From: SMTP%"gkleyweg at laplace.csb.yale.edu" 6-JUN-1996 16:44:02.47
To: gerard at xray.bmc.uu.se
CC:
Subj:
From: Gerard Kleywegt <gkleyweg at laplace.csb.yale.edu>
Date: Thu, 6 Jun 1996 10:57:23 -0400 (EDT)
Message-Id: <199606061457.KAA14897 at kepler.csb.yale.edu>
To: gerard at xray.bmc.uu.se
* B-factor restraints test @ 960604
***********************************
* compare default B restraints in X-PLOR with Dale's restraints
as posted on the xplor newsgroup
(NOTE: this post does not quite implement Dale's method:
- XPLOR would need something like: bsigma=(selection)=(selection)=target
as it is now, every atom gets the target of the last bsigma
statement it fits; for example:
bsigma = ( name N or name CA ) = 4.6
bsigma = ( name CA or name C ) = 7.4
-> CA will get a target of 7.4 anyway
- Dale's set has *directionality*)
(NOTE: critique on Dale's paper: he never used Rfree to show that you
actually get better models at any resolution !)
* first try with CRABPII holo, 1.8 A data, use near-final model
still with Rfree (i.e., prior to final refinement against all data)
do the following for several resolutions:
- set all bs to 15 + Gaussian term as per normal xplor
- refine with default xplor restraints
- set bs to 15 + gaussian again
- refine with pseudo-Dale restraints
Resol R/Rfree start Normal Bs Dale's Bs
2.0 0.270/0.287 0.202/0.226 0.193/0.220
2.2 0.259/0.275 0.197/0.220 0.185/0.216
2.4 0.250/0.267 0.191/0.218 0.178/0.212
2.6 0.242/0.263 0.184/0.219 0.169/0.214
3.0 0.230/0.252 0.175/0.211 0.161/0.205
-> in all cases pseudo-Dale is ~0.5 % better in Rfree
however, also R is lower, but usually 2-3 times as much as Rfree
-> pseudo-Dale seems to be slightly more accurate, but
it also increases the extent of over-fitting (since R drops
quite a bit more than Rfree)
* try the same with CBH2 native data (1.8 A):
Resol R/Rfree start Normal Bs Dale's Bs
2.0 0.232/0.247 0.169/0.198 0.159/0.197
2.4 0.215/0.232 0.156/0.193 0.143/0.191
3.0 0.196/0.210 0.140/0.182 0.123/0.179
-> same picture: 0.1-0.3% drop in Rfree at the expense of
a drop in R which is 5-10 * larger
* -> stick to the old restraints in X-PLOR
--------------------------------------------------------
Gerard CD Kleywegt
Presently at Yale (mailto:gkleyweg at laplace.csb.yale.edu)
Normally in Uppsala (mailto:gerard at xray.bmc.uu.se)
