satisfactory result with the new version phenix.real_space_refine.

The other concern of me was that, I have noticed there were publications In Nature and Science which wrote they use phenix.real_space_refine to got the results in Nature and Science. The Phenix they used should be the versions earlier than version 1.10. Considering what I mentioned above, the Nature and Science results may be not so correct, if new version of phenix was considered as much better than the old version.

Thus am I the only user who communicated with you on the high clashing score given by the new version of phenix？Can you give some comments on what I mentioned above on the high clashing score given by the new version phenix.real_spac_refine?

Best regards.

Smith