i mean does phenix differentiate in refinment between SN, SN2+ and SN4+?
In the phenix.refine log file look for this section:

============================== Scattering factors =============================


� � � � � � � � ----------X-ray scattering dictionary----------

Number of scattering types: 4
� Type �Number � �sf(0) � Gaussians
� �Zn2+ � � 1 � � 27.88 � � � 1
� �O � � � 20 � � �7.97 � � � 2
� �N � � � 12 � � �6.97 � � � 2
� �C � � � 33 � � �5.97 � � � 2
� sf(0) = scattering factor at diffraction angle 0.

The "Type" is exact including charge. The label is one of the entries from Int Tab Vol C Tab. 6.1.1.4. For SN this is your list above (SN, SN2+, SN4+).

Ralf