RE: [ccp4bb]: planarity restraint in refmac5

["Bernhard Rupp" <br@llnl.gov>]

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My experience in agreement with Garib's advice is that the 
X-ray weights are probably set high in default. I occasionally
run a regularization and refine few cycles with x-ray weights 
low (Garib suggested 0.1, or lower at low res ( < 3.0)).

In 4 cases I ran recently the Rfree dropped while closing
the gap to R from 5 to 2-3% (R got higher). Same holds for bonds,
I noticed that with standard weight for example CD-SD, SD-CG METS 
have a tendency to depart a lot from their positions. I also
had modest data in a rather flexible protein, so take
what I say with a gain of salt. However, same was obseved on some
bonds in 1.5 A with Rf20.5 R 18.6. Judging from that,
the procedure improves both your crossvalidation/refinement 
and the geometry. In the maps, the deviations we talk about
are nearly imperceptible, so there is no real reason to accept
such obviously unprobable deviations (except if you are possessed
by lowering standard Rfactors and ready to accept a rough rap sheet 
from what-check)....     

BR
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Dr. Bernhard Rupp
Macromolecular Crystallography and Structural Genomics  
LLNL-BBRP L448                               Phone (925) 423-3273
University of California                     Phax  (925) 424-3130
Livermore, CA 94551                          email    br@llnl.gov
URL                                 http://www-structure.llnl.gov
TB Structural Genomics Consortium  http://www.doe-mbi.ucla.edu/TB
EU Mirror  http://www.ccp14.ac.uk/ccp/web-mirrors/llnlrupp/
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> -----Original Message-----
> From: owner-ccp4bb@dl.ac.uk [mailto:owner-ccp4bb@dl.ac.uk]On Behalf Of
> Huiying Li
> Sent: Friday, July 13, 2001 9:50 AM
> To: ccp4bb@dl.ac.uk
> Subject: [ccp4bb]: planarity restraint in refmac5
> 
> 
> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
> 
> 
> After running 10 cycles of refinement with REFMAC5 through CCP4i GUI, I
> have noticed the planarity of all the aromatic side chains (Phe, Tyr,
> Trp) was distorted. Is this normal as a 0.02A deviation from the
> planarity is allowed in the library file, mon_lib_prot.cif, or had I done
> something wrong?
> 
> The related settings I used:
> Setup Restraints: "Do not check anything"
> Scaling Fobs and Fc: Bulk solvent scaling and Apply anisotropic scaling
> Other parameters: Damp shifts Pdamp 0.5 Bdamp 0.5 
> Geometric parameters: all the restraints was turned on except NCS
> 
> Thanks for any help.
> 
> Huiying Li
> --------------------------------------------------
> Huiying Li, Ph. D
> Department of Molecular Biology and Biochemistry
> University of California at Irvine
> Irvine, CA 92697, USA
> Tel: 949-824-4322(or -1797);  Fax: 949-824-3280
> email: hli@bragg.bio.uci.edu
> --------------------------------------------------
> 
>