Dear Modeller users
I generated some protein by Modeller. When I checked the log file, I found a lot of restraint violations. I have a question. How can I remove restrain violations ? Which package should I use to get rid of violation and when do I use that package? ex. after generating model ...
Please check my log file. I need comments since I want to generate very good model from Modeller. Thanks.
Hyun.
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Summary of the restraint violations:
NUM ... number of restraints. NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. RVIOL ... relative difference from the best value. NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). RMS_2 ... RMS(feature, best_value, NUMB). MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i ------------------------------------------------------------------------------------------------------ 1 Bond length potential : 6142 0 2 0.006 0.006 70.031 1.000 2 Bond angle potential : 8336 4 21 2.162 2.162 743.97 1.000 3 Stereochemical cosine torsion poten: 4014 0 98 43.785 43.785 1174.1 1.000 4 Stereochemical improper torsion pot: 2594 0 0 1.541 1.541 132.21 1.000 5 Soft-sphere overlap restraints : 15521 0 0 0.004 0.004 35.949 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 9 Distance restraints 1 (CA-CA) : 21580 0 19 0.290 0.290 7962.2 1.000 10 Distance restraints 2 (N-O) : 21708 0 37 0.370 0.370 8395.3 1.000 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 13 Mainchain Omega dihedral restraints: 788 0 4 4.353 4.353 176.07 1.000 14 Sidechain Chi_1 dihedral restraints: 648 0 13 80.203 80.203 236.97 1.000 15 Sidechain Chi_2 dihedral restraints: 490 0 7 81.340 81.340 168.21 1.000 16 Sidechain Chi_3 dihedral restraints: 132 0 1 65.670 65.670 86.936 1.000 17 Sidechain Chi_4 dihedral restraints: 54 0 0 89.199 89.199 37.293 1.000 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 23 Distance restraints 3 (SDCH-MNCH) : 6500 0 0 0.364 0.364 5270.9 1.000 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 25 Phi/Psi pair of dihedral restraints: 786 63 79 24.691 47.736 -19.470 1.000 26 Distance restraints 4 (SDCH-SDCH) : 1300 0 1 0.828 0.828 1103.2 1.000 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000