SWISS-MODEL Repository

Template's ligands section 
Ligands in the template: BGC: 3, BMA: 1, GAL: 1, NAG: 2, XYS: 2. 
Ligands in the template that will be assessed: BGC4, BGC5, BGC6, BMA3, GAL9, NAG1, NAG2. 
Model's ligands section 
NAG1 
One or more ligand's atoms are closer than 1.5 Angstroem to one or more atoms that belong to the model or to other ligands. 
Given the properties calculated previously, the ligand z.NAG1 will not be included in the model. 
NAG1: conservation:False, RMSD:False, included: False 
 
NAG2 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.NAG2 will not be included in the model. 
NAG2: conservation:False, RMSD:False, included: False 
 
BMA3 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.BMA3 will not be included in the model. 
BMA3: conservation:False, RMSD:False, included: False 
 
BGC4 
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 z.BGC4 will not be included in the model. 
BGC4: conservation:False, RMSD:False, included: False 
 
BGC5 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.BGC5 will not be included in the model. 
BGC5: conservation:False, RMSD:False, included: False 
 
BGC6 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.BGC6 will not be included in the model. 
BGC6: conservation:False, RMSD:False, included: False 
 
GAL9 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.GAL9 will not be included in the model. 
GAL9: conservation:False, RMSD:False, included: False 
 
No ligands were included in the model.

Quaternary Structure Annotation of the Template 
 1umz 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: 1umz.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 Analysis of evolutionary and family specific aspects revealed conservation of the oligomeric structure 
 Hence, the oligomeric structures of the target and the template can be assumed to be similar (=MONOMER) 
 The corresponding reliability score is 0.534 (>0.5 indicates similarity) 
 Model was succesfully built as MONOMER.

 - Start SMR-Pipeline for:9110c97f6d6f1ed6fd38b5e7844e173a on BC2-cluster at Tue Feb 19 20:28:50
2013 


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

 - 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:1): model based on new templates
 - Send 1 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -               ******************************************************************
 - building model based on 1umzA (49-281) 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:9110c97f6d6f1ed6fd38b5e7844e173a on BC2-cluster at Tue Feb 19 20:30:34
2013