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Hi Gerwald,<br>
<br>
<blockquote cite="mid:48F614A4.8000209@brown.edu" type="cite">
<pre wrap="">I just started using phenix.refine and it's working quite well so far. I
ran the optimize weight strategy at the end of a test refinement and it
lowered the Rfree as intended. Unfortunately, when I ran the next refine
job based on the output .def file, it seems that the 'best weights'
found in the previous run were not conserved as the geometry and R
factors got a lot worse.
</pre>
</blockquote>
<br>
The "best weights" are good per macro-cycle. That is what is the "best
weight" for macro-cycle #1 is not necessarily the best one for
macro-cycle #2, etc. This is why they are not preserved for next runs. <br>
<br>
<blockquote cite="mid:48F614A4.8000209@brown.edu" type="cite">
<pre wrap="">Where can I find the weights determined by the optimize run and how can
I fix those for further refinement?
</pre>
</blockquote>
<br>
If you run phenix.refine with "optimize_wxc=true", then you will see
something like this:<br>
<br>
<font face="Courier New, Courier, monospace">================================
xyz refinement ===============================<br>
<br>
Start r_work= 0.2359 r_free= 0.2576 bonds= 0.004 angles= 1.08<br>
r_work= 0.2304 r_free= 0.2504 bonds= 0.003 angles= 1.14 scale=
1.00<br>
r_work= 0.2286 r_free= 0.2476 bonds= 0.003 angles= 1.22 scale=
1.40<br>
r_work= 0.2279 r_free= 0.2465 bonds= 0.004 angles= 1.26 scale=
1.80<br>
r_work= 0.2271 r_free= 0.2454 bonds= 0.004 angles= 1.32 scale=
2.20<br>
r_work= 0.2266 r_free= 0.2447 bonds= 0.005 angles= 1.35 scale=
2.60<br>
r_work= 0.2262 r_free= 0.2442 bonds= 0.005 angles= 1.39 scale=
3.00<br>
r_work= 0.2258 r_free= 0.2436 bonds= 0.005 angles= 1.41 scale=
3.40<br>
r_work= 0.2256 r_free= 0.2433 bonds= 0.006 angles= 1.44 scale=
3.80<br>
r_work= 0.2253 r_free= 0.2429 bonds= 0.006 angles= 1.47 scale=
4.20<br>
r_work= 0.2251 r_free= 0.2426 bonds= 0.006 angles= 1.49 scale=
4.60<br>
r_work= 0.2249 r_free= 0.2425 bonds= 0.007 angles= 1.51 scale=
5.00<br>
r_work= 0.2245 r_free= 0.2417 bonds= 0.008 angles= 1.56 scale=
6.00<br>
r_work= 0.2242 r_free= 0.2420 bonds= 0.008 angles= 1.60 scale=
7.00<br>
r_work= 0.2238 r_free= 0.2408 bonds= 0.009 angles= 1.63 scale=
8.00<br>
r_work= 0.2236 r_free= 0.2413 bonds= 0.010 angles= 1.68 scale=
9.00<br>
r_work= 0.2234 r_free= 0.2409 bonds= 0.010 angles= 1.71 scale=
10.00<br>
r_work= 0.2314 r_free= 0.2516 bonds= 0.003 angles= 1.11 scale=
0.85<br>
r_work= 0.2331 r_free= 0.2538 bonds= 0.003 angles= 1.05 scale=
0.70<br>
r_work= 0.2362 r_free= 0.2566 bonds= 0.003 angles= 0.98 scale=
0.55<br>
Final r_work= 0.2238 r_free= 0.2408 bonds= 0.009 angles= 1.63<br>
</font><br>
In this particular case, the best result is:<br>
<br>
<font face="Courier New, Courier, monospace">r_work= 0.2238 r_free=
0.2408 bonds= 0.009 angles= 1.63 scale= 8.00<br>
</font><br>
meaning that if you want to fix it then "wxc_scale=8" keyword in your
subsequent phenix.refine run (I should replace "scale" with "wxc_scale"
to make it more obvious).<br>
<br>
Pavel.<br>
<br>
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