SWISS-MODEL Repository

Template's ligands section 
Ligands in the template: FUL: 1, MAN: 1. 
Ligands in the template that will be assessed: FUL2005, MAN2004. 
Model's ligands section 
MAN2004 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand A.MAN2004 will not be included in the model. 
MAN2004: conservation:False, RMSD:False, included: False 
 
FUL2005 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand A.FUL2005 will not be included in the model. 
FUL2005: conservation:False, RMSD:False, included: False 
 
No ligands were included in the model.

Quaternary Structure Annotation of the Template 
 4aqs 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: 4aqs.pdb1.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 (=MONOMER) 
 The target structure was calculated as SINGLE CHAIN 
 The corresponding reliability score is 0.164 (>0.5 indicates similarity)

 - Start SMR-Pipeline for:a6326cdf8fd806bb9123b0c40164dfe7 on BC2-cluster at Thu Feb 21 16:58:29
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 C found
 - No template with C found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with C found
 - No template with A found
 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:16): model based on new templates
 - Send 16 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -   *********************
 - building model based on 4aqsA (49-511) was successful 
 -                                             **
 - building model based on 1tleA (991-1039) was successful 
 -                                           ******
 - building model based on 1kloA (949-1092) was successful 
 -                                              *****
 - building model based on 1kloA (1012-1132) was successful 
 -                                    ****
 - building model based on 1kloA (789-884) was successful 
 -                                       ***
 - building model based on 2y38A (855-932) was successful 
 -                     *****
 - building model based on 1kloA (447-567) was successful 
 -                    *******
 - building model based on 1npeB (416-567) was successful 
 -                 *********
 - building model based on 4aqsA (355-561) was successful 
 -                                            *******
 - building model based on 4aqsA (960-1126) was successful 
 -                                                ******
 - building model based on 2gy5A (1044-1172) was not successful go to next best template
 -                                                ******
 - building model based on 2gy7B (1044-1172) was successful 
 -                                     *****
 - building model based on 2gy5A (800-912) was successful 
 -                                              *******
 - building model based on 4aqsA (1010-1174) was successful 
 -                                         *********
 - building model based on 4aqsA (883-1077) was successful 
 -                                       ******
 - building model based on 1kloA (857-990) was successful 
 -                                     *******
 - building model based on 4aqsA (806-972) 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:a6326cdf8fd806bb9123b0c40164dfe7 on BC2-cluster at Thu Feb 21 17:09:15
2013