cryo-EM

3a5x (7194 atoms)

method	bond	angle	clashscore	rama_outlier	rama_favor	rotamer	CC_mask
initial	0.013	1.530	117.79	2.85	86.59	8.72	0.292
cctbx_refine	0.001	0.4	2.36	0.61	93.50	2.05	0.3025
xtb_refine	0.010	1.70	2.5	0.81	93.90	4.36	0.3050
terachem_refine	0.014	1.4	1.53	0	96.75	4.62	0.3051

3j63_chain_A (1436 atoms)

method	bond	angle	clashscore	rama_outlier	rama_favor	rotamer	CC_mask
initial	0.004	1.007	50.84	4.49	85.39	5.48	0.6747
cctbx_refine	0.002	0.5	4.18	0	96.63	5.48	0.6711
xtb_refine	0.011	1.67	3.5	0	91.01	4.11	0.6530
terachem_refine	0.013	1.535	0.70	0	100.00	1.37	0.6386

5fn5_chain_c(3787 atoms)

method	bond	angle	clashscore	rama_outlier	rama_favor	rotamer	CC_mask
initial	0.012	2.001	14.27	2.07	90.87	18.13	0.6430
cctbx_refine	0.002	0.51	5.0	0.83	91.70	7.25	0.6540
xtb_refine	0.009	1.5	2.9	0.41	90.04	8.29	0.6555
terachem_refine	0.013	1.58	1.8	0	96.28	11.92	0.6441

5ly6(7399 atoms)

method	bond	angle	clashscore	rama_outlier	rama_favor	rotamer	CC_mask
initial	0.005	0.942	92.04	4.9	74.2	36.08	0.6239
cctbx_refine	0.002	0.48	4.6	4.26	77.61	10.41	0.6564
xtb_refine	0.011	1.86	1.8	2.13	87.21	7.75	0.6623
terachem_refine	0.014	1.87	7.0	2.56	85.07	17.92	0.6555

command used

0. if ligand included, phenix.pdbtool keep="protein" *.pdb
1. phenix.map_box mask_atoms=true soft_mask=true keep_origin=false keep_input_unit_cell_and_grid=false *.pdb *.map
2. qr.finalise *.pdb