==============================
// MC-Sym 4.2 script generated by MC-Fold 1.0
// Please cite: Parisien M, Major F. Nature. (2008) 452:51-55.


//========== Sequence ==========

sequence( r A1 GUGGUCUGAUGAGGCGAAAGCCGAAACUCGUAAGAGUCACCAC )
//             ((((((...(((((((..)))))))(((((..)))))))))))



//========== Cycles ==========

ncm_01 = library(
	pdb( "MCSYM-DB/4/GAAA/*.pdb.gz" ) #1:#4 <- A16:A19
	rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) )

ncm_02 = library(
	pdb( "MCSYM-DB/2_2/CGAG/*.pdb.gz" ) #1:#2, #3:#4 <- A15:A16, A19:A20
	rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) )

ncm_03 = library(
	pdb( "MCSYM-DB/2_2/GCGC/*.pdb.gz" ) #1:#2, #3:#4 <- A14:A15, A20:A21
	rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) )

ncm_04 = library(
	pdb( "MCSYM-DB/2_2/GGCC/*.pdb.gz" ) #1:#2, #3:#4 <- A13:A14, A21:A22
	rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) )

ncm_05 = library(
	pdb( "MCSYM-DB/2_2/AGCG/*.pdb.gz" ) #1:#2, #3:#4 <- A12:A13, A22:A23
	rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) )

ncm_06 = library(
	pdb( "MCSYM-DB/2_2/GAGA/*.pdb.gz" ) #1:#2, #3:#4 <- A11:A12, A23:A24
	rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) )

ncm_07 = library(
	pdb( "MCSYM-DB/2_2/UGAA/*.pdb.gz" ) #1:#2, #3:#4 <- A10:A11, A24:A25
	rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) )

ncm_08 = library(
	pdb( "MCSYM-DB/4/GUAA/*.pdb.gz" ) #1:#4 <- A30:A33
	rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) )

ncm_09 = library(
	pdb( "MCSYM-DB/2_2/CGAG/*.pdb.gz" ) #1:#2, #3:#4 <- A29:A30, A33:A34
	rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) )

ncm_10 = library(
	pdb( "MCSYM-DB/2_2/UCGA/*.pdb.gz" ) #1:#2, #3:#4 <- A28:A29, A34:A35
	rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) )

ncm_11 = library(
	pdb( "MCSYM-DB/2_2/CUAG/*.pdb.gz" ) #1:#2, #3:#4 <- A27:A28, A35:A36
	rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) )

ncm_12 = library(
	pdb( "MCSYM-DB/2_2/ACGU/*.pdb.gz" ) #1:#2, #3:#4 <- A26:A27, A36:A37
	rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) )

ncm_13 = library(
	pdb( "MCSYM-DB/2_2/UCCA/*.pdb.gz" ) #1:#2, #3:#4 <- A5:A6, A38:A39
	rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) )

ncm_14 = library(
	pdb( "MCSYM-DB/2_2/GUAC/*.pdb.gz" ) #1:#2, #3:#4 <- A4:A5, A39:A40
	rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) )

ncm_15 = library(
	pdb( "MCSYM-DB/2_2/GGCC/*.pdb.gz" ) #1:#2, #3:#4 <- A3:A4, A40:A41
	rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) )

ncm_16 = library(
	pdb( "MCSYM-DB/2_2/UGCA/*.pdb.gz" ) #1:#2, #3:#4 <- A2:A3, A41:A42
	rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) )

ncm_17 = library(
	pdb( "MCSYM-DB/2_2/GUAC/*.pdb.gz" ) #1:#2, #3:#4 <- A1:A2, A42:A43
	rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) )

lnk_01 = library(
	pdb( "MCSYM-DB/ss2/AA/*.pdb.gz" ) #1:#2 <- A25:A26
	rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) )

lnk_02 = library(
	pdb( "MCSYM-DB/ss2/UC/*.pdb.gz" ) #1:#2 <- A37:A38
	rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) )

lnk_03 = library(
	pdb( "MCSYM-DB/ss4/CUGA/*.pdb.gz" ) #1:#4 <- A6:A9
	rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) )



//=========== Backtrack ===========
// assemble the whole structure:

structure = backtrack(

	//----- multi-brached loop -----
	ncm_07
	merge( lnk_01 2.0 )
	merge( ncm_12 2.0 )
	merge( lnk_02 2.0 )
	merge( ncm_13 2.0 )
	merge( lnk_03 2.0 )

	//----- stem_1 -----
	merge( ncm_06 2.0 )
	merge( ncm_05 2.0 )
	merge( ncm_04 2.0 )
	merge( ncm_03 2.0 )
	merge( ncm_02 2.0 )
	merge( ncm_01 2.0 )

	//----- stem_2 -----
	merge( ncm_11 2.0 )
	merge( ncm_10 2.0 )
	merge( ncm_09 2.0 )
	merge( ncm_08 2.0 )

	//----- stem_3 -----
	merge( ncm_14 2.0 )
	merge( ncm_15 2.0 )
	merge( ncm_16 2.0 )
	merge( ncm_17 2.0 )
)



// ========= Distance Restraints =========
// this distance restraint will force the coaxial
// stacking of stems 2 and 3
distance( A25:PSY  A26:PSY  0.0  5.0 )



// ========= Constraints / Restraints =========

clash                 ( structure 1.5 !( pse || lp || hydrogen ) )

ribose_rst            ( structure
                        pucker = C3p_endo, glycosyl = anti,
                        method = ccm, threshold = 2.0 )

backtrack_rst         ( structure
                        width_limit = 25%, height_limit = 100%,
// for breadth-first-like search:
			method = probabilistic )
// for depth-first-like search:
//                      method = exhaustive )



// ========= Exploration Initialization =========
explore(
	structure
	option( model_limit = 100, time_limit = 1h, seed = 3210 )
	rmsd( 3.0 sidechain && !( pse || lp || hydrogen ) )
	pdb( "hammer" zipped )
)