A method for automatic building of protein structures has been developed. The method is based on the concept of flexible structure units. A structure unit is a fragment (group) of about ten atoms that is positioned in the electron density by a phased rotation and translation function. The positions, orientations and internal torsion angles of all structure units are refined by a phased flexible refinement. Individual structure units are connected into polyalanine chains. The sequence is aligned by combined marker and rotamer methods. The side chains are built either by the marker method and a full conformational search or by the rotamer method. Side chains are independent structure units. The structure unit represents a generalized atom and the group model can be refined by the least-squares method. The protein model is built with an accuracy of about 0.2 A at resolutions of 1.2-1.9 A. Partial results can be obtained at resolutions of between 2.0 and 2.3 A.