[phenixbb] 0 for wxc_scale and wxu_scale?
Michaela Kramer, Biochemisches Inst.
mkramer at bioc.uzh.ch
Wed Nov 26 00:15:28 PST 2008
I am refining a structure with a resolution of 2.1 Angstroem using Phenix.
The spacegroup is P 31 2 1 (No. 152) with a twin fraction of 0.37 and twin
law -h,-k,l.
In the refinement procedure the NCS (4 chains) constraints are on, using
individual sites, ADP and occupancy refinement.
In the last refinement step, I use the option to optimize the values for
wxu_scale and wxc_scale. These values are optimizes to 0 for wxc_scale and
close to 0 for wxu_scale (0.2)
When I tried this at earlier refinement stages wxu_scale was also here
optimized in some refinement macrocycles to 0.
Interestingly I obtain better R values (0.1948/0.2184), than without the
optimization by using the default values (0.1391/0.2438 Rwork/Rfree).
In addition to that the statistics are better: clashscore 14.41 (compared to
25.73 without wxc_scale & wxu_scale optimization), rotamer outliers 2.33%
(compared o 4.66%) and Ramachandran favoured (Molprobity).
How is it possible that wxu_scale and wxc_scale can be optimized to 0 by
having better statistics?
The total refinement target is defined as
Etotal= wxc_scale x wxc x Exray + wc x Egeom
As I understand it, the crystallographic refinement target (Exray) would now
not be considered in the refinement procedure.
Would this refinement procedure be valid?
And how is wxc (output of target weights: x-ray data) defined?
Thank you very much for your help
Michaela
Here is the output belonging to the optimization:
Refinement Macrocycle 1 of 3
========================== Target weights: x-ray data
=========================
|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc
|
| wxc = 1.649809 wxc_scale = 0.500 wc = 1.000
|
| angle between x-ray and geometry gradient vectors: 93.128 (deg)
|
|
|
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu
|
| wxc = 0.888942 wxc_scale = 1.000 wc = 1.000
|
| angle between Xray and ADP gradient vectors: 85.407 (deg)
|
|-----------------------------------------------------------------------------|
================================ xyz refinement
===============================
Start r_free = 0.2118
scale= 0.0000 total_weight= 0.0000 r_free= 0.2181 0
scale= 1.0000 total_weight= 1.6498 r_free= 0.2336 0
scale= 1.5000 total_weight= 2.4747 r_free= 0.2379 1
scale= 2.0000 total_weight= 3.2996 r_free= 0.2412 2
scale= 0.6667 total_weight= 1.0999 r_free= 0.2297 0
scale= 0.5000 total_weight= 0.8249 r_free= 0.2245 1
scale= 0.4000 total_weight= 0.6599 r_free= 0.2226 2
Best r_free = 0.2181
================================ ADP refinement
===============================
----------Individual ADP refinement----------
Start r_free = 0.2181
scale= 0.0000 total_weight= 0.0000 r_free= 0.2247 0
scale= 1.0000 total_weight= 0.8889 r_free= 0.2262 0
scale= 1.5000 total_weight= 1.3334 r_free= 0.2293 1
scale= 2.0000 total_weight= 1.7779 r_free= 0.2310 2
scale= 0.6667 total_weight= 0.5926 r_free= 0.2236 0
scale= 0.5000 total_weight= 0.4445 r_free= 0.2221 0
scale= 0.4000 total_weight= 0.3556 r_free= 0.2208 0
scale= 0.3333 total_weight= 0.2963 r_free= 0.2203 0
scale= 0.2857 total_weight= 0.2540 r_free= 0.2195 0
scale= 0.2500 total_weight= 0.2222 r_free= 0.2191 0
scale= 0.2222 total_weight= 0.1975 r_free= 0.2186 0
scale= 0.2000 total_weight= 0.1778 r_free= 0.2183 0
Best r_free = 0.2183
Refinement Macrocycle 2 of 3
========================== Target weights: x-ray data
=========================
|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc
|
| wxc = 1.737535 wxc_scale = 0.500 wc = 1.000
