Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    55:77 56:76 57:75 59:73 204:241 205:240 206:239 207:238
	    208:237 209:236 256:286 257:285 259:283 260:282 303:342 304:341
	    305:340 307:337 308:336 309:335
	Energy of Broken Structure: -62.2
	Energy of Pseudo-Helices:   -28.5
	Pseudoknot Energy Penalty:  30.7
	Total Free Energy:          -60.0
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-402
		Stack = -1.5  for stack of 2-401
		Stack = -2.1  for stack of 3-400
		Stack = -3.3  for stack of 4-399
		Stack = -3.4  for stack of 5-398
		Stack = -2.4  for stack of 6-397
	Helix total = -16.0
	Multiloop = 5.1  for closure of 7-396
		Stack = -3.4  for stack of 379-395
		Stack = -2.4  for stack of 380-394
		Stack = -3.3  for stack of 381-393
		Stack = -3.3  for stack of 382-392
	Helix total = -12.4
	Hairpin = 4.4  for closure of 383-391
		Stack = -2.4  for stack of 20-375
		Stack = -2.5  for stack of 21-374
		Stack = 0.3  for stack of 22-373
		Stack = -0.5  for stack of 23-372
		Stack = -2.1  for stack of 24-371
		Stack = -2.2  for stack of 25-370
		Stack = -1.3  for stack of 26-369
	Helix total = -10.7
	Internal/bulge = 2.9  for closure of 27-368	Size = 11
		Stack = -3.3  for stack of 34-362
	Helix total = -3.3
	Internal/bulge = 1.7  for closure of 35-361	Size = 6
		Stack = -2.1  for stack of 39-357
		Stack = -2.5  for stack of 40-356
	Helix total = -4.6
	Internal/bulge = 4.5  for closure of 41-355	Size = 5
		Stack = -2.1  for stack of 43-350
		Stack = -1.1  for stack of 44-349
		Stack = -2.1  for stack of 45-348
		Stack = -3.4  for stack of 46-347
	Helix total = -8.7
	Multiloop = 3.4  for closure of 47-346
		Stack = -2.5  for stack of 288-323
		Stack = -2.1  for stack of 289-322
		Stack = -2.1  for stack of 290-321
		Stack = -2.2  for stack of 291-320
	Helix total = -8.9
	Internal/bulge = 4.0  for closure of 292-319	Size = 5
	Helix total = 0.0
	Internal/bulge = 2.9  for closure of 296-316	Size = 5
		Stack = -2.4  for stack of 299-312
		Stack = -3.3  for stack of 300-311
	Helix total = -5.7
	Hairpin = 4.1  for closure of 301-310
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 242-274	Size = 2
		Stack = -3.4  for stack of 244-272
		Stack = -2.4  for stack of 245-271
		Stack = -2.5  for stack of 246-270
		Stack = -1.5  for stack of 247-269
	Helix total = -9.8
	Internal/bulge = 1.2  for closure of 248-268	Size = 2
		Stack = -1.3  for stack of 250-266
		Stack = -0.9  for stack of 251-265
		Stack = -1.4  for stack of 252-264
		Stack = -1.5  for stack of 253-263
		Stack = -2.1  for stack of 254-262
	Helix total = -7.2
	Hairpin = 5.4  for closure of 255-261
		Stack = -3.3  for stack of 188-226
		Stack = -2.4  for stack of 189-225
		Stack = -2.2  for stack of 190-224
		Stack = -0.9  for stack of 191-223
	Helix total = -8.8
	Internal/bulge = 4.6  for closure of 192-222	Size = 11
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 198-215	Size = 2
		Stack = -2.5  for stack of 200-213
		Stack = -3.3  for stack of 201-212
	Helix total = -5.8
	Hairpin = 4.4  for closure of 202-211
		Stack = -1.4  for stack of 164-186
		Stack = -1.3  for stack of 165-185
		Stack = -2.2  for stack of 166-184
		Stack = -2.1  for stack of 167-183
		Stack = -2.1  for stack of 168-182
		Stack = -3.3  for stack of 169-181
	Helix total = -12.4
	Hairpin = 5.7  for closure of 170-180
	Helix total = 0.0
	Internal/bulge = 2.2  for closure of 125-144	Size = 4
		Stack = -3.4  for stack of 128-141
		Stack = -2.1  for stack of 129-140
	Helix total = -5.5
	Hairpin = 4.0  for closure of 130-139
		Stack = -2.4  for stack of 48-65
		Stack = -2.4  for stack of 49-64
		Stack = -2.1  for stack of 50-63
		Stack = -2.4  for stack of 51-62
	Helix total = -9.3
	Hairpin = 5.0  for closure of 52-61


	Total energy = -62.2



