A less exact answer, albeit less precise and informative than the very
nice PDF and the very useful Polygon ideas, is:
"very well done, but have another look at this couple of Ramachandran
outliers and also consider loosening up the geometry a bit".
;-)
A.
On Dec 14, 2009, at 17:04, Pavel Afonine wrote:
Hi,
the exact answer to your question is here:
http://cci.lbl.gov/~afonine/for_ak/validation.pdf
In particular, your question below is spelled out is discussed staring
from slide #2.
Pavel.
On 12/14/09 7:50 AM, rui wrote:
Hi, All,
I have a general question for refinement. I tried to refine a dataset
that is about 2.3A and got R/Rfree is about o.18/0.24. RMS(angles):
0.77, RMS(bonds): 0.003
however, when I check with molprobity, There are still some outliers
and some bad contact that is overlap > 0.4 A.
Ramachandran outliers: 0.2% (Goal: < 0.2%)
Ramachandran favored: 97.7% (Goal: > 98%)
Rotamer outliers: 1.4% (Goal: 1%)
C-beta outliers: 0 (Goal: 0)
Clashscore: 14.16
Generally speaking, should I remove all those bad contact or is there
any miminum requirement that ok, the structure is acceptable? I know
the refinement can be endless, but I just want to get an idea how far
away I'm . Thanks.
R
P please don't print this e-mail unless you really need to
Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member
Department of Biochemistry (B8)
Netherlands Cancer Institute,
Dept. B8, 1066 CX Amsterdam, The Netherlands
Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791
