Hello, I generated my new ligand using smiles string in Phenix with elbow to generate my ligand cif and pdb file. I then open these in Coot along with my protein model and mtz and fitted this new ligand into my density. However Refmac failed with the following details in my log file:
PDB_code:4F80 PDB_name:IMMUNE SYSTEM PDB_date:16-MAY-12 -------------------------------- ERROR : atom :C01 LIG 1 EE is absent in the library ERROR : atom :C02 LIG 1 EE is absent in the library ERROR : atom :C03 LIG 1 EE is absent in the library ERROR : atom :C04 LIG 1 EE is absent in the library ERROR : atom :C05 LIG 1 EE is absent in the library ERROR : atom :O06 LIG 1 EE is absent in the library ERROR : atom :P07 LIG 1 EE is absent in the library ERROR : atom :O08 LIG 1 EE is absent in the library ERROR : atom :O09 LIG 1 EE is absent in the library ERROR : atom :O10 LIG 1 EE is absent in the library ATTENTION: atom:C28 LIG 1 EE is missing in the structure ATTENTION: atom:C26 LIG 1 EE is missing in the structure ATTENTION: atom:C24 LIG 1 EE is missing in the structure ATTENTION: atom:C22 LIG 1 EE is missing in the structure ATTENTION: atom:C21 LIG 1 EE is missing in the structure ATTENTION: atom:C4 LIG 1 EE is missing in the structure ATTENTION: atom:N3 LIG 1 EE is missing in the structure ATTENTION: atom:C20 LIG 1 EE is missing in the structure ATTENTION: atom:C17 LIG 1 EE is missing in the structure ATTENTION: atom:C5 LIG 1 EE is missing in the structure ATTENTION: atom:C6 LIG 1 EE is missing in the structure ATTENTION: atom:N1 LIG 1 EE is missing in the structure ATTENTION: atom:C7 LIG 1 EE is missing in the structure ATTENTION: atom:C15 LIG 1 EE is missing in the structure ATTENTION: atom:C13 LIG 1 EE is missing in the structure ATTENTION: atom:N12 LIG 1 EE is missing in the structure ATTENTION: atom:C10 LIG 1 EE is missing in the structure ATTENTION: atom:C8 LIG 1 EE is missing in the structure Number of chains : 5 Total number of monomers : 217 Number of atoms : 2162 Number of missing atoms : 18 Number of rebuilt atoms : 908 Number of unknown atoms : 10 Number of deleted atoms : 0 IERR = 1 There is an error. See above ===> Error: Fatal error. Cannot continue <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> Refmac_5.8.0123: Fatal error. Cannot continue Times: User: 2.1s System: 0.1s Elapsed: 0:04 </pre> </html> What went wrong? Am I missing any steps in my ligand fitting? Appreciate your feedback. Regards, Sze Yi
