Hi Jose Antonio Cuesta Seijo,
- at 3.1A I would try 1) refining individual isotropic ADPs, 2) combined
strategy of refining TLS+individual isotropic ADPs, 3) combined strategy
of refining TLS+group isotropic ADPs with one or two definable isotropic
B-factor per residue. Look at Rfree and Rfree-Rwork to decide which
strategy worked best.
In addition, you can run "1)" and "2)" with X-ray/restraints target
weight optimization option turned ON.
- try re-setting all B-factors to the average value with this command:
phenix.pdbtools model.pdb set_b_iso=50.0
and try refinement again.
- the fact that group B-factor refines to a large value for certain
residues may mean that these residues do not fit the density well. In
this case it is questionable what is better: a) apply restraints to
group B and like this to force smaller B-factors of adjacent residues
that fit density well to be biased by the "bad" large B-factors or
misfitting residues, or b) have the truth values at the price of
unpleasant B-factor distribution. I don't know the answer.
Please let me know if you have specific questions about using
phenix.refine in this context.
Pavel.
On 1/28/10 1:34 AM, Jose Antonio Cuesta Seijo wrote:
Dear all,
I am refining a 3.1Å structure with Phenix.refine, using two ADP
groups per residue.
When doing refinement in Refmac, the way to go would be to tighten the
weights quite a bit to make up for the low resolution, resulting in
small deviations in bond lenghts and angles from the ideal values and
also in quite small ADP variations from atom to atom, typically in the
range of, say, 5%.
Now, doing the same refinement with Phenix.refine and 2 ADP groups per
residue, the manual claims that the weights do not normally need to be
touched. Judging by the values of R and R free (19.5% and 23.9%)
compared to other protocols and with Refmac, it certainly does a good
job. But the spread in ADP values in the refined model is strikingly
high. Below is a extract from the pdb file. Note for example the jump
from B=81.7 to B=163.8 for the main chains of ILE180 and LYS181, or
the 163.8 to 113.5 between the main chain and the side chain of
LYS181. Similar examples are all over the 1000+ residues in this
structure.
Is this normal? All global quality indicators look OK to me...
Cheers,
Jose Antonio Cuesta Seijo.
ATOM 8338 N ARG F 178 65.398 30.884 -0.261 1.00
84.90 N
ATOM 8339 CA ARG F 178 66.532 31.758 -0.521 1.00
84.90 C
ATOM 8340 CB ARG F 178 67.576 31.628 0.583
1.00131.99 C
ATOM 8341 CG ARG F 178 67.044 31.967 1.952
1.00131.99 C
ATOM 8342 CD ARG F 178 68.084 32.695 2.778
1.00131.99 C
ATOM 8343 NE ARG F 178 67.464 33.433 3.873
1.00131.99 N
ATOM 8344 CZ ARG F 178 66.894 34.627 3.737
1.00131.99 C
ATOM 8345 NH1 ARG F 178 66.865 35.222 2.551
1.00131.99 N
ATOM 8346 NH2 ARG F 178 66.350 35.224 4.787
1.00131.99 N
