SWISS-MODEL Repository

Template's ligands section 
Ligands in the template: ZN: 3. 
Ligands in the template that will be assessed: ZN1, ZN2, ZN3. 
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: 0.040 
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 
 
ZN3 
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.ZN3 will be included in the final model. 
ZN3: conservation:True, RMSD:True, included: True 
 
The new model with the included ligands was saved successfully.

Quaternary Structure Annotation of the Template 
 2iyk 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: 2iyk.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:d8cb3d86db31a0d67c979f07e01f5a0b on BC2-cluster at Sat Feb 23 03:40:04
2013 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  3
 - But still uncovered regions of the target sequence detected, go for: HHSEARCH

 - Run HHSearch to detect more templates...
FATAL - No md5 found in hash for: 4i1sA
 - Generate new template library
 - Run template selection against modfied template library 
 - Summarize templates: 
 - No template with D found
 - No template with E found
 - No template with D found
 - No template with E found
 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:3): model based on new templates
 - Send 3 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -         ***********
 - building model based on 2iykB (113-267) was successful 
 -                      *********************************************
 - building model based on 2xzpA (289-920) was successful 
 -         **********************************************************
 - building model based on 2wjyA (111-919) 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:d8cb3d86db31a0d67c979f07e01f5a0b on BC2-cluster at Sat Feb 23 03:48:58
2013