Editing Phase problem (section)

=== Refining initial phases ===
In many cases, an initial set of phases are determined, and the electron density map for the diffraction pattern is calculated.  Then the map is used to determine portions of the structure, which portions are used to simulate a new set of phases.  This new set of phases is known as a ''refinement''. These phases are reapplied to the original amplitudes, and an improved electron density map is derived, from which the structure is corrected.  This process is repeated until an error term (usually <math>R_\textrm{free}</math>) has stabilized to a satisfactory value. Because of the phenomenon of [[phase bias]], it is possible for an incorrect initial assignment to propagate through successive refinements, so satisfactory conditions for a structure assignment are still a matter of debate. Indeed, some spectacular incorrect assignments have been reported, including a protein where the entire sequence was threaded backwards.<ref name="Kleywegt2000">{{cite journal|last1=Kleywegt|first1=Gerard J.|title=Validation of protein crystal structures|journal=Acta Crystallographica Section D|volume=56|issue=3|year=2000|pages=249–265|doi=10.1107/S0907444999016364|pmid=10713511|doi-access=free}}</ref>