[phenixbb] phenix.refine frozen
Roberto Steiner
roberto.steiner at kcl.ac.uk
Wed Feb 10 23:13:53 PST 2010
Hi there,
I would appreciate some feedback on the following:
I am playing around with phenix.refine which comes with Phenix distro
1.6-289 for Mac-Intel. When running a normal refinement job
(ind site + grouped ADPs + ncs+TorsionSimulatedAnnealing)
phenix.refine gets stuck after bulk solvent modelling and scaling.
The last things I see in the log page are:
====================== bulk solvent modeling and scaling
======================
|--(resolution: 3.50 - 58.55 A; n_refl. =
55140)------------------------------|
|
|
| r_work= 0.2687 r_free= 0.2800 ksol= 0.38 Bsol= 10.09 scale=
1.148 |
|
|
| overall anisotropic scale matrix (Cartesian basis;
B11,B22,B33,B12,B13,B23):|
| (-2.67,-2.67,5.34,0.00,0.00,-0.00); trace/3=
0.00 |
|
|
| maximum likelihood estimate for coordinate error: 0.41
A |
| x-ray target function (ml) for work reflections:
7.216427 |
|
-----------------------------------------------------------------------------|
========================== Target weights: x-ray data
=========================
and that's it. For completeness, I must report that I changed the
defaults of wxc_scale and wxu_scale (but surely that cannot be the
problem...).
Switching off the TorsionSimAnnealing does not help.
Additionally, if I click on the abort button on the bottom-left of the
page nothing happens. On the other hand
if I click on the abort icon at the top of the page I get the message
"You are not currently running any calculations. Do you want to close
this window?"
If I say Ok the following message appears:
"There is at least one process running; are you sure you want to exit
before it is finished"
Other tasks (phenix.xtriage for example) seem to run fine.
Any suggestion?
Best
Roberto
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