SSBOND 1 CYS C 107 CYS C 138 SSBOND 2 CYS C 124 CYS C 139 SSBOND 3 CYS C 137 CYS C 149 SSBOND 4 CYS D 107 CYS D 138 SSBOND 5 CYS D 124 CYS D 139 SSBOND 6 CYS D 137 CYS D 149
phi 4 -88.2 -48.2 psi 4 -59.2 -19.2 phi 5 -84.8 -44.8 psi 5 -57.3 -17.3 phi 6 -86.6 -46.6 psi 6 -58.9 -18.9 .... 49 79 1 5.0 HD1 H 49 12 1 5.0 HD1 H 4 52 2 5.0 HD1 H 4 59 2 5.0 HD1 H ....In the angular section, the angle is marked "phi" or "psi", which is followed by residue index and the lower and upper angle boundary. In the distance section, the first two numbers are the indices of the residues followed by peak index (the peak is ambiguous if the index is repeated in several lines), the upper distance boundary and proton types. From the menu the user can select the following items of equations 3 and 4 in Lubecka and Liwo, J.Comput.Chem., 43, 2047 (2022) scaling factor in the log-exp ambiguous-restraint penalty function (scal_peak; factor alpha in equation 3), restraint well-depth (fordepth_peak; factor A in equation 4), and the slope of the flat-top part of the penalty function (slope_peak; factor kappa in equation 4). See Lubecka and Liwo, J.Comput.Chem., 43, 2047 (2022) for details. Use of NMR restraints requires the use of the scale-consistent NEWCT-9P variant of UNRES.
... 2 5 2.5 8.0 1 1.0 1.0 2 6 2.5 8.0 1 1.0 1.0 3 6 2.5 8.0 1 1.0 1.0 ...where the first two integers are residue indices. If the first residue is not glycine, add 1 to each index according to UNRES style, in which the first residue is a dummy if the first full residue is not glycine. The next two numbers are the lower and the upper distance bouundary. The next integer is 1 for sidechain-sidechain contacts and 0 for Calpha-Calpha contacts. The last two numbers are the well depth and well-wall breadth of the flat-bottom bounded restraint function (constants A and sigma in equation 3 of Lubecka and Liwo, J. Comput. Chem., 40, 2164 (2019).
... DSS ilink=39 jlink=53 score=15 DSS ilink=39 jlink=88 score=15 DSS ilink=5 jlink=39 score=15 ...The first item is crosslink identifier, the next two items are the indices of the bridged residues (1 added if the first residue is not glycine), the last item is the scaling factor of the pseudopotential. The following bridges are available:
... ilink=39 jlink=53 bridge=BS3 ilink=25 jlink=27 bridge=BS3 ...The first and the second item are the indices of cross-linked residues (add 1 if the first residue is not glycine), the last is cross-link type. The following bridges are available: