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Conclusions
Brunger, A. T., Adams, P. D., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., Pannu, N. S., Read, R. J., Rice, L. M. and Simonson, T.  International Tables for Crystallography (2012). Vol. F, Section 18.6.10, p. 517 [ doi:10.1107/97809553602060000860 ]
... searches to atomic resolution refinement. References Stout, G. H. & Jensen, L. H. (1989). X-ray Structure Determination, p. 33. New ...

Conclusions
Brunger, A. T., Adams, P. D. and Rice, L. M.  International Tables for Crystallography (2012). Vol. F, Section 18.2.8, p. 472 [ doi:10.1107/97809553602060000856 ]
... initial models, e.g. those obtained by weak molecular-replacement solutions (Rice & Brünger, 1994; Adams et al., 1997, 1999). Simulated ... 181-190. Brunger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., ...

Ensemble models
Brunger, A. T., Adams, P. D. and Rice, L. M.  International Tables for Crystallography (2012). Vol. F, Section 18.2.7, pp. 471-472 [ doi:10.1107/97809553602060000856 ]
... 165-175. Burling, F. T., Weis, W. I., Flaherty, K. M. & Brunger, A. T. (1996). Direct observation of protein solvation ... Burley, S. K., Brunger, A. T., Hendrickson, W. A. & Karplus, M. (1991). Exploration of disorder in protein structures by X ... 10, 340-358. Kuriyan, J., Petsko, G. A., Levy, R. M. & Karplus, M. (1986). Effect of anisotropy and anharmonicity ...

Multi-start refinement and structure-factor averaging
Brunger, A. T., Adams, P. D. and Rice, L. M.  International Tables for Crystallography (2012). Vol. F, Section 18.2.6, p. 471 [ doi:10.1107/97809553602060000856 ]
... structure factors from each of the models can be averaged (Rice et al., 1998). This averaging tends to reduce the ... structure of aspartate aminotransferase. J. Mol. Biol. 203, 803-816. Rice, L. M., Shamoo, Y. & Brunger, A. T. (1998). Phase ...

Examples
Brunger, A. T., Adams, P. D. and Rice, L. M.  International Tables for Crystallography (2012). Vol. F, Section 18.2.5, pp. 470-471 [ doi:10.1107/97809553602060000856 ]
... nger, 1988; Fujinaga et al., 1989; Kuriyan et al., 1989; Rice & Brünger, 1994; Adams et al., 1997). In another ... Biol. 203, 803-816. Brunger, A. T., Kuriyan, J. & Karplus, M. (1987). Crystallographic R factor refinement by molecular dynamics. Science, 235, 458-460. Fujinaga, M., Gros, P. & van Gunsteren, W. F. (1989). Testing ...

An intuitive explanation of simulated annealing
Brunger, A. T., Adams, P. D. and Rice, L. M.  International Tables for Crystallography (2012). Vol. F, Section 18.2.4.4, p. 470 [ doi:10.1107/97809553602060000856 ]
An intuitive explanation of simulated annealing 18.2.4.4. An intuitive explanation of simulated annealing The goal of any optimization problem is to find the global minimum of a target function. In the case of crystallographic refinement, one searches for the conformation or conformations of the molecule that best fit the diffraction data ...
     [more results from section 18.2.4 in volume F]

A priori chemical information
Brunger, A. T., Adams, P. D. and Rice, L. M.  International Tables for Crystallography (2012). Vol. F, Section 18.2.3.2, p. 468 [ doi:10.1107/97809553602060000856 ]
... is sometimes used to reduce the radii, and n = 2, m = 2 or n = 1, m = 4. van der Waals attraction and electrostatic interactions are usually ... Methods Enzymol. 115, 252-270. Parkinson, G., Vojtechovsky, J., Clowney, L., Brunger, A. T. & Berman, H. M. (1996). New ...
     [more results from section 18.2.3 in volume F]

Cross validation
Brunger, A. T., Adams, P. D. and Rice, L. M.  International Tables for Crystallography (2012). Vol. F, Section 18.2.2, pp. 466-467 [ doi:10.1107/97809553602060000856 ]
... crystallography. Methods Enzymol. 277, 366-396. Hsu, I. N., Delbaere, L. T. J., James, M. N. G. & Hoffman, T. (1977). Penicillopepsin from Penicillium janthinellum ...

Introduction
Brunger, A. T., Adams, P. D. and Rice, L. M.  International Tables for Crystallography (2012). Vol. F, Section 18.2.1, p. 466 [ doi:10.1107/97809553602060000856 ]
... by the introduction of torsion-angle refinement methods (Diamond, 1971; Rice & Brünger, 1994), which decrease the number of adjustable parameters ... London), 355, 472-474. Brunger, A. T., Kuriyan, J. & Karplus, M. (1987). Crystallographic R factor refinement by molecular dynamics. Science ... 165-175. Burling, F. T., Weis, W. I., Flaherty, K. M. & Brunger, A. T. (1996). Direct observation of protein ...

Enhanced macromolecular refinement by simulated annealing
Brunger, A. T., Adams, P. D. and Rice, L. M.  International Tables for Crystallography (2012). Vol. F, ch. 18.2, pp. 466-473 [ doi:10.1107/97809553602060000856 ]
... by the introduction of torsion-angle refinement methods (Diamond, 1971; Rice & Brünger, 1994), which decrease the number of adjustable parameters ... is sometimes used to reduce the radii, and n = 2, m = 2 or n = 1, m = 4. van der Waals attraction and electrostatic interactions are ...

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