Deep network has been utilized in designing a deformable registration framework for end-to-end optimization.Deep deformable registration minimizes a cost that is an upper bound to the sum of squared difference image registration cost.Proposed deep deformable registration improves diffeomorphic and log-demons registration significantly on 3D brain MRI data.The network architecture used in this research is a variation of a fully convolutional SKIP architecture.Prior to this work, convnet was used in learning features for registration; in contrast, this work uses it for optimization. Deformable registration is ubiquitous in medical image analysis. Many deformable registration methods minimize sum of squared difference (SSD) as the registration cost with respect to deformable model parameters. In this work, we construct a tight upper bound of the SSD registration cost by using a fully convolutional neural network (FCNN) in the registration pipeline. The upper bound SSD (UB-SSD) enhances the original deformable model parameter space by adding a heatmap output from FCNN. Next, we minimize this UB-SSD by adjusting both the parameters of the FCNN and the parameters of the deformable model in coordinate descent. Our coordinate descent framework is end-to-end and it can work with any deformable registration method that uses SSD. We demonstrate experimentally that our method enhances the accuracy of deformable registration algorithms significantly on two publicly available 3D brain MRI data sets.