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

Previous message:
Subject: Re: scala maxbat compile problems
From: jp d yoyoq {- at -} YAHOO {- dot -} COM
Date: 2009-10-09

Next message:
Subject: [Fwd: NCS in REFMAC (was Re: )]
From: Vellieux Frederic Frederic {- dot -} Vellieux {- at -} IBS {- dot -} FR
Date: 2009-10-10

Subject:
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2009-10-09

Hello Vandana, so you are saying your Rfree=27.7 and Rwork=27.0.

Let's stop shaking the air with throwing out hypothesis (someone, likely
you, will need to verify them and this is some work) and start with the
simplest option -- look in PDB at the structures deposited at similar
resolution as yours, that is in the range, say, from 2.9 to 3.1A:

Histogram of Rwork for all model in PDB at resolution 2.9-3.1:
0.139 - 0.160 : 1
0.160 - 0.181 : 16
0.181 - 0.202 : 122
0.202 - 0.223 : 251
0.223 - 0.243 : 259
0.243 - 0.264 : 161
0.264 - 0.285 : 69 <<< your structure
0.285 - 0.306 : 21
0.306 - 0.327 : 8
0.327 - 0.348 : 4
Histogram of Rfree for all model in PDB at resolution 2.9-3.1:
0.181 - 0.205 : 4
0.205 - 0.229 : 35
0.229 - 0.254 : 128
0.254 - 0.278 : 274 <<< your structure
0.278 - 0.302 : 285
0.302 - 0.326 : 127
0.326 - 0.350 : 46
0.350 - 0.375 : 9
0.375 - 0.399 : 2
0.399 - 0.423 : 2
Histogram of Rfree-Rwork for all model in PDB at resolution 2.9-3.1:
-0.025 - -0.008 : 3
-0.008 - 0.010 : 20 <<< your structure
0.010 - 0.027 : 100
0.027 - 0.045 : 269
0.045 - 0.062 : 315
0.062 - 0.080 : 133
0.080 - 0.097 : 54
0.097 - 0.115 : 12
0.115 - 0.132 : 3
0.132 - 0.150 : 3

Hm... I think you got the message. Not necessarily your structure is
incorrect, it just simply needs some closer look and possibly some more
work -:) It might turn out that a few cycles of refinement just enough.

Please let me know if you want to discuss it some more.

All the best!
Pavel.

On 10/9/09 12:28 AM, Vandana Kukshal wrote:
> hi
> i am solving one structure
>
> in which after refinement i got R factor=27
> and R free =27.7
> i want to know that is it correct or i did some over refinment
>
> the Resolution is 3.0 A

CCP4bb navigation

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

Previous message:
Subject: Re: scala maxbat compile problems
From: jp d yoyoq {- at -} YAHOO {- dot -} COM
Date: 2009-10-09

Next message:
Subject: [Fwd: NCS in REFMAC (was Re: )]
From: Vellieux Frederic Frederic {- dot -} Vellieux {- at -} IBS {- dot -} FR
Date: 2009-10-10