Additional measures

Alignment accuracy measures are based on the sequence independent superposition generated by the LGA server (ver. 11/2000) using 4.0 Angstroms distance cutoff.

AL-0 : The number of residues in the model for which corresponding residue in the target is correct one, and the distance between them is less than 4.0 Angstroms is reported. This gives the number of correctly aligned residues.

AL-4 : The number of positions for which the model residue corresponds to a residue in the target within +/-4 residues, and the distance is less than 4.0 Angstroms is reported. This gives the number aligned within 4 residues of the correct value.

AL4+ : The number of positions for which the distance between model residue and a residue in the target is less than 4.0 Angstroms is reported. This gives the number of all aligned residues.

2. Lesk windows.

Local RMS deviation is calculated in a runnung window for several values of the window length. There are four window lengths used for calculations: 6, 15, 25 and 40 residues.

LW-6 : The mean value of RMSD for the 6-residue running window is reported.

LW-15 : The minimum value of RMSD within the 15-residue running window is reported.

LW-25 : The minimum value of RMSD within the 25-residue running window is reported.

LW-40 : The minimum value of RMSD within the 40-residue running window is reported.

3. CA-CA Deviation plots.

Using GDT method the target and model structures are superimposed in a sequence dependent manner. The maximum number (GDT-4) of CA atom pairs which are closer than 4.0Angstrom are used to obtain final superposition. Each superposition is represented as a single colored bar where:
      residues superimposed below 2.0 A are in GREEN
      residues superimposed below 4.0 A are in YELLOW
      residues superimposed below 8.0 A are in ORANGE
      residues superimposed above 8.0 A are in RED