SWISS-MODEL Repository

Template's ligands section 
Ligands in the template: ZN: 2. 
Ligands in the template that will be assessed: ZN1, ZN2. 
Model's ligands section 
ZN1 
All the residues interacting with the ligand are completely conserved between model and template. 
The RMSD between the interacting residues of model and template is smaller than 2 Angstrom: 0.050 
Given the properties calculated previously, the ligand z.ZN1 will be included in the final model. 
ZN1: conservation:True, RMSD:True, included: True 
 
ZN2 
All the residues interacting with the ligand are completely conserved between model and template. 
The RMSD between the interacting residues of model and template is smaller than 2 Angstrom: 0.050 
Given the properties calculated previously, the ligand z.ZN2 will be included in the final model. 
ZN2: conservation:True, RMSD:True, included: True 
 
The new model with the included ligands was saved successfully.

Quaternary Structure Annotation of the Template 
 2kwq is annotated as MONOMER 
 The template structure (2kwq) was solved by NMR and does not contain any quaternary structure annotation 
 The template is annotated by the number of chains found in the PDB file 
      
 
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:95eba7a6d260a3d407d9a22761696c0e on BC2-cluster at Sun Apr 21 22:19:44
2013 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  2
 - But still uncovered regions of the target sequence detected, go for: HHSEARCH

 - No A3m found

 - Run HHSearch to detect more templates...
FATAL - No templates found in HHSEARCH, strange
 - 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 2kwqA (770-857) was successful 
 -                        ****************
 - building model based on 3h15A (247-416) 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:95eba7a6d260a3d407d9a22761696c0e on BC2-cluster at Sun Apr 21 22:21:28
2013