Hi everyone,

I am refining a ~3A structure using phenix 1.21.2-5419. I am at the final stages of the refinement but I am seeing some positive density on some hydrophobic residues (mainly Ile and Leu) together with a negative density around those residues (image attached).  At first, I guessed that might be related to solvent mask, so I turned on optimize_mask. That did not solve the issue, although slightly decreased R values. Diffraction data was processed with autoproc+staraniso and does not seem to be twinned (normal intensity stats + map deteriorates if twinning refinement is applied).

Does anyone have a guess about that?

Best,
Lucas

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Lucas Souza dos Santos
Laboratório de Biologia Estrutural Aplicada (LBEA)
Departamento de Microbiologia
Instituto de Ciências Biomédicas II - USP
Cidade Universitária - São Paulo - SP
CEP 05508-000