Re: [ccp4bb] restrained refinement in Refmac

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

Previous message:
Subject: Re: Proper Reference for Phil Evans Program POINTLESS
From: "Winter, G (Graeme)" g {- dot -} winter {- at -} DL {- dot -} AC {- dot -} UK
Date: 2007-07-10

Next message:
Subject: Re: Proper Reference for Phil Evans Program POINTLESS
From: "F {- dot -} Xavier_Gomis-Rüth" xgrcri {- at -} IBMB {- dot -} CSIC {- dot -} ES
Date: 2007-07-10

Subject: Re: restrained refinement in Refmac
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-07-10

It looks like as if your PDB is corrupt. For example there atoms B
that should not be present inamino acids.

Garib

On 9 Jul 2007, at 19:55, JINJIN ZHANG wrote:

>
>
> Hello all,
>
> I'm working on a protein-DNA complex. My protein is a trimer and
> the crystal has 3 trimers in an AU. I used a pdb file including
> three subunits as a search model when I did molecular replacement
> in CCP4. I did a rigid body refinement in Recfmac the R-factor and
> R-free did not go down. Then I tried to do restrained refinement by
> using MTZ and PDB file ourput from MR but failed. The log file is
> attached at the bottom of this message. It looked like something
> wrong with the PDB file input. But I used the same PDB file to run
> rigid body refinement and did not get any error message. How can
> this happen?
>
> I sincerely appreciate any comment and suggestion.
>
> Best,
>
> Jinjin
>
>
>
> --- title of input coord file ---
>
> PDB_code:XXXX
> PDB_name:----
> PDB_date:XX-XXX-XX
> --------------------------------
> WARNING : atom :OT1 ARG AA 226 is absent in the library
> ATTENTION: atom:O ARG AA 226 is missing in the structure
> WARNING : atom :B SER BB -1 is absent in the library
> ATTENTION: atom:C SER BB -1 is missing in the structure
> WARNING : atom :B HIS BB 0 is absent in the library
> ATTENTION: atom:C HIS BB 0 is missing in the structure
> WARNING : atom :B MET BB 1 is absent in the library
> ATTENTION: atom:C MET BB 1 is missing in the structure
> WARNING : atom :B THR BB 2 is absent in the library
> ATTENTION: atom:C THR BB 2 is missing in the structure
> WARNING : atom :B PRO BB 3 is absent in the library
> ATTENTION: atom:C PRO BB 3 is missing in the structure
> WARNING : atom :B ASP BB 4 is absent in the library
> ATTENTION: atom:C ASP BB 4 is missing in the structure
> WARNING : atom :B ILE BB 5 is absent in the library
> ATTENTION: atom:C ILE BB 5 is missing in the structure
> WARNING : atom :B ILE BB 6 is absent in the library
> ATTENTION: atom:C ILE BB 6 is missing in the structure
> WARNING : atom :B LEU BB 7 is absent in the library
> ATTENTION: atom:C LEU BB 7 is missing in the structure
> WARNING : atom :B GLN BB 8 is absent in the library
> ATTENTION: atom:C GLN BB 8 is missing in the structure
> WARNING : atom :B ARG BB 9 is absent in the library
> ATTENTION: atom:C ARG BB 9 is missing in the structure
> WARNING : atom :B THR BB 10 is absent in the library
> ATTENTION: atom:C THR BB 10 is missing in the structure
> WARNING : atom :B GLY BB 11 is absent in the library
> ATTENTION: atom:C GLY BB 11 is missing in the structure
> WARNING : atom :B ILE BB 12 is absent in the library
> ATTENTION: atom:C ILE BB 12 is missing in the structure
> WARNING : atom :B ASP BB 13 is absent in the library
> ATTENTION: atom:C ASP BB 13 is missing in the structure
> WARNING : atom :B VAL BB 14 is absent in the library
> ATTENTION: atom:C VAL BB 14 is missing in the structure
> WARNING : atom :B ARG BB 15 is absent in the library
> ATTENTION: atom:C ARG BB 15 is missing in the structure
> WARNING : atom :B ALA BB 16 is absent in the library
> ATTENTION: atom:C ALA BB 16 is missing in the structure
> WARNING : atom :B VAL BB 17 is absent in the library
> ... and more ...
> ATTENTION: atom:C VAL BB 17 is missing in the structure
> ... and more ...
> Number of chains : 9
> Total number of monomers : 2052
> Number of atoms : 17226
> Number of missing atoms : 693
> Number of rebuilt atoms : 0
> Number of unknown atoms : 693
> Number of deleted atoms : 0
>
> Number of bonds restraints : 14889
> Number of angles restraints : 18801
> Number of torsions restraints : 7878
> Number of chiralities : 1746
> Number of planar groups : 2244
> IERR = 1
>
> There is error. See above
> ===> Error: Fatal error. Cannot continue
> Refmac_5.2.0019: Fatal error. Cannot continue
> Times: User: 0.0s System: 0.0s Elapsed: 0:39
>
>
> **********************************************************************
> *****
> * Information from CCP4Interface script
> **********************************************************************
> *****
> The program run with command: refmac5 XYZIN "C:/Ccp4Temp/
> lam-6-14-07-P1/trimer_molrep1.pdb" XYZOUT "C:/Ccp4Temp/lam-6-14-07-
> P1/lam6-14_11_4_pdb_1.tmp" HKLIN "C:/Ccp4Temp/lam-6-14-07-P1/
> ScalAveraged.mtz" HKLOUT "C:/Ccp4Temp/lam-6-14-07-P1/
> lam6-14_11_6_mtz_1.tmp" LIBOUT "C:/Ccp4Temp/lam-6-14-07-P1/
> lam6-14_11_lib.cif"
> has failed with error message
> Refmac_5.2.0019: Fatal error. Cannot continue
> **********************************************************************
> *****
>
>
> #CCP4I TERMINATION STATUS 0 Refmac_5.2.0019: Fatal error. Cannot
> continue
> #CCP4I TERMINATION TIME 06 Jul 2007 15:08:36
> #CCP4I MESSAGE Task failed

CCP4bb navigation

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

Previous message:
Subject: Re: Proper Reference for Phil Evans Program POINTLESS
From: "Winter, G (Graeme)" g {- dot -} winter {- at -} DL {- dot -} AC {- dot -} UK
Date: 2007-07-10

Next message:
Subject: Re: Proper Reference for Phil Evans Program POINTLESS
From: "F {- dot -} Xavier_Gomis-Rüth" xgrcri {- at -} IBMB {- dot -} CSIC {- dot -} ES
Date: 2007-07-10