|
| angle between x-ray and geometry gradient vectors: 89.612 (deg)
|
|
|
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu
|
| wxc = 0.228155 wxc_scale = 1.000 wc = 1.000
|
| angle between Xray and ADP gradient vectors: 155.392 (deg)
|
|-----------------------------------------------------------------------------|
================================ xyz refinement
===============================
Start r_free = 0.2179
scale= 0.0000 total_weight= 0.0000 r_free= 0.2223 0
scale= 1.0000 total_weight= 1.7375 r_free= 0.2272 0
scale= 1.5000 total_weight= 2.6063 r_free= 0.2310 1
scale= 2.0000 total_weight= 3.4751 r_free= 0.2332 2
scale= 0.6667 total_weight= 1.1584 r_free= 0.2267 0
scale= 0.5000 total_weight= 0.8688 r_free= 0.2258 1
scale= 0.4000 total_weight= 0.6950 r_free= 0.2269 2
Best r_free = 0.2223
================================ ADP refinement
===============================
----------Individual ADP refinement----------
Start r_free = 0.2223
scale= 0.0000 total_weight= 0.0000 r_free= 0.2228 0
scale= 1.0000 total_weight= 0.2282 r_free= 0.2235 0
scale= 1.5000 total_weight= 0.3422 r_free= 0.2256 1
scale= 2.0000 total_weight= 0.4563 r_free= 0.2275 2
scale= 0.6667 total_weight= 0.1521 r_free= 0.2219 0
scale= 0.5000 total_weight= 0.1141 r_free= 0.2213 0
scale= 0.4000 total_weight= 0.0913 r_free= 0.2207 0
scale= 0.3333 total_weight= 0.0761 r_free= 0.2204 0
scale= 0.2857 total_weight= 0.0652 r_free= 0.2201 0
scale= 0.2500 total_weight= 0.0570 r_free= 0.2197 0
scale= 0.2222 total_weight= 0.0507 r_free= 0.2195 0
scale= 0.2000 total_weight= 0.0456 r_free= 0.2194 0
Best r_free = 0.2194
Macrocycle 2 of 3
========================== Target weights: x-ray data
=========================
|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc
|
| wxc = 2.157676 wxc_scale = 0.500 wc = 1.000
|
| angle between x-ray and geometry gradient vectors: 93.409 (deg)
|
|
|
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu
|
| wxc = 0.228399 wxc_scale = 1.000 wc = 1.000
|
| angle between Xray and ADP gradient vectors: 140.390 (deg)
|
|-----------------------------------------------------------------------------|
================================ xyz refinement
===============================
Start r_free = 0.2163
scale= 0.0000 total_weight= 0.0000 r_free= 0.2189 0
scale= 1.0000 total_weight= 2.1577 r_free= 0.2299 0
scale= 1.5000 total_weight= 3.2365 r_free= 0.2340 1
scale= 2.0000 total_weight= 4.3154 r_free= 0.2341 2
scale= 0.6667 total_weight= 1.4385 r_free= 0.2282 0
scale= 0.5000 total_weight= 1.0788 r_free= 0.2255 1
scale= 0.4000 total_weight= 0.8631 r_free= 0.2249 2
Best r_free = 0.2189
================================ ADP refinement
===============================
----------Individual ADP refinement----------
Start r_free = 0.2189
scale= 0.0000 total_weight= 0.0000 r_free= 0.2218 0
scale= 1.0000 total_weight= 0.2284 r_free= 0.2231 0
scale= 1.5000 total_weight= 0.3426 r_free= 0.2250 1
scale= 2.0000 total_weight= 0.4568 r_free= 0.2272 2
scale= 0.6667 total_weight= 0.1523 r_free= 0.2215 0
scale= 0.5000 total_weight= 0.1142 r_free= 0.2209 0
scale= 0.4000 total_weight= 0.0914 r_free= 0.2201 0
scale= 0.3333 total_weight= 0.0761 r_free= 0.2197 0
scale= 0.2857 total_weight= 0.0653 r_free= 0.2195 0
scale= 0.2500 total_weight= 0.0571 r_free= 0.2193 0
scale= 0.2222 total_weight= 0.0508 r_free= 0.2191 0
scale= 0.2000 total_weight= 0.0457 r_free= 0.2190 0
Best r_free = 0.2190
Michaela Kramer
PhD student
Institute of Biochemistry
Winterthurerstrasse 190
8057 Zuerich
Switzerland
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