Flexible optical network is a promising technology to accommodate high-capacity demands in next-generation networks. To ensure uninterrupted communication, existing lightpath provisioning schemes are mainly done with the assumption of worst-case resource under-provisioning and fixed channel spacing, which preserves an excessive signal-to-noise ratio (SNR) margin. However, under a resource over-provisioning scenario, the excessive SNR margin restricts the transmission bit-rate, leading to physical layer resource waste and stranded transmission capacity. To tackle this challenging problem, we leverage an iterative feedback tuning algorithm to provide a just-enough SNR margin, so as to maximize the network throughput. Specifically, the proposed algorithm is implemented in three steps. First, starting from the high SNR margin setup, we establish an integer linear programming model as well as a heuristic algorithm to maximize the network throughput by solving the problem of routing, modulation format, forward error correction, baud-rate selection, and spectrum assignment. Second, we optimize the channel spacing of the lightpaths obtained from the previous step, thereby increasing the available physical layer resources. Finally, we iteratively reduce the SNR margin of each lightpath until the network throughput cannot be increased. Through numerical simulations, we confirm the throughput improvement in different networks and with different baud-rates. In particular, we find that our algorithm enables over 20\% relative gain when network resource is over-provisioned, compared to the traditional method preserving an excessive SNR margin.