Dear all,
I have fit my ligand into its density with coot. Then, I add the ligand into
the protein's pdb and try to do refine with refmac5. First, the error comes,
error message
Refmac_5.5.0109: New ligand has been encountered. Stopping now
The next time, I input the .cif file generated by the first run of refmac5 and
rerun the program. And the error comes as,
ERROR : atom :04 5CD 225 XX is absent in the library
ATTENTION: atom:4__0 5CD 225 XX is missing in the structure
ERROR : atom :04 5CD 224 Bb is absent in the library
ATTENTION:
atom:4__0 5CD 224 Bb is missing in the structure
Number of chains : 7
Total number of monomers : 750
Number of atoms : 3691
Number of missing atoms : 2
Number of rebuilt atoms : 0
Number of unknown atoms : 2
Number of
deleted atoms : 0
Number of bonds restraints : 3452
Number of angles restraints : 4672
Number of torsions restraints : 2372
Number of chiralities : 512
Number of planar groups : 612
IERR = 1
There is error. See above
===> Error: Fatal error. Cannot continue
Refmac_5.5.0109: Fatal error. Cannot continue
Times: User: 13.8s System: 0.1s Elapsed: 0:14
Could anybody please help me to solve this problem?
Thank you all for your attention.
Best wishes,
Vinson Liang
