[phenixbb] R-merge and MOLREP

Nathaniel Echols nechols at lbl.gov
Tue Jul 12 19:20:23 PDT 2011

On Tue, Jul 12, 2011 at 6:53 PM, Yuri <yuri.pompeu at ufl.edu> wrote:
> 1-I see a  reasonable chi-square value 1.69 but r-merge 0.15 (0.49 at 2.75
> A). It was 0.20 before I excluded some bad frames.
> I thought this R value is a bit high... Is it? Mosaicty was around 1.00.

It is on the high side, but I've seen worse.  Others might have ideas
on how to improve it, but some datasets are like this, and sometimes
the processed data works just fine for refinement.  (Some peer
reviewers enjoy complaining about crystallography statistics,

> 2- My search model has an identity of around 40%. I tried MOLREP. Seems I
> got a solution LLG=486 PAK=10 TFZ ~30 RFZ ~20.
> My R-free before any refinement is 0.54. Two questions here, a) I think I
> only fully understand the meaning of LLG, what about PAK and both Z-values?

Do you mean MOLREP the program, or just shorthand for molecular
replacement?  I'm assuming the latter since I don't think MOLREP
reports statistics like those, but the answer does depend on the

I believe PAK is the number of bad clashes between place molecules;
for a 40% identical model 10 clashes isn't terribly surprising (I
believe the cutoff is 15 or so).  Running Sculptor on the search model
will trim off some of the most divergent parts and probably decrease
the clashes and improve your solution in general - this is highly
recommended and will make rebuilding much easier later.

RFZ and TFZ are "Z-scores" for the rotation and translation functions
respectively.  RFZ in Phaser isn't very relevant, but TFZ (along with
non-negative LLG) is the most important indicator of whether the
structure is solved.  A TFZ above 8 with a single copy placed almost
always means that MR worked; if you have multiple copies it might need
to be higher (I'm not sure what the exact rules are).  These
statistics look very encouraging, anyway.

> b)is this R-free acceptable or is it also a little high?

This is normal for an unrefined MR solution, especially if it isn't
sequence identical - what matters is whether it decreases
significantly when you refine.


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