>> "...They might
>> also get rectified when you use all of your data for refinement, meaning
>> when you are not using any R free..."
>>
>>
> Sorry to go off on a little tangent here - but doesn't refining against
> ALL
> of your data generally mean that your RFree is no longer your "free" and
> cannot be used for cross-validation...
I meant at the final stage of refinement, when we are satisfied with the
progress and result of refinement
Arti Pandey
I was always taught that the reflections within the test set are
> sacrosanct
> - is this not also the case for circa atomic resolution data? Perhaps
> someone more learned than I could shed a little light on this...
>
> Dave
>
> Hallo to all out there,
>> >
>> > I have a problem refining a structure against a 1.33 A resolution data
>> > set. Using REFMAC (version 5.2.0019, also tested version 5.3) with
>> > isotropic B-factor refinement resulted in an valid model with R /
>> > R(free) of 17.8 / 19.2%.
>> >
>> > To finish the model I tried to use anisotropic refinement which should
>> > be possible/reasonable because of an observable to parameter ratio of
>> > about 2.8. This refinement yielded to a much better R / R(free)-Factor
>> > of 14.1 / 16.8% and converged after about 15 cycles of anisotropic
>> > refinement. However the problem is that running a few cycles of
>> > refinement resulted in warnings, logged as "Problem in
>> MAKE_U_POSITIVE".
>> >
>> > So what would be the right solution to overcome this problem?
>> >
>> > Some further information about the data set:
>> >
>> > spacegroup P 6(5) 2 2, one protomer per ASU
>> > cell axis 76.615 76.615 209.787 90.00 90.00 120.00
>> > unique reflections 83156 (6220)
>> > Completeness 98.6 % (87.9%)
>> > I/Sigma 21.4 (3.5)
>> > Rmrgd-F 5.9% (35.0%)
>> >
>> > Maybe the refmac-script will be of some help (some other BFAC
>> restraints
>> > and SPHE/RBON parameter tested, the following example takes care of
>> > reasonable distribution of anisotropy):
>> >
>> > #!/bin/bash
>> > refmac5 hklin ../gz_ccp4.mtz \
>> > hklout gz_aniso_01f.mtz \
>> > xyzin ./gz_iso.pdb \
>> > xyzout gz_aniso_01f.pdb \
>> > libin ../llp_citrat_fitted.cif \
>> > << end_ip > refmac.log
>> > LABI FP=F_cit_01 SIGFP=SIGF_cit_01 FREE=FreeR_flag
>> > LABO FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT
>> > FOM=FOM
>> > NCYC 20
>> > REFI TYPE RESTRAINED
>> > REFI RESI MLKF
>> > REFI METH CGMAT
>> > REFI RESO 25 1.33
>> > REFI BREF ANISOTROPIC
>> > SCAL TYPE BULK
>> > SCAL LSSC ANISO NCYCLES 10
>> > SCAL MLSC NCYCLES 10
>> > WEIG MATRIX 1.25
>> > SPHE 30.0
>> > RBON 30.0
>> > BFAC 0.5 2.0 4.0 4.0 6.0
>> > MAKE CHECK ALL
>> > MAKE HYDROGEN ALL
>> > MAKE HOUT NO
>> > MAKE PEPTIDE NO
>> > MAKE CISPEPTIDE NO
>> > MAKE SSBRIDGE NO
>> > MAKE CHAIN YES
>> > MAKE SYMMETRY YES
>> > MONI MANY TORS 10 DIST 10 ANGL 10 VAND 10 PLANE 10 CHIR 10 BFAC 10
>> BSPH
>> > 10 RBOND 10
>> > BINS 20
>> > PNAM gz
>> > DNAM gz
>> > USEC
>> > END
>> > end_ip
>> >
>> > The final refinement statistic:
>> >
>> > Resolution limits = 25.000 1.330
>> > Number of used reflections = 81889
>> > Percentage observed = 98.6122
>> > Percentage of free reflections = 1.5000
>> > Overall R factor = 0.1409
>> > Free R factor = 0.1681
>> > Overall weighted R factor = 0.1348
>> > Free weighted R factor = 0.1641
>> > Overall correlation coefficient = 0.9763
>> > Free correlation coefficient = 0.9688
>> > Overall figure of merit = 0.9183
>> > ML based su of positional parameters = 0.0274
>> > ML based su of thermal parameters = 1.5420
>> > rmsBOND = 0.014
>> > rmsANGLE = 1.569
>> >
>> > Thanks in advance,
>> > georg zocher
>> >
>> >
>>
>
>
>
> --
> ---------------------------------------
> David Briggs, PhD.
> Father & Crystallographer
> www.dbriggs.talktalk.net
> iChat AIM ID: DBassophile
>
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