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[ccp4bb] Refmac refinement problem
 

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CCP4bb <-- 2007 <-- March 2007 <-- 31 March 2007
Previous message:
Subject: Re: (bigger) fragment identification of limited proteolysis w/ mass-spec
From: tea {- dot -} pavkov {- at -} UNI-GRAZ {- dot -} AT tea {- dot -} pavkov {- at -} UNI-GRAZ {- dot -} AT
Date: 2007-03-31 		Next message:
Subject: Re: Refmac refinement problem
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-03-31


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

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CCP4bb <-- 2007 <-- March 2007 <-- 31 March 2007
Previous message:
Subject: Re: (bigger) fragment identification of limited proteolysis w/ mass-spec
From: tea {- dot -} pavkov {- at -} UNI-GRAZ {- dot -} AT tea {- dot -} pavkov {- at -} UNI-GRAZ {- dot -} AT
Date: 2007-03-31 		Next message:
Subject: Re: Refmac refinement problem
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-03-31


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