SWISS-MODEL Repository

Template's ligands section 
Template without ligands. 
No ligands were included in the model.

Quaternary Structure Annotation of the Template 
 3im5 is annotated as MONOMER 
 The oligomeric state of the structure was assigned by the authors of the corresponding PDB entry 
 The following biological unit was used to build the template structure: 3im5.pdb2.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 The quaternary structure can be assumed to be identical 
 Model was succesfully built as MONOMER.

 - Start SMR-Pipeline for:f90935b4c470d1d12353ecdde59b660a on BC2-cluster at Fri Feb 22 06:01:40
2013 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  1
 - But still uncovered regions of the target sequence detected, go for: HHSEARCH

FATAL - No A3m found

 - Run HHSearch to detect more templates...
 - Generate new template library
 - Run template selection against modfied template library 
 - Summarize templates: 
 - Warning: Oligomer Prediction was not successfull!

 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:9): model based on new templates
 - Send 9 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 - ***
 - building model based on 3im5B (15-199) was successful 
 - ********
 - building model based on 2xoaA (15-532) was successful 
 -              *
 - building model based on 3nrtA (854-942) was successful 
 -                                             ***
 - building model based on 4ervA (2833-3033) was successful 
 -                *
 - building model based on 3nrtE (967-1056) was successful 
 -              ***
 - building model based on 4ervA (854-1055) was successful 
 -                  **
 - building model based on 3tojA (1072-1204) was successful 
 -                                            ***
 - building model based on 3rqrA (2749-2919) was successful 
 -                                                                   *
 - building model based on 1rroA (4205-4263) was successful 
 - Repository Pipeline parameter

   Cut-off parameters to model the target based on a BLAST target-template alignment
    Evalue :                                     0.0001
    Minimum Template size (aa) for ranking :     25
    Minimum Sequence identity :                  60

   Cut-off parameters to model the target based on a HHSearch target-template alignment
    Evalue :                                     0.0001
    Probability :                                50
    MAC :                                        0.3

   Parameters for model selection
    Minimal number of uncovered target
     residues after BLAST to run HHSEARCH :      50
    Minimal number of uncovered target
     residues to model an additional template :  25
    
 - Finish SMR-Pipeline for:f90935b4c470d1d12353ecdde59b660a on BC2-cluster at Fri Feb 22 06:10:53
2013