PAfonine at lbl.gov
Mon May 4 18:53:25 PDT 2009
I see. I suggest to run two refinements:
- with NCS and "optimize_wxc=true optimize_wxu=true" options, and
- without NCS and with "optimize_wxc=true optimize_wxu=true".
This will make it weight-choice independent and so easier to understand.
Otherwise, since NCS term is included in weights calculation, using or
not using NCS may change the X-ray/Restrains weight which may have
larger effects than using/not using NCS itself.
On 5/4/09 6:48 PM, Maia Cherney wrote:
> Hi Pavel,
> The resolution is 2.15 A. The NCS was always on during the refinement
> until we got low R factors (19.2% and 21.2%). Then the NCS was turned
> off for the final refinement and the R factors increased, which is
> strange as they should be going down when you apply less restraints.
> There are five restraint groups in the asym. unit.
> Pavel Afonine wrote:
>> Hi Maia,
>> - I'm wondering why this puzzles you?
>> - The gap Rfree-Rwork seems suspiciously small, although I can't tell
>> without knowing the resolution.
>> - Overall, better R-factors (Rwork, Rfree and Rfree-Rwork) mean that
>> among many possible refinement strategies you have chosen the one that
>> is better than the others.
>> What is the resolution?
>> What are the R-factor before using NCS?
>> What will be the R-factors after you turn NCS back off?
>> On 5/4/09 12:27 PM, Maia Cherney wrote:
>>> Hi everybody,
>>> I am wondering why my final structure refined with NCS=True has lower R
>>> factors (19.2% and 21.2%) than without NCS by approximately 1.5%.
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
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