"...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 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
