Hi Zeynep,
Thank you for attaching your .sam file.
This thread is about using POA irradiance as input, but your file is using the default DNI and DHI as input. In your case, the module "deviation from STC" loss is high because of shading. The partial shading model calculates shading loss as a reduction in DC output, and as the screenshot of your 3D shading scene shows, there is significant shading between modules.
You are have enabled both beam irradiance losses by time step and solar azimuth-by-altitude beam irradiance shading, which seems like you might be double-counting the effect of shading. You have also enabled self shading by enabling, although because GCR = 0.3 self shading is not having a large impact. I think I would recommend using one shading model instead of three.
Best regards,
Paul.