>> "...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 >
