SWISS-MODEL Repository

Template's ligands section 
Ligands in the template: CL: 2, MG: 2. 
Ligands in the template that will be assessed: MG1, MG2. 
Model's ligands section 
MG1 
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: 0.060 
Given the properties calculated previously, the ligand z.MG1 will be included in the final model. 
MG1: conservation:True, RMSD:True, included: True 
 
MG2 
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.MG2 will be included in the final model. 
MG2: conservation:True, RMSD:True, included: True 
 
The new model with the included ligands was saved successfully.

Quaternary Structure Annotation of the Template 
 2jd4 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: 2jd4.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:c8612e37bf93f39a831b14dad0c3c5da on BC2-cluster at Fri Feb 22 12:51:48
2013 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  1
 - But still uncovered regions of the target sequence detected, go for: HHSEARCH

 - Run HHSearch to detect more templates...
 - Generate new template library
 - Run template selection against modfied template library 
 - Summarize templates: 
 - Skip Template HHsearch issue
 - Skip Template HHsearch issue
 - 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 C found
 - No template with D found
 - No template with A found
 - No template with C found
 - No template with D found
 - No template with B found
 - No template with D 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:22): model based on new templates
 - Send 22 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                                                                       **********
 - building model based on 2jd4B (2709-3083) was successful 
 -  **********
 - building model based on 2y38A (29-403) was successful 
 -                       *
 - building model based on 1tleA (855-908) was successful 
 -                      ****
 - building model based on 1kloA (819-955) was successful 
 -                                                        **************
 - building model based on 2wjsA (2134-2680) was not successful go to next best template
 -                                      ***
 - building model based on 1kloA (1426-1558) was successful 
 -                    *****
 - building model based on 4aqsA (749-941) was successful 
 -                                     ***
 - building model based on 1kloA (1371-1503) was successful 
 -                    ***
 - building model based on 1kloA (718-843) was not successful go to next best template
 -                    ***
 - building model based on 1npeB (718-843) was successful 
 -           ****
 - building model based on 4aqsA (371-523) was successful 
 -                         ***
 - building model based on 2gy5A (918-1033) was not successful go to next best template
 -                         ***
 - building model based on 2gy7B (918-1033) was not successful go to next best template
 -  ************
 - building model based on 4aqsA (42-491) was successful 
 -                      ****
 - building model based on 4aqsA (826-989) was successful 
 -                                                         ***
 - building model based on 3sh5A (2149-2260) was successful 
 -                          ***
 - building model based on 1kloA (957-1088) was successful 
 -                            ***
 - building model based on 1kloA (1023-1154) was successful 
 -                                                             ****
 - building model based on 3pveA (2316-2467) was successful 
 -                         ****
 - building model based on 1kloA (909-1049) was successful 
 -                                                                  ****
 - building model based on 2h0bD (2508-2658) was not successful go to next best template
 -                                                                  ****
 - building model based on 2h0bA (2508-2658) was not successful go to next best template
 -                                                                  ****
 - building model based on 2h0bC (2508-2658) was not successful go to next best template
 -                                                                  ****
 - building model based on 2h0bB (2508-2658) was not successful go to next best template
 -                                     *****
 - building model based on 4aqsA (1369-1548) was successful 
 -                       ******
 - building model based on 4aqsA (856-1083) was successful 
 -                    *****
 - building model based on 4aqsA (715-891) was successful 
 -                                                         ********
 - building model based on 2jd4B (2152-2475) was successful 
 -                                                             *********
 - building model based on 1dykA (2306-2659) was successful 
 -                        ******
 - building model based on 4aqsA (899-1138) was successful 
 -                                                             ********************
 - building model based on 3qcwB (2323-3082) was not successful go to next best template
 -                                                             ********************
 - building model based on 3qcwA (2323-3082) was not successful go to next best template
 -                                                             ********************
 - building model based on 3r05A (2323-3082) was not successful go to next best template
 -                                                             ********************
 - building model based on 3r05B (2323-3082) was not successful go to next best template
 -                                                             ********************
 - building model based on 3poyA (2323-3082) was not successful go to next best template
 -                                                         ******************
 - building model based on 3qcwB (2140-2823) was successful 
 -                                                         ***********************
 - building model based on 3qcwB (2141-3029) was not successful go to next best template
 -                                                         ***********************
 - building model based on 3qcwA (2141-3029) was not successful go to next best template
 -                                                         ***********************
 - building model based on 3r05A (2141-3029) was not successful go to next best template
 -                                                         ***********************
 - building model based on 3r05B (2141-3029) was not successful go to next best template
 -                                                         ***********************
 - building model based on 3poyA (2141-3029) was not successful go to next best template
 -                                                                  **********
 - building model based on 2jd4A (2499-2893) 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:c8612e37bf93f39a831b14dad0c3c5da on BC2-cluster at Fri Feb 22 13:33:50
2013