Hi Abhinaba,
Based on your screenshot of the validation summary, your model contains 480 residues spread over 80 chains. Does that match what is in your sample? Is it possible that some or all of these amino acids need to be merged into larger polypeptide chain(s)? Perhaps it is not a coincidence that the number of chains is equal to the number of bonds of unrealistic length.
Best, Kaspar
Thanks Phil and Pavel for pointing it out. The error is likely (I think) of the NH2 ligands not being detected as proper amide linkage.
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Hi Abhinaba,
Here is my interpretation of this…
The geometry statistics are overall fine, except for the impossibly bad bond rmsd (overall, and greater than 4σ). This can't be true for an okay model. So I'd stop deposition and check/fix that first! It’s also amazing how one can mess up bond lengths so badly
without actually damaging the angles—very interesting!
Overall, CCmask suggests the model fits the map okay as a whole. To get a better local picture, you’d need to check values per chain and residue.
I wouldn’t worry about the atom inclusion score at all—it’s a pretty meaningless quality metric, and I could spend an hour or two explaining why.
Bottom line: Based on the information you’ve supplied, your biggest concern should be bad covalent bonds.
Good luck!
Pavel
Dear Community,
I'm trying to deposit an EM volume map and the corresponding model to the PDB. Though validation in Phenix doesn't show anything wrong, the deposition
validation indicates a low atom inclusion score. Not sure why the error… Thanks in advance for any insights.
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