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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

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

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