qr-helix-3nir

This is a helix extracted from Crystal structure of small protein crambin at 0.48 A resolution. Except for its high resolution feature, its sidechain is complete and diverse.

Analysis of optimization results

H bond analysis

Total number of H bonds: 9.

Reference H-bond distances range (min,max,mean): 2.005 2.325 2.139

"use_hydrogens=False" is used for bond rmsn analysis.

perturbed:

model	min	max	mean	recovered	bond_rmsd	rama_favored	clashscore
0.3	1.921	2.639	2.237	64.44	0.0171	100.00	0.00
0.6	1.937	3.279	2.584	22.22	0.0186	95.00	4.93
0.9	1.909	4.178	2.712	28.89	0.0190	92.50	0.00
1.2	2.189	5.793	3.702	3.33	0.0185	76.67	0.45
1.5	1.630	6.461	3.880	5.56	0.0189	83.33	3.59

cctbx_opt:

model	min	max	mean	recovered	bond_rmsd	rama_favored	clashscore
0.3	1.988	2.616	2.257	52.22	0.0035	100.00	0.00
0.6	2.094	2.939	2.441	35.56	0.0032	91.67	0.00
0.9	2.057	4.825	2.832	23.33	0.0033	85.83	0.00
1.2	2.079	5.752	3.472	12.22	0.0034	83.33	0.90
1.5	1.695	6.724	3.880	11.11	0.0035	82.50	0.90

xtb_opt_stpmax_0.2:

model	min	max	mean	recovered	bond_rmsd	rama_favored	clashscore
0.3	1.811	2.219	1.936	100.00	0.0112	91.67	4.04
0.6	1.795	2.601	2.006	88.89	0.0113	91.67	4.48
0.9	1.805	2.722	2.028	88.89	0.0113	91.67	4.48
1.2	1.769	4.554	2.420	63.33	0.0116	75.83	1.79
1.5	1.802	4.397	2.784	42.22	0.0115	71.67	2.69

xtb_opt_stpmax_0.3:

model	min	max	mean	recovered	bond_rmsd	rama_favored	clashscore
0.3/	1.810	2.186	1.931	100.00	0.0112	91.67	4.42
0.6/	1.798	2.577	2.005	88.89	0.0111	91.67	4.48
0.9/	1.803	2.716	2.030	88.89	0.0113	91.67	4.48
1.2/	1.766	4.550	2.364	67.78	0.0115	82.50	2.69
1.5/	1.774	4.344	2.711	44.44	0.0114	70.00	0.90

xtb_opt_stpmax_0.4:

model	min	max	mean	recovered	bond_rmsd	rama_favored	clashscore
0.3/	1.811	2.209	1.934	100.00	0.0112	91.67	4.48
0.6/	1.798	2.574	2.002	88.89	0.0112	91.67	4.48
0.9/	1.802	2.716	2.025	88.89	0.0113	91.67	4.48
1.2/	1.766	4.318	2.253	72.22	0.0114	88.33	5.38
1.5/	1.776	4.133	2.662	46.67	0.0113	72.50	1.35

xtb_opt_stpmax_0.5:

model	min	max	mean	recovered	bond_rmsd	rama_favored	clashscore
0.3/	1.813	2.193	1.936	100.00	0.0094	91.67	4.48
0.6/	1.795	2.564	1.995	88.89	0.0094	91.67	4.48
0.9/	1.797	2.689	2.013	88.89	0.0095	91.67	4.48
1.2/	1.767	3.391	2.181	75.56	0.0095	91.67	5.83
1.5/	1.753	3.909	2.503	56.67	0.0095	78.33	1.79

terachem_opt_water

model	min	max	mean	recovered	bond_rmsd	rama_favored	clashscore
0.3	1.783	2.024	1.867	100.00	0.0150	100.00	0.00
0.6	1.791	2.309	1.897	97.78	0.0150	100.00	0.00
0.9	1.789	2.318	1.903	93.33	0.0150	100.00	0.00
1.2	1.781	2.314	1.902	98.89	0.0149	100.00	0.90
1.5	1.735	3.604	2.250	67.78	0.0149	93.33	0.00

terachem_opt_final

model	min	max	mean	recovered	bond_rmsd	rama_favored	clashscore
0.3	1.783	2.024	1.867	100.00	0.0150	100.00	0.00
0.6	1.791	2.300	1.896	98.89	0.0150	100.00	0.00
0.9	1.789	2.318	1.903	93.33	0.0150	100.00	0.00
1.2	1.781	2.314	1.902	98.89	0.0149	100.00	0.90
1.5	1.786	2.665	1.921	95.56	0.0149	100.00	1.35

simulated map are generated by commands:

1. phenix.fmodel helix_3nir_6_19.pdb high_res=4 low_res=6
2. phenix.mtz2map helix_3nir_6_19.pdb.mtz include_fmodel=True
3. mv helix_3nir_6_19.pdb_fmodel.ccp4 map.ccp4