2. Submit to PINE. Try to submit backbone only one time and backbone + sidechain the other time. See the probabilities for side chain, and you think they are good mostly 80%, you use PINE results. Use PINE-SPARKY to validate them. If they are not good, use only backbone and do the superfast methods.
https://www.youtube.com/watch?v=vSlT7y5hT5glist=PLmYqoarOFAZ-aInZ5uM2pV63e7yMSHSuZindex=6
https://www.youtube.com/watch?v=l50CE-M1KE0list=PLmYqoarOFAZ-aInZ5uM2pV63e7yMSHSuZindex=8
3. Check your nomenclature and assignment confidence.
https://www.youtube.com/watch?v=I0mNdR3MHiwlist=PLmYqoarOFAZ-aInZ5uM2pV63e7yMSHSuZindex=30
https://www.youtube.com/watch?v=KqPstgautBElist=PLmYqoarOFAZ-aInZ5uM2pV63e7yMSHSuZindex=29
4. Run PONDEROSA-C/S
https://www.youtube.com/watch?v=zjO8Xh6VgV0list=PLmYqoarOFAZ-aInZ5uM2pV63e7yMSHSuZindex=14
5. Validate distance and angle constraints with Ponderosa Analyzer and PyMOL.
https://www.youtube.com/watch?v=L7vM_PrSnrglist=PLmYqoarOFAZ9Um_2DNL6Bw-gy92VJscfWindex=9
https://www.youtube.com/watch?v=12qKSA6Ku00list=PLmYqoarOFAZ9Um_2DNL6Bw-gy92VJscfWindex=10
https://www.youtube.com/watch?v=Tq7e8VK9ivElist=PLmYqoarOFAZ9Um_2DNL6Bw-gy92VJscfWindex=13
6. Iterate until you get reasonably good structure
https://www.youtube.com/watch?v=gqb8e_mNBk0list=PLmYqoarOFAZ9Um_2DNL6Bw-gy92VJscfWindex=14
7. Use final step option for large sampled structure generation
8. Validate structure quality.
https://www.youtube.com/watch?v=zPslIiR6Y1slist=PLmYqoarOFAZ9Um_2DNL6Bw-gy92VJscfWindex=18
Let me know if you need further help.
Cheers,
Woonghee