| DISTANCE GEOMETRY AND RESTRAINED MOLECULAR DYNAMICS |
A SET OF FOUR STRUCTURES WERE OBTAINED USING METRIC MATRIX DISTANCE GEOMETRY, AND SUBSEQUENTLY REFINED BY DISTANCE-RESTRAINED MOLECULAR DYNAMICS USING A SET OF INTER-PROTON DISTANCES AND DIHEDRAL ANGLE RESTRAINTS DERIVED FROM THE NMR DATA. THE FOUR DISTANCE-REFINED STRUCTURES WERE REFINED FURTHER USING RELAXATION-MATRIX BASED NOE INTENSITY-RESTRAINED MOLECULAR DYNAMICS. ALL CALCULATIONS WERE CARRIED OUT USING THE X-PLOR PROGRAM. THE FINAL FOUR STRUCTURES WERE OBTAINED BY CONJUGATE GRADIENT MINIMIZATION OF THE STRUCTURES OBTAINED BY RELAXATION MATRIX BASED NOE INTENSITY-RESTRAINED MOLECULAR DYNAMICS. THE UNWEIGHTED R(1/6) VALUE WAS USED TO MONITOR THE REFINEMENT. THE R(1/6)-FACTOR IS DEFINED: R(1/6) = SUM{|I(OBS)^(1/6) - K*I(CALC)^(1/6)|} / SUM{I(OBS)^(1/6)}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|
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