If possible please elaborate your question.
However its better to compare the same values of SAVES server for the template model (template pdb).
By comparing you can predict the reason for the errors.
GOOD LUCK!!!
target protein dont have the homology wd PDB so i made the model through I-tasser. then I got the saves values 30% so i did energy minimization and i checked saves i got 16% saves values..now I am worried what to do.I have checked the instability index , it also not valid.
What pdb, I don't understand and secondly homology modelling prerequisite need a template. So if feasible tell me How much sequence alignment you got for target model with any pdb and i will tell you another way to do homology modelling on the basis of the pairwise sequence alignment.
Do multi-template modelling in Modeler. It is better than I-Tasser and will help. If the issue persists, go for a minimum of 1ns dynamics of modeled protein and check the stability.
@ Ponne , @Jamal ,Thanks all of u for the answers . I can go through the multiple template ..but probs is : Target seq blast against pdb and i get only 21% query coverage and 25% identity and only 4 templates wd same output. I select the template on >30% identity and >=85% query coverage..but in this case i dont get this criteria..so how can i select the mutiple template.
Low identity is due to low query coverage (in your case). If all the four templates had different domains matching to your query, then you can very well consider them for multi-template modeling.
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