Two of the lower resolution structures have rmsd of 0.002 Å. _____________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, U-M Medical School Room 3220B, MSRB III | [email protected] | +1 (734) 764-3353

On Jul 25, 2017, at 7:03 PM, Nigel Moriarty wrote:

Mark

Can you verify the RMSD range for bonds? Is it, "0.005-0.002" as stated or "0.005-0.02"?

Cheers

Nigel

--- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

...

On Tue, Jul 25, 2017 at 3:52 PM, Mark Saper wrote: Hi all,

A reviewer points out that my refined structures (which have already been deposited in PDB) have very small RMSD values for bond lengths (0.005–0.002) (refinement resolutions are 2.0–2.8 Å), and that my weights should be decreased. The weights were calculated with “Optimize XYZ Weight” option turned ON. This seems to be the case with all of the structures that I have refined during the past 5 years. My impression from previous discussions is that deriving explicit weights from these optimized ones is not straightforward and so I have never tried to relax the weights. Moreover inspecting the optimization results in the log file, suggest that changing the weights to increase the RMSD would increase the Rfree. (I can post this if its helpful).

How do I address the reviewer’s concerns?

Thanks, Mark _______________________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, U-M Medical School Room 3220B, MSRB III [email protected] +1 (734) 764-3353

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Dear Luke, I missed where your quote comes from, so please apologise if I address you incorrectly. The statement We prefer to maintain Rfree and (Rfree-Rwork) both as small as possible to minimize the possibility of overfitting. is not quite right: there is an expected gap between Rfree and Rwork, i.e. if this gap becomes too small, something is wrong, e.g. a real contamination of Rfree by an oversight of Twinning, NCS, or a higher space group (Ian Tickle's articles on this topic is probably the best reference and available at Acta Cryst). Best, Tim On Wednesday, July 26, 2017 1:45:55 AM CEST Luke Rice wrote:

Mark,

I think a reasonable strategy is to acknowledge the concern, inform the reviewer about what changes if you do as asked, and use that as a data-driven way of justifying your decision. I pasted below what worked for me when I had to address a similar issue in review.

...

“the geometry is too tight” This is a frequently debated point among crystallographers, and there is no clear consensus. Given the challenges of our data (anisotropy, moderate completeness and resolution), we do not believe there is sufficient information content in the data to warrant significant deviations from ideal bond lengths and angles. Test refinements using different weights between the X-ray and stereochemical terms bear this out: allowing the geometry to relax by choosing a weight such that bond and angle deviations in the refined model are 0.01 Å and 1.3° results in Rfree decreasing by 0.3% while Rwork decreases 2.5%. Thus, we could have achieved a slightly lower Rfree at the expense of significantly greater decrease in Rwork. We prefer to maintain Rfree and (Rfree-Rwork) both as small as possible to minimize the possibility of overfitting.

Good luck,

Luke

...

On Jul 25, 2017, at 5:52 PM, Mark Saper wrote:

Hi all,

A reviewer points out that my refined structures (which have already been deposited in PDB) have very small RMSD values for bond lengths (0.005–0.002) (refinement resolutions are 2.0–2.8 Å), and that my weights should be decreased. The weights were calculated with “Optimize XYZ Weight” option turned ON. This seems to be the case with all of the structures that I have refined during the past 5 years. My impression from previous discussions is that deriving explicit weights from these optimized ones is not straightforward and so I have never tried to relax the weights. Moreover inspecting the optimization results in the log file, suggest that changing the weights to increase the RMSD would increase the Rfree. (I can post this if its helpful).

How do I address the reviewer’s concerns?

Thanks, Mark _______________________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, U-M Medical School Room 3220B, MSRB III [email protected] +1 (734) 764-3353

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