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
