Re: [ccp4bb] When can I say the refinement is done?

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: overexpression of unintended protein
From: Karthik S biokarthik {- at -} GMAIL {- dot -} COM
Date: 2009-12-15

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Subject: Re: When can I say the refinement is done?
From: Bernhard Rupp br {- at -} RUPPWEB {- dot -} ORG
Date: 2009-12-15

page 682 :-)

BR

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Pavel
Afonine
Sent: Monday, December 14, 2009 9:24 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] When can I say the refinement is done?

This is pointed out (in absolutely unobvious way - I wish I can add voice to
that PDF) at the slide #19 -:)

(except loosening weights).

P.

On 12/14/09 8:35 AM, Anastassis Perrakis wrote:

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

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: overexpression of unintended protein
From: Karthik S biokarthik {- at -} GMAIL {- dot -} COM
Date: 2009-12-15

Next message:
Subject: Rosetta vs Modeller
From: subhendu chakraborti chakraborti {- dot -} subhendu {- at -} GMAIL {- dot -} COM
Date: 2009-12-15