*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
Dear All,
I am nearing the end of refining a structure at 2.2A. I did a final
run with refmac without TLS giving:
Ncyc Rfact Rfree FOM LLG rmsBOND rmsANGLE
rmsCHIRAL $$
$$
0 0.243 0.279 0.770 412162.4 0.010 1.192 0.084
1 0.242 0.279 0.771 411994.7 0.010 1.189 0.085
2 0.242 0.279 0.770 412122.6 0.010 1.189 0.084
3 0.242 0.279 0.770 412108.9 0.010 1.189 0.085
4 0.242 0.279 0.770 412124.6 0.010 1.189 0.085
5 0.242 0.279 0.770 412108.7 0.010 1.190 0.085
6 0.242 0.279 0.771 412086.2 0.010 1.190 0.085
7 0.242 0.279 0.770 412110.0 0.010 1.189 0.085
8 0.242 0.279 0.771 412081.1 0.010 1.190 0.085
9 0.242 0.279 0.771 412098.3 0.010 1.189 0.085
10 0.242 0.279 0.771 412101.6 0.010 1.189 0.085
NB. The geometry may be over-constrained, but this is not the issue (or
at least I don't think so).
I then did a run with TLS, resetting the B-factors to constant, but
everything else the same.
This gave:
Ncyc Rfact Rfree FOM LLG rmsBOND rmsANGLE
rmsCHIRAL $$
$$
0 0.313 0.347 0.641 431881.8 0.0 0.0 0.0
1 0.280 0.314 0.703 424572.2 0.0 0.0 0.0
2 0.266 0.301 0.730 420938.2 0.0 0.0 0.0
3 0.260 0.294 0.742 418564.2 0.0 0.0 0.0
4 0.257 0.290 0.747 417039.8 0.0 0.0 0.0
5 0.255 0.288 0.751 416035.8 0.0 0.0 0.0
6 0.254 0.286 0.753 415380.3 0.0 0.0 0.0
7 0.253 0.285 0.753 414950.6 0.010 1.189 0.085
8 0.232 0.267 0.777 409181.2 0.017 1.373 0.096
9 0.229 0.265 0.782 408371.9 0.014 1.338 0.091
10 0.227 0.261 0.787 407502.1 0.012 1.290 0.092
11 0.226 0.261 0.787 407380.1 0.012 1.283 0.092
12 0.226 0.260 0.790 407000.4 0.012 1.276 0.092
13 0.225 0.260 0.789 407016.7 0.012 1.280 0.092
14 0.225 0.259 0.791 406774.3 0.012 1.278 0.091
15 0.225 0.259 0.790 406858.1 0.012 1.279 0.092
16 0.225 0.259 0.791 406687.7 0.012 1.279 0.092
17 0.225 0.259 0.790 406779.6 0.012 1.286 0.092
As you can see the TLS refinement improved teh R-factors by 2% (but not
noticeably the maps).
However I am curious about the blip in the rmsBOND and rmsANGLE values
once real
refinement started. And it never go back to what is was before.
Any comments as to why this happens after TLS refinement?
thanks
Stephen
**********************************************************************
Dr. Stephen Cusack,
Head of Grenoble Outstation of EMBL
Group leader in structural biology of protein-RNA complexes and viral proteins
Joint appointment in EMBL Gene Expression Programme
**********************************************************************
Email: [EMAIL PROTECTED]
Website: http://www.embl-grenoble.fr
Tel: (33) 4 76 20 7238 Secretary (33) 4 76 20 7306
Fax: (33) 4 76 20 7786 or (33) 4 76 20 7199
Postal address: EMBL c/o ILL, BP181, 38042 Grenoble Cedex 9, France
Delivery address: EMBL c/o ILL, Polygone Scientifique,
6 Rue Jules Horowitz, 38042 Grenoble, France
**********************************************************************
