My knowledge of Fortran is dated, but the ESU_R and ESU_RFREE are
calculated in refmac like this
HESU_CRUIC = SQRT(FLOAT(N_REFINED_ATOMS)/FLOAT(NREFMNPAR))*
+ COMPL**(-0.333333)*HD_HIGH*HRFAC_SHELL_WORK(NB1)
HESU_FREE = SQRT(FLOAT(N_REFINED_ATOMS)/FLOAT(NREFA(1,NB1)))*
+ COMPL**(-0.333333)*HD_HIGH*HRFAC_SHELL_FREE(NB1)
Completeness and resolution are the same in both, so for the ratio of
the two you get
ESU_R/ESU_RFREE=SQRT(Nrefl/(Nrefl-Npar))*(R/Rfree)
First factor will always be >1, second <1. It seems to me that R/Rfree
stays roughly constant at various resolutions, so ESU_R > ESU_RFREE will
hold at lower resolutions, where Nrefl is small.
Now to specific numbers in your case:
R=18.343, Rfree=23.766, Nrefl=8006, Npar=4*1577=6308
(it appears to me that with isotropic Bfactors refmac indeed uses
Npar=4*Natoms)
This gives
ESU_R/ESU_RFREE ~1.68, in perfect agreement with stated ESU's
(0.468/0.279~1.68)
Ed.
On Mon, 2010-01-11 at 12:12 +0100, Mueller, Juergen-Joachim wrote:
>
> Dear all,
> a solved 2.6 Ang. structure shows the following estimated coordinate
> errors
> REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
> REMARK 3 ESU BASED ON R VALUE (A):
> 0.468
> REMARK 3 ESU BASED ON FREE R VALUE (A):
> 0.279
> REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A):
> 0.217
>
> Similar values are calculated by REFMAC independent of its version.
> The reverse order
> (at least for Rvalue and Rfree) makes more sense to me. Using the
> formula for the ESDs given in the REFMAC documentation also a reverse
> order seems to be correct (Parameters are given in the full pdb-header
> attached).
> Unclear to me is whether the restraints are included in the item
> Nparam or not. I choose Nparam=4 x Natom. Or what could be the reason
> for discrepancy?
> Any comments are welcome
> Jürgen
>
>
--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
----------------------------------------------
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Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
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------------------------------ / Lao Tse /
