Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    48:67 49:66 50:65 51:64 52:63 202:237 203:236 204:235
	    205:234 206:233 257:286 258:285 260:284 261:283 262:282 305:344
	    306:343 308:341 309:339 310:338
	Energy of Broken Structure: -57.8
	Energy of Pseudo-Helices:   -25.7
	Pseudoknot Energy Penalty:  31.8
	Total Free Energy:          -51.7
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-404
		Stack = -1.5  for stack of 2-403
		Stack = -2.1  for stack of 3-402
		Stack = -3.3  for stack of 4-401
		Stack = -2.5  for stack of 5-400
		Stack = -1.4  for stack of 6-399
	Helix total = -14.1
	Multiloop = 5.1  for closure of 7-398
		Stack = -3.4  for stack of 381-397
		Stack = -2.4  for stack of 382-396
		Stack = -3.3  for stack of 383-395
		Stack = -3.3  for stack of 384-394
	Helix total = -12.4
	Hairpin = 4.4  for closure of 385-393
		Stack = -2.4  for stack of 20-377
	Helix total = -2.4
	Internal/bulge = 0.5  for closure of 21-376	Size = 2
		Stack = -1.4  for stack of 23-374
		Stack = -2.1  for stack of 24-373
		Stack = -2.5  for stack of 25-372
	Helix total = -6.0
	Internal/bulge = 1.9  for closure of 26-371	Size = 2
	Helix total = 0.0
	Internal/bulge = 3.7  for closure of 28-369	Size = 9
		Stack = -3.3  for stack of 34-364
		Stack = -2.1  for stack of 35-363
	Helix total = -5.4
	Internal/bulge = 0.6  for closure of 36-362	Size = 4
		Stack = -3.3  for stack of 39-359
		Stack = -2.5  for stack of 40-358
	Helix total = -5.8
	Internal/bulge = 4.5  for closure of 41-357	Size = 5
		Stack = -2.1  for stack of 43-352
		Stack = -1.1  for stack of 44-351
		Stack = -2.1  for stack of 45-350
		Stack = -3.4  for stack of 46-349
	Helix total = -8.7
	Multiloop = 6.2  for closure of 47-348
		Stack = -2.5  for stack of 290-326
		Stack = -1.4  for stack of 291-325
		Stack = -2.5  for stack of 292-324
		Stack = -2.1  for stack of 293-323
	Helix total = -8.5
	Internal/bulge = 2.9  for closure of 294-322	Size = 5
	Helix total = 0.0
	Internal/bulge = 3.7  for closure of 298-319	Size = 4
		Stack = -2.2  for stack of 300-315
		Stack = -3.3  for stack of 301-314
		Stack = -3.3  for stack of 302-313
	Helix total = -8.8
	Hairpin = 4.7  for closure of 303-312
		Stack = -2.2  for stack of 238-272
		Stack = -2.1  for stack of 239-271
		Stack = -1.5  for stack of 240-270
		Stack = -2.4  for stack of 241-269
	Helix total = -8.2
	Internal/bulge = 4.9  for closure of 242-268	Size = 6
		Stack = -2.4  for stack of 249-267
		Stack = -2.1  for stack of 250-266
		Stack = -2.1  for stack of 251-265
		Stack = -3.4  for stack of 252-264
	Helix total = -10.0
	Hairpin = 5.0  for closure of 253-263
		Stack = -2.1  for stack of 185-224
		Stack = -2.1  for stack of 186-223
		Stack = -2.2  for stack of 187-222
		Stack = -2.4  for stack of 188-221
		Stack = -3.3  for stack of 189-220
		Stack = -2.4  for stack of 190-219
	Helix total = -14.5
	Internal/bulge = 4.4  for closure of 191-218	Size = 6
		Stack = -3.3  for stack of 193-212
		Stack = -1.4  for stack of 194-211
		Stack = -2.1  for stack of 195-210
		Stack = -3.4  for stack of 196-209
		Stack = -2.1  for stack of 197-208
	Helix total = -12.3
	Hairpin = 5.5  for closure of 198-207
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 127-181	Size = 2
	Helix total = 0.0
	Internal/bulge = -0.7  for closure of 129-179	Size = 4
		Stack = -2.2  for stack of 132-176
	Helix total = -2.2
	Internal/bulge = 3.1  for closure of 133-175	Size = 8
	Helix total = 0.0
	Internal/bulge = 1.7  for closure of 138-170	Size = 6
		Stack = -3.4  for stack of 142-166
		Stack = -2.1  for stack of 143-165
	Helix total = -5.5
	Internal/bulge = 5.3  for closure of 144-164	Size = 9
		Stack = -1.4  for stack of 145-154
		Stack = 1.3  for stack of 146-153
	Helix total = -0.1
	Hairpin = 5.5  for closure of 147-152
		Stack = -2.2  for stack of 55-83
		Stack = -1.3  for stack of 56-82
		Stack = -2.1  for stack of 57-81
		Stack = -2.2  for stack of 58-80
		Stack = -2.1  for stack of 59-79
	Helix total = -9.9
	Hairpin = 4.6  for closure of 60-78


	Total energy = -57.8



