Validating analysis time window
Validating analysis time window - ukraine online dating scammer
This approximation works decently on a global structural level, but often leaves chemically impossible geometries in place.
Phenix, like most crystallographic software, uses the Engh and Huber (1991) restraints for proteins, nucleic acids, and other common molecules, here in the form of the CCP4 monomer library.
Although it is possible to run validation with only a model, we recommend including experimental data, as interpreting geometry outliers only makes sense in the context of the electron density maps.
The analyses performed by Phenix include: Any non-protein molecule will be included in the real-space fit evaluation, and if CIF files are provided, geometric outliers will be detected as well.
Once hydrogens have been added, is run to analyze the atomic contacts.
All atomic overlaps worse than 0.4A are listed, and a global "clash score" is reported for the entire structure (calculated as 1000 * (number of bad overlaps) / (number of atoms)).
An initial tab shows the target and actual values for assorted validation criteria (mostly specific to proteins).
See below for advice on interpreting these results.Large deviations (greater than 4 sigma) from the restrained values usually indicate something seriously wrong with the model, and should not be taken as examples of genuine structural strain unless the electron density for that feature is exceptionally good (usually only at ultra-high-resolution, i.e.better than 1.0 Angstrom) and the deviation is no more than approximately 7 sigma.Other restraints come from CIF files provided by the user; these can be generated by phenix.elbow and associated programs.These restraints are used in refinement to prevent distortions of model geometry, and to increase the observation-to-parameter ratio.At resolutions below 3.0A, any outliers should be considered errors.