SWISS-MODEL Repository

Template's ligands section 
Ligands in the template: ANP: 1, MG: 1. 
Ligands in the template that will be assessed: ANP901, MG903. 
Model's ligands section 
ANP901 
ANP901 interacts, within a radius of 3 Angstroem, with the following ions: MG903. They will be considered as a single ligand. 
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: 0.090 
Given the properties calculated previously, the ligand ANP901 will be included in the model. 
ANP901: conservation:True, RMSD:True, included: True 
 
The new model with the included ligands was saved successfully.

Quaternary Structure Annotation of the Template 
 1zxm 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: 1zxm.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 Not all chains of the complex were                      identified 
 Please use the advancend features of the SwissModel Project Mode 
   
 The target structure was calculated as SINGLE CHAIN

 - Start SMR-Pipeline for:318306e83530cb706180952152299ce0 on BC2-cluster at Thu Feb 14 04:56:03
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

 - Warning: sequence length exceeded the limit of 1500 residues
 - HHsearch profile build is skipped
FATAL - No A3m found

 - No template with A found
 - 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 1zxmA (28-404) was successful 
 -                        ****************************************
 - building model based on 4fm9A (433-1187) 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:318306e83530cb706180952152299ce0 on BC2-cluster at Thu Feb 14 06:18:45
2013