The fragment binding data used in this study was a subset of the 55 complex structures and 1 apo structure with associated affinity data published by L. Öster et al. All 55 complex structures were re-refined using phenix.refine (version 1.14.3283) with AFITT4 55 generated MMFF94s gradients on the small molecule ligand-complexes used in phenix.refine (PHENIX-AFITT). All refinements using phenix.refine or PHENIX-AFITT used six refinement macrocycles. The resulting structures were aligned to the apo structure (PDBID:5AHX) using defaults options for protein alignment in the OpenEye SpruceTK. The ten fragment complex structures used for prediction (PDBID:5AI0, 5AI6, 5AIB, 5AIC, 5AK4, 5AKG, 5AKX, 5ALE, 5ALV, 5AM2) were further re-refined in an attempt estimate the occupancy of the fragment in the binding site and to determine if an automated ligand placement algorithm (AFITT) agreed with the conformation and placement done by L. Öster et al. The re-refinement protocol was as follows: 1) remove the ligand and refine using phenix.refine the resulting protein, excipients and solvent; 2) AFITT was used to automatically fit fragment to the resulting difference density; 3) the new fragment placement was checked to see if significantly different from the deposited placement; 4) the new complex was re-refined using PHENIX-AFITT; and 5) the structure was refined with occupancy refinement of the ligand turned on and automatically generated Translational, Librational, and Screw (TLS) constraints for PHENIX-AFITT. The refinement and occupancy data for all ten structures can be found in supporting data tables S3, S2 and S1. The median root mean square deviation (RMSD) between the deposited and re-refined ligands was 0.11 Å with a maximum of 1.4 Å for 6N6 (PDBID:5AK4).