[phenixbb] some general refine questions

William Scott wgscott at chemistry.ucsc.edu
Sat Jun 30 11:16:08 PDT 2007


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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