>Hello Georg,
Some of the atoms in your model are ending up with a negative value of U,
hence the warning. You might want to look at any disorder associated with
these atoms and refine their occupancies. If that doesnt help try
tightening the restraints that you are using for refinement. They might
also get rectified when you use all of your data for refinement, meaning
when you are not using any R free.
Hope one of these works for you.
Arti Pandey
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
>
>
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