[ccp4bb] restrained refinement in Refmac

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

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

Previous message:
Subject: Re: Spam: Spam: looking for test data
From: Serge Cohen s {- dot -} cohen {- at -} NKI {- dot -} NL
Date: 2007-07-09

Next message:
Subject: Postdoctoral Positions
From: Rachelle Gaudet gaudet {- at -} MCB {- dot -} HARVARD {- dot -} EDU
Date: 2007-07-09

Subject: restrained refinement in Refmac
From: JINJIN ZHANG zhang {- dot -} 508 {- at -} OSU {- dot -} EDU
Date: 2007-07-09

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
</pre>
</html>
***************************************************************************
* 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: Spam: Spam: looking for test data
From: Serge Cohen s {- dot -} cohen {- at -} NKI {- dot -} NL
Date: 2007-07-09

Next message:
Subject: Postdoctoral Positions
From: Rachelle Gaudet gaudet {- at -} MCB {- dot -} HARVARD {- dot -} EDU
Date: 2007-07-09