SWISS-MODEL Repository

Template's ligands section 
Ligands in the template: ALA: 1, CO: 1, EDO: 2, FE: 1, GOL: 1. 
Ligands in the template that will be assessed: CO1316, FE1315. 
Model's ligands section 
FE1315 
Not all the residues interacting with the ligand are completely conserved between model and template. 
No RMSD calculation will be performed. 
Given the properties calculated previously, the ligand D.FE1315 will not be included in the final model. 
FE1315: conservation:False, RMSD:False, included: False 
 
CO1316 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand D.CO1316 will not be included in the final model. 
CO1316: conservation:False, RMSD:False, included: False 
 
No ligands were included in the model.

Quaternary Structure Annotation of the Template 
 2vc5 is annotated as DIMER 
 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: 2vc5.pdb2.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 Analysis of evolutionary and family specific aspects revealed non-conservation of the oligomeric structure 
 Hence, the oligomeric structures of the target and the template cannot be assumed to be similar (=DIMER) 
 The target structure was calculated as SINGLE CHAIN 
 The corresponding reliability score is 0.294 (>0.5 indicates similarity) 
 To build the complex the following chains of the complex has been additionally identified: 2vc5C 

 - Start SMR-Pipeline for:2172477c88a04cd4268b49effcc8ceb5 on BC2-cluster at Fri Feb 22 00:07:05
2013 


 - Analyze BLAST summary ... 
 - No templates found with BLAST (seqid-cutoff: 60): go to HHSEARCH

FATAL - No A3m found

 - Run HHSearch to detect more templates...
 - Generate new template library
 - Run template selection against modfied template library 
 - Summarize templates: 
 - No template with B found
 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:2): model based on new templates
 - Send 2 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                 *****************************************************
 - building model based on 2vc5D (69-298) was successful 
 -  ******************************************************************************
 - building model based on 3k2gD (4-344) 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:2172477c88a04cd4268b49effcc8ceb5 on BC2-cluster at Fri Feb 22 00:29:52
2013