ATOM 8347 C ARG F 178 67.152 31.347 -1.839 1.00
84.90 C
ATOM 8348 O ARG F 178 66.738 30.357 -2.443 1.00
84.90 O
ATOM 8349 N ILE F 179 68.143 32.107 -2.287 1.00
80.99 N
ATOM 8350 CA ILE F 179 68.954 31.666 -3.406 1.00
80.99 C
ATOM 8351 CB ILE F 179 69.698 32.817 -4.083 1.00
53.62 C
ATOM 8352 CG1 ILE F 179 68.754 33.995 -4.333 1.00
53.62 C
ATOM 8353 CD1 ILE F 179 68.390 34.216 -5.806 1.00
53.62 C
ATOM 8354 CG2 ILE F 179 70.308 32.325 -5.389 1.00
53.62 C
ATOM 8355 C ILE F 179 69.970 30.657 -2.884 1.00
80.99 C
ATOM 8356 O ILE F 179 70.677 30.914 -1.913 1.00
80.99 O
ATOM 8357 N ILE F 180 70.026 29.500 -3.528 1.00
81.67 N
ATOM 8358 CA ILE F 180 70.864 28.417 -3.061 1.00
81.67 C
ATOM 8359 CB ILE F 180 70.161 27.066 -3.218 1.00
71.36 C
ATOM 8360 CG1 ILE F 180 68.850 27.090 -2.446 1.00
71.36 C
ATOM 8361 CD1 ILE F 180 68.964 27.820 -1.114 1.00
71.36 C
ATOM 8362 CG2 ILE F 180 71.038 25.955 -2.707 1.00
71.36 C
ATOM 8363 C ILE F 180 72.180 28.418 -3.811 1.00
81.67 C
ATOM 8364 O ILE F 180 73.218 28.106 -3.240 1.00
81.67 O
ATOM 8365 N LYS F 181 72.137 28.768 -5.092
1.00163.76 N
ATOM 8366 CA LYS F 181 73.356 28.961 -5.872
1.00163.76 C
ATOM 8367 CB LYS F 181 74.053 27.627 -6.155
1.00113.58 C
ATOM 8368 CG LYS F 181 73.432 26.812 -7.280
1.00113.58 C
ATOM 8369 CD LYS F 181 74.307 25.615 -7.656
1.00113.58 C
ATOM 8370 CE LYS F 181 74.291 24.546 -6.571
1.00113.58 C
ATOM 8371 NZ LYS F 181 75.015 23.306 -6.984
1.00113.58 N
ATOM 8372 C LYS F 181 73.033 29.687 -7.172
1.00163.76 C
ATOM 8373 O LYS F 181 71.889 29.673 -7.629
1.00163.76 O
ATOM 8374 N LYS F 182 74.039 30.325 -7.760
1.00126.44 N
ATOM 8375 CA LYS F 182 73.849 31.088 -8.988
1.00126.44 C
ATOM 8376 CB LYS F 182 74.588 32.421 -8.897
1.00131.41 C
ATOM 8377 CG LYS F 182 74.235 33.203 -7.652
1.00131.41 C
ATOM 8378 CD LYS F 182 74.885 34.575 -7.634
1.00131.41 C
ATOM 8379 CE LYS F 182 74.466 35.367 -6.393
1.00131.41 C
ATOM 8380 NZ LYS F 182 75.076 36.730 -6.349
1.00131.41 N
ATOM 8381 C LYS F 182 74.338 30.303 -10.192
1.00126.44 C
ATOM 8382 O LYS F 182 75.506 29.930 -10.252
1.00126.44 O
ATOM 8383 N LEU F 183 73.447 30.052 -11.146
1.00161.61 N
ATOM 8384 CA LEU F 183 73.819 29.331 -12.360
1.00161.61 C
ATOM 8385 CB LEU F 183 72.591 29.005 -13.214
1.00100.55 C
ATOM 8386 CG LEU F 183 71.470 28.218 -12.534
1.00100.55 C
ATOM 8387 CD1 LEU F 183 70.602 27.516 -13.569
1.00100.55 C
ATOM 8388 CD2 LEU F 183 72.058 27.219 -11.558
1.00100.55 C
ATOM 8389 C LEU F 183 74.810 30.141 -13.183
1.00161.61 C
ATOM 8390 O LEU F 183 74.988 31.337 -12.943
1.00161.61 O
ATOM 8391 OXT LEU F 183 75.443 29.616 -14.103
1.00100.55 O
------------------------------------------------------------------------
***************************
Jose Antonio Cuesta-Seijo
Biophysical Chemistry Group
Department of Chemistry
University of Copenhagen
Tlf: +45-35320261
Universitetsparken 5
DK-2100 Copenhagen, Denmark
***************************
