I have a protein (90aa length) structure with 2.3A resolution and space group P21 refined to Rfree/R to around 0.27 / 0.20. There are 3 protein dimers in one asym unit. For two dimers (chain A, B, C, D), I can see clearly continuous electron density from residue 10 to residue 89. However for the third dimer (chain E and F), I can only see clearly continuous density between residue 10 to residue 72 and lost tracing of the main chain.  I did see a large electron density blob close to the third dimer. (https://goo.gl/photos/R1SaHPKS6VLfcesb7 ; Green is positive density at 3 sigma and blue is FWT PHWT at 2sigma and 1sigma ). I do not know how to explain this blob. It seems to me that this blob is unlikely protein fragments (some parts of the blob is so chunky). Even if it's true that it's certain protein fragment between residue 73 to residue 89 of chain E or chain F, then the position of this fragment is totally different from the position of its fragment counterparts in chain A,B, C,D. I assume NCS copies (in this case maybe 3 copies) should have the same morphology as to each other.  

It also seems to me that this density is not from my crystal growth or harvest conditions, which has: Bis-Tris; PEG3350; PEG400 and NaCl. 

I do not know if Phenix Autobuild could build this automatically for me, but I'll try this later.

Thanks in advance for any input on this.

The density link is: https://goo.gl/photos/R1SaHPKS6VLfcesb7