Subject: [modeller_usage] Confusion between two models
From: hari krishna <>
Date: Mon, 20 Feb 2012 12:49:18 +0530
Dear All,
I am trying to model a protein containing 859 amino acids. After loop modeling and refinement of two different models, I have doubt in chosing which model for further usage.. Becuase the stereochemical quality was good for one model (85% in favorable region) and for the second model its about 65%. Except this all other parameters like Z-score, energy, residue error plot and DOPE score favors the second model. In this case which one i need to choose. Please help me in this regard. I am attaching the procheck program results. Also the second model superimpose well to their homology proteins compared to the first model
MODEL 1
+----------<<< P R O C H E C K S U M M A R Y >>>----------+ | | | input_atom_only.pdb 2.5 858 residues |
| | *| Ramachandran plot: 85.4% core 11.4% allow 2.1% gener 1.1% disall | | |
*| All Ramachandrans: 49 labelled residues (out of 854) | +| Chi1-chi2 plots: 5 labelled residues (out of 502) | | Main-chain params: 6 better 0 inside 0 worse |
| Side-chain params: 5 better 0 inside 0 worse | | | *| Residue properties: Max.deviation: 15.7 Bad contacts: 57 |
*| Bond len/angle: 10.7 Morris et al class: 1 1 3 | | | | G-factors Dihedrals: -0.07 Covalent: -0.36 Overall: -0.18 |
| | | M/c bond lengths: 97.8% within limits 2.2% highlighted | *| M/c bond angles: 90.5% within limits 9.5% highlighted 1 off graph |
| Planar groups: 100.0% within limits 0.0% highlighted | | | +----------------------------------------------------------------------------+
+ May be worth investigating further. * Worth investigating further.
MODEL 2
+----------<<< P R O C H E C K S U M M A R Y >>>----------+
| | | input_atom_only.pdb 2.5 859 residues | | |
*| Ramachandran plot: 64.7% core 28.0% allow 4.6% gener 2.7% disall | | | *| All Ramachandrans: 147 labelled residues (out of 825) |
*| Chi1-chi2 plots: 16 labelled residues (out of 472) | +| Main-chain params: 4 better 0 inside 2 worse | | Side-chain params: 5 better 0 inside 0 worse |
| | *| Residue properties: Max.deviation: 9.3 Bad contacts: 0 | *| Bond len/angle: 7.1 Morris et al class: 3 2 2 |
*| 5 cis-peptides | +| G-factors Dihedrals: -0.90 Covalent: -0.13 Overall: -0.57 | | |
| M/c bond lengths:100.0% within limits 0.0% highlighted | | M/c bond angles: 90.2% within limits 9.8% highlighted | *| Planar groups: 57.1% within limits 42.9% highlighted 69 off graph |
| | +----------------------------------------------------------------------------+ + May be worth investigating further. * Worth investigating further.