*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
Dear Tea
You do not need to worry about it. Scaling is different in different
programs and if you use TLS then you may get even larger
differences of Rfactors between REFMAC and SFCHECK. Sfcheck can not
handle TLS yet.
regards
Garib
On 25 Aug 2006, at 10:09, Tea Pavkov wrote:
*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
Dear all,
I refined my structure using REFMAC5 and afterwards I ran PROCHECK/
SFCHECK.
And I got a higher R-factor and Rfree than the ones reported by
REFMAC. Is
it something to be worried about? What could cause this difference?
Thank you in advance!
Tea
This is the first part of the output:
--- Model ---
Number of atoms: 3428 ( 255 water molecules)
% VOLUME not occupied by model : 41.8
<B> / for atomic model / : 41.74
sigma(B) : 9.48
Matthews coefficient : 2.79
corresponding % solvent : 55.58
Reported R-factor : 0.204
Number of chains: 2
----------------------------------------------
--- Refinement ---
Program : REFMAC 5.2.0005
Resolution: 15.00 - 2.20
Reported R-factor : 0.204
Rfree : 0.271
----------------------------------------------
--- Structure factors ---
Resolution /input data/ : 24.56 - 2.10
Number of reflections : 27435 ( in_file : 27435)
Number of reflections with I > sigma(I) : 27214
Number of reflections with I > 3sigma(I): 17431
R_stand(I) = <sig(I)>/<I> : 0.070
Number of acceptable reflections: 24795
for resolution : 24.56 - 2.20
reflections out from resolution : 2640
Optical Resolution: 1.74
Expected Optical Resolution for complete data set: 1.74
/ Optical resolution - expected minimal distance between
two resolved peaks in the electron density map./
Number of max possible refls : 26779 actual : 24795
Completeness : 92.6 %
R_stand(F) = <sig(F)>/<F> :0.067
Boverall /estimated by Patterson/ : 35.13
Minimal estimated error : 0.0367
Anisotropic distribution of Structure Factors:
Ratio of Eigen values : 0.5927 0.5942 1.0000
----------------------------------------------
--- Model and Structure factors---
R-factor : 0.2367
Correlation factor : 0.9241
R-factor(for s/F >= 2.0 and resol. 15.0 - 2.20 A)= 0.2385
N_refls : 24527
Rfree,Rrest : 0.306 0.235
Nfree,Nrest : 1246 23281
Corr-factor(for s/F >= 2.0 and resol. 15.0 - 2.20 A)= 0.9223
<u> /error in coords by Luzzati plot/ : 0.2933
Scaling /by Patterson/ Scale,Btemp,Boff : 0.928 -4.24 256.00
Anisothermal scaling:
Beta: -0.89504 -0.90240 5.35325 0.00000 -0.43827 0.00000
Solvent correction: Ks,Bs: 0.721 250.024
Maximal estimated error : 0.1595
DPI : 0.2059
---------------------------------------------------------
Mag. Pavkov Tea
Institute of Chemistry - Structural Biology
Karl-Franzens-University Graz
Heinrichstrasse 28, 8010 Graz, Austria
Phone: ++43 316 380 5414
Fax: ++43 316 380 9850
http://PhysChem.kfunigraz.ac.at/sb
---------------------------------------------------------
