[phenixbb] depositing phenix-refined coordinates

[Enrico Malito]

Hi All,
I have just completed the refinement of 2 structures by phenix, and  
I'm really really impressed.
Particularly impressed by elbow and LigandFit, just wonderful.
However, I would be very grateful if someone could point me to the topic
already posted in the message below by Dr. Scott few days ago,  
exactly at:
"a quick description for depositing phenix-refined coordinates?",
though the full message contained very interesting points I would  
love to hear about
(I also performed refinement by refmac/phenix, and observed kind of a  
similar trend
for those numbers).

Thanks in advance.
EM

***
Enrico Malito
Ben-May Department for Cancer Research
Center for Integrative Science, W423J
The University of Chicago,
929 E. 57th Street,
Chicago, IL, 60637
Tel: 773-702-4608
Fax: 773-702-6260


On Jun 30, 2007, at 1:16 PM, William Scott wrote:

> Hi folks:
>
> With the helpful advice of the phenix crew, I've re-refined 2goz, an
> entry in the pdb in which I used refmac5 the first time around.
>
> There was a small error in the pdb:  One nucleotide (C8 in chain A)
> was rotated 180 degrees about the glycosylic bond from where it
> should have been.  The net result is one oxygen atom was in the wrong
> place in the structure, and this was apparent within the difference
> Fourier. After I rotated the base and re-refined in refmac, the
> Rfactor and other stats remained essentially unchanged (so this fix
> has nothing to do with the following):
>
>
> My refinement results in Refmac:
>
> REMARK   3   R VALUE            (WORKING SET) : 0.191
> REMARK   3   FREE R VALUE                     : 0.241
>
> REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS
> WEIGHT
> REMARK   3   BOND LENGTHS REFINED ATOMS        (A):     1503 ;
> 0.009 ;    0.021
> REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):  2331 ; 1.676 ;
> 3.000
>
>
>
> Then I refined in phenix.
>
> I get
>
> REMARK Final: r_work = 0.1737 r_free = 0.2224 bonds = 0.003 angles =
> 0.745
>
>
>
> So the working and free R factor are both lower, and the geometry is
> substantially tighter.
>
> If I relax the weights in phenix, even to get rms bonds of around
> 0.006, the free-R goes up, which tells me this is not something I am
> justified in doing.
>
> Phil Evans once told me that anything tighter than about 0.01
> (conservatively) was science-fiction, in that this is within the
> error of the idealized libraries for bond lengths.
>
> Other people have asked me about this too, and I didn't know how to
> reply.
>
> Is bonds = 0.003 angles = 0.745  realistic, or have I done something
> wrong?  Even if I do structure idealization in Refmac, I can't get
> the rms bonds below about 0.005 (and my understanding is that it uses
> the same monomer library).
>
> Why is the weight multiplied by 0.5 by default?  Since changing that
> to 1.0 slightly increases freeR, I assume it is the default for some
> reason.
>
> All the best,
>
> Bill
>
>
> PS:  Could someone point me to a quick description for depositing
> phenix-refined coordinates?  (The latest phenix installer seems to
> have omitted the docs.)
>
>
> William G. Scott
>
> contact info:  http://chemistry.ucsc.edu/~wgscott
>
>
>
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