You cannot use this prototxt as it is for training as there is no 'phase: train' involved in the prototxt. This prototxt is used for inference, You cannot use it for training. Please find the prototxt file that was used for training and use that file or rewrite the deploy.prototxt file so that it has training phase.
To rewrite please refer to the train_test.prototxt I have attached (see line 8 and line 144). This file is provided by Xilinx and to use this you need special caffe framework that is provided by xilinx to run it. So I suggest you to rewrite your prototxt file by taking train_test.prototxt as reference or else refer caffe tutorials on how to write a prototxt file.