Re: [ccp4bb] Refmac refinement problem

Protein crystallography Programs for crystallography X-ray detectors
Basic tutorials:
Protein Peptide

CCP4bb navigation

CCP4bb <-- 2007 <-- March 2007 <-- 31 March 2007

Previous message:
Subject: Refmac refinement problem
From: Todd Holyoak tholyoak {- at -} KUMC {- dot -} EDU
Date: 2007-03-31

Next message:
Subject: Re: (bigger) fragment identification of limited proteolysis w/ mass-spec
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2007-03-31

Subject: Re: Refmac refinement problem
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-03-31

I think your pdb header has cis conformation fnormation. Remove them
from the pdb header then it should work. If not, please let me know.

Garib

On 31 Mar 2007, at 22:16, Todd Holyoak wrote:

> All,
>
> We are currently refining a 1.6A structure with Refmac5. There are a
> few loops with backbone geometries that Refmac seems to have an issue
> with. There is clear density for the modeled conformations, however
> when doing restrained refinement the following errors are encountered
> and the restraints place the refined loops in an entirely incorrect
> orientation
> in order to satisfy the restraints.
>
> WARNING : TRANS peptide bond (not be changed CIS) angle = 173.39
> ch:AA res: 22 SER --> 23 LEU
> WARNING : TRANS peptide bond (not be changed CIS) angle = 116.53
> ch:AA res: 185 GLY --> 186 ASP
> WARNING : TRANS peptide bond (not be changed CIS) angle = 175.20
> ch:AA res: 202 LEU --> 203 LYS
> WARNING : TRANS peptide bond (not be changed CIS) angle = 166.00
> ch:AA res: 374 ASP --> 375 GLU
> WARNING : TRANS peptide bond (not be changed CIS) angle = 161.52
> ch:AA res: 375 GLU --> 376 PRO
> WARNING : TRANS peptide bond (not be changed CIS) angle = 171.15
> ch:AA res: 376 PRO --> 377 LEU
> WARNING : TRANS peptide bond (not be changed CIS) angle = 163.99
> ch:AA res: 521 LYS --> 522 ASN
> WARNING : TRANS peptide bond (not be changed CIS) angle = 175.63
> ch:AA res: 522 ASN --> 523 GLY
> WARNING : TRANS peptide bond (not be changed CIS) angle = 179.92
> ch:AA res: 523 GLY --> 524 LYS
> WARNING : TRANS peptide bond (not be changed CIS) angle = 145.57
> ch:AA res: 572 VAL --> 573 ASN
> WARNING : TRANS peptide bond (not be changed CIS) angle = 173.89
> ch:AA res: 574 VAL --> 575 GLU
>
>
> Is there any way to reduced the restraints in the particular loop
> regions? Through the gui it only seems possible to reduce the
> restraints in a global fashion.
>
> Thanks
> Todd
>

CCP4bb navigation

CCP4bb <-- 2007 <-- March 2007 <-- 31 March 2007

Previous message:
Subject: Refmac refinement problem
From: Todd Holyoak tholyoak {- at -} KUMC {- dot -} EDU
Date: 2007-03-31

Next message:
Subject: Re: (bigger) fragment identification of limited proteolysis w/ mass-spec
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2007-03-31