cryo-EM

3a5x (7194 atoms)

method	bond	angle	clash	rama_out	rama_favor	rotamer	EMRinger	CC_mask
initial	0.013	1.530	117.79	2.85	86.59	8.72	0.80	0.292
cctbx_refine	0.002	1.14	3.9	0.41	92.28	2.56	-0.08	0.3091
xtb_refine	0.010	1.73	3.3	0.61	94.31	3.33	0.40	0.3311
terachem_refine	0.010	1.47	0.14	0	96.75	5.13	0.89	0.3001

3j63_chain_A (1436 atoms)

method	bond	angle	clash	rama_out	rama_favor	rotamer	EMRinger	CC_mask
initial	0.004	1.007	50.84	4.49	85.39	5.48	2.36	0.6747
cctbx_refine	0.002	0.749	3.48	0	98.88	4.11	1.17	0.6553
xtb_refine	0.012	1.705	3.48	0	94.38	4.11	1.83	0.6546
terachem_refine	0.013	1.535	0.70	0	100.00	1.37	1.17	0.6386

5fn5_chain_c(3787 atoms)

method	bond	angle	clash	rama_out	rama_favor	rotamer	EMRinger	CC_mask
initial	0.012	2.001	14.27	2.07	90.87	18.13	0.79	0.6430
cctbx_refine	0.003	1.19	5.81	0.83	92.53	8.29	-0.10	0.6645
xtb_refine	0.01	1.55	2.64	0.83	90.87	9.33	0.79	0.6573
terachem_refine	0.012	1.741	0	0	95.85	7.77	0.79	0.6648

5ly6(7399 atoms)

method	bond	angle	clash	rama_out	rama_favor	rotamer	EMRinger	CC_mask
initial	0.005	0.942	92.04	4.9	74.2	36.08	0.49	0.6239
cctbx_refine	0.002	0.66	4.87	3.62	79.10	3.39	1.05	0.6441
xtb_refine	0.011	1.86	1.8	2.13	87.21	7.75	0.93	0.6623
terachem_refine	0.012	1.61	1.08	2.1	89.98	11.14	0.93	0.6394

6i5a(2396 atoms)

method	bond	angle	clash	rama_out	rama_favor	rotamer	EMRinger	CC_mask
initial	0.012	1.840	6.69	1.32	97.35	0.74	3.94	0.8156
cctbx_refine	0.002	0.570	1.67	1.32	95.36	0.00	3.73	0.8118
xtb_refine	0.011	1.590	2.09	1.32	94.70	0.74	3.57	0.8066
terachem_refine	0.010	1.407	0.84	1.32	98.68	0.00	3.99	0.8106

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