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
</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
