C-score is a confidence score for estimating the quality of predicted models. It is calculated based on the significance of threading template alignments and the convergence parameters of the structure assembly simulations. C-score is typically in the range of [-5,2], where a C-score of higher value signifies a model with a high confidence and vice-versa.

The Z-score of a protein is defined as the energy separation between the native fold and the average of an ensemble of misfolds in the units of the standard deviation of the ensemble. The Z-score is often used as a way of testing the knowledge-based potentials for their ability to recognise the native fold from other alternatives.

They are self explanatory.

References:

• http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2144000/
• http://zhanglab.ccmb.med.umich.edu/I-TASSER/example/cscore.txt