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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