XmlmmCIF equivalent: refine_analyze Data items in the REFINE_ANALYZE category record details about the refined structure that are often used to analyze the refinement and asses its quality. A given computer program may or may not produce values corresponding to these data names. XmlmmCIF equivalent: refine_analyze/Luzzati_coordinate_error_free The estimated coordinate error obtain from the plot of the R value versus sin(theta)/lambda for the reflections treated as a test set in refinement. Ref: Luzzati, V. (1952). Acta Cryst. 5, 134-136. XmlmmCIF equivalent: refine_analyze/Luzzati_coordinate_error_obs The estimated coordinate error obtained from the plot of the R value versus sin(theta)/lambda for reflections classified as observed. Ref: Luzzati, V. (1952). Acta Cryst. 5, 134-136. XmlmmCIF equivalent: refine_analyze/Luzzati_d_res_low_free The value of the low resolution cutoff used in constructing the Luzzati plot for reflections treated as a test set in refinement. Ref: Luzzati, V. (1952). Acta Cryst. 5, 134-136. XmlmmCIF equivalent: refine_analyze/Luzzati_d_res_low_obs The value of the low resolution cutoff used in constructing the Luzzati plot for reflections classified as observed. Ref: Luzzati, V. (1952). Acta Cryst. 5, 134-136. XmlmmCIF equivalent: refine_analyze/Luzzati_sigma_a_free The value of sigma~a~ used in constructing the Luzzati plot for the reflections treated as a test set in refinement. The details of the estimation of sigma~a~ can be specified in _refine_analyze.Luzzati_sigma_a_free_details. Ref: Luzzati, V. (1952). Acta Cryst. 5, 134-136. XmlmmCIF equivalent: refine_analyze/Luzzati_sigma_a_free_details The details of the estimation of sigma~a~ for the reflections treated as a test set in refinement. Ref: Luzzati, V. (1952). Acta Cryst. 5, 134-136. XmlmmCIF equivalent: refine_analyze/Luzzati_sigma_a_obs The value of sigma~a~ used in constructing the Luzzati plot for reflections classified as observed. The details of the estimation of sigma~a~ can be specified in _refine_analyze.Luzzati_sigma_a_obs_details. Ref: Luzzati, V. (1952). Acta Cryst. 5, 134-136. XmlmmCIF equivalent: refine_analyze/Luzzati_sigma_a_obs_details Special aspects of the estimation of sigma~a~ for the reflections classified as observed. Ref: Luzzati, V. (1952). Acta Cryst. 5, 134-136. XmlmmCIF equivalent: refine_analyze/RG_d_res_high The value of the high-resolution cutoff in angstroms used in calculation of the Hamilton generalized R factor (RG) stored in refine_analyze.RG_work and _refine_analyze.RG_free. Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510. XmlmmCIF equivalent: refine_analyze/RG_d_res_low The value of the low-resolution cutoff in angstroms used in calculation of the Hamilton generalized R factor (RG) stored in refine_analyze.RG_work and _refine_analyze.RG_free. Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510. XmlmmCIF equivalent: refine_analyze/RG_free The Hamilton generalized R factor for all reflections that satisfy the resolution limits established by _refine_analyze.RG_d_res_high and _refine_analyze.RG_d_res_low for the free R set of reflections that were excluded from the refinement. sum_i sum_j w_{i,j}(|Fobs|_i - G|Fcalc|_i)(|Fobs|_j - G|Fcalc|_j) Rg = Sqrt( ----------------------------------------------------------------------------------------------------- ) sum_i sum_j w_{i,j} |Fobs|_i |Fobs|_j where |Fobs| = the observed structure factor amplitudes |Fcalc| = the calculated structure factor amplitudes G = the scale factor which puts |Fcalc| on the same scale as |Fobs| w_{i,j} = the weight for the combination of the reflections i and j. sum_i and sum_j are taken over the specified reflections When the covariance of the amplitude of reflection i and reflection j is zero (i.e. the reflections are independent) w{i,i} can be redefined as w_i and the nested sums collapsed into one. sum_i w_i(|Fobs|_i - G|Fcalc|_i)^2 Rg = Sqrt( ---------------------------------------------------- ) sum_i w_i |Fobs|_i^2 Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510. XmlmmCIF equivalent: refine_analyze/RG_free_work_ratio The observed ratio of RGfree to RGwork. The expected RG ratio is the value that should be achievable at the end of a structure refinement when only random uncorrelated errors exist in data and model provided that the observations are properly weighted. When compared with the observed RG ratio it may indicate that a structure has not reached convergence or a model has been over-refined with no corresponding improvement in the model. In an unrestrained refinement the ratio of RGfree/RGwork with only random uncorrelated errors at convergence depends only on the number of reflections and the number of parameters as: sqrt[(f + m) / (f - m) ] where f = number of included structure amplitudes and target distances, and m = number of parameters being refined. In the restrained case, RGfree is calculated from a random selection of residuals including both structure amplitudes and restraints. When restraints are included in refinement the RG ratio requires a term for the contribution to the minimized residual at convergence, Drest, due to those restraints: Drest = r - sum (w_i . (a_i)^t . (H)^-1 a_i where r is the number of geometrical, temperature factor and other restraints H is the (m,m) normal matrix given by A^t.W.A W is the (n,n) symmetric weight matrix of the included observations A is the least-squares design matrix of derivatives of order (n,m) a_i is the ith row of A Then the expected RGratio becomes sqrt [ (f + (m - r + Drest))/ (f - (m - r + Drest)) ] The expected RGfree/RGwork is not yet included in the mmCIF dictionary. Ref: "Rfree and the Rfree ratio. Part I: derivation of expected values of cross-validation residuals used in macromolecular least-squares refinement". Tickle, I. J., Laskowski, R. A. and Moss, D.S. (1998). Acta Cryst. D, in the press. XmlmmCIF equivalent: refine_analyze/RG_work The Hamilton generalized R factor for all reflections that satisfy the resolution limits established by _refine_analyze.RG_d_res_high and _refine_analyze.RG_d_res_low and for those reflections included in the working set when a free R set of reflections are omitted from the refinement. sum_i sum_j w_{i,j}(|Fobs|_i - G|Fcalc|_i)(|Fobs|_j - G|Fcalc|_j) Rg = Sqrt( ---------------------------------------------------------------------------------------------- ) sum_i sum_j w_{i,j} |Fobs|_i |Fobs|_j where |Fobs| = the observed structure factor amplitudes |Fcalc| = the calculated structure factor amplitudes G = the scale factor which puts |Fcalc| on the same scale as |Fobs| w_{i,j} = the weight for the combination of the reflections i and j. sum_i and sum_j are taken over the specified reflections When the covariance of the amplitude of reflection i and reflection j is zero (i.e. the reflections are independent) w{i,i} can be redefined as w_i and the nested sums collapsed into one. sum_i w_i(|Fobs|_i - G|Fcalc|_i)^2 Rg = Sqrt( --------------------------------------------------------------------------------------- ) sum_i w_i |Fobs|_i^2 Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510. XmlmmCIF equivalent: refine_analyze/number_disordered_residues The number of discretely disorded residues in the refined model. XmlmmCIF equivalent: refine_analyze/occupancy_sum_hydrogen The sum of the occupancies of the hydrogen atoms in the refined model. XmlmmCIF equivalent: refine_analyze/occupancy_sum_non_hydrogen The sum of the occupancies of the non-hydrogen atoms in the refined model. XmlmmCIF equivalent: refine_analyze/entry_id This data item is a pointer to _entry.id in the ENTRY category.