Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    56:81 57:80 59:78 60:77 61:76 196:227 197:226 198:225
	    199:224 200:223 202:221 243:277 245:275 246:274 247:273 248:272
	    249:271 250:270 295:333 296:332 297:331 300:328 301:327
	Energy of Broken Structure: -76.5
	Energy of Pseudo-Helices:   -42.3
	Pseudoknot Energy Penalty:  32.5
	Total Free Energy:          -86.3
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-393
		Stack = -1.5  for stack of 2-392
		Stack = -2.1  for stack of 3-391
		Stack = -3.3  for stack of 4-390
		Stack = -2.2  for stack of 5-389
		Stack = -2.1  for stack of 6-388
	Helix total = -14.5
	Multiloop = 5.1  for closure of 7-387
		Stack = -3.3  for stack of 370-386
		Stack = -3.4  for stack of 371-385
		Stack = -2.4  for stack of 372-384
		Stack = -3.3  for stack of 373-383
	Helix total = -12.4
	Hairpin = 4.4  for closure of 374-382
		Stack = -2.4  for stack of 20-366
		Stack = -3.3  for stack of 21-365
		Stack = -1.5  for stack of 22-364
		Stack = -0.5  for stack of 23-363
		Stack = -2.1  for stack of 24-362
		Stack = -2.5  for stack of 25-361
	Helix total = -12.3
	Internal/bulge = 3.6  for closure of 26-360	Size = 11
		Stack = -1.4  for stack of 33-354
		Stack = -2.4  for stack of 34-353
	Helix total = -3.8
	Internal/bulge = -2.2  for closure of 35-352	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.3  for closure of 37-350	Size = 1 BP stack across bulge = -2.1
		Stack = 0.3  for stack of 39-349
		Stack = -2.1  for stack of 40-348
		Stack = -3.4  for stack of 41-347
		Stack = -1.4  for stack of 42-346
	Helix total = -6.6
	Internal/bulge = 3.7  for closure of 43-345	Size = 3
		Stack = -2.1  for stack of 44-341
		Stack = -1.1  for stack of 45-340
		Stack = -2.1  for stack of 46-339
		Stack = -3.4  for stack of 47-338
	Helix total = -8.7
	Multiloop = 2.1  for closure of 48-337
		Stack = -2.2  for stack of 278-316
		Stack = -0.9  for stack of 279-315
		Stack = -0.9  for stack of 280-314
		Stack = -2.4  for stack of 281-313
	Helix total = -6.4
	Internal/bulge = 1.9  for closure of 282-312	Size = 3
		Stack = -2.1  for stack of 285-310
	Helix total = -2.1
	Internal/bulge = 2.3  for closure of 286-309	Size = 4
		Stack = -3.4  for stack of 288-305
		Stack = -1.4  for stack of 289-304
		Stack = -2.5  for stack of 290-303
	Helix total = -7.3
	Hairpin = 5.1  for closure of 291-302
		Stack = -1.4  for stack of 232-261
		Stack = -1.5  for stack of 233-260
		Stack = -2.4  for stack of 234-259
		Stack = -3.3  for stack of 235-258
		Stack = -2.2  for stack of 236-257
		Stack = -1.3  for stack of 237-256
		Stack = -2.1  for stack of 238-255
		Stack = -2.5  for stack of 239-254
	Helix total = -16.7
	Internal/bulge = 1.2  for closure of 240-253	Size = 2
	Helix total = 0.0
	Hairpin = 5.0  for closure of 242-251
		Stack = -3.3  for stack of 178-215
		Stack = -3.3  for stack of 179-214
	Helix total = -6.6
	Internal/bulge = 1.2  for closure of 180-213	Size = 2
	Helix total = 0.0
	Internal/bulge = 4.6  for closure of 182-211	Size = 4
		Stack = -1.0  for stack of 187-210
		Stack = -2.2  for stack of 188-209
		Stack = -2.1  for stack of 189-208
		Stack = -0.6  for stack of 190-207
		Stack = -1.0  for stack of 191-206
		Stack = 1.3  for stack of 192-205
		Stack = -1.4  for stack of 193-204
	Helix total = -7.0
	Hairpin = 5.0  for closure of 194-203
		Stack = -2.4  for stack of 164-174
		Stack = -3.4  for stack of 165-173
		Stack = -3.3  for stack of 166-172
	Helix total = -9.1
	Hairpin = 5.4  for closure of 167-171
		Stack = -0.5  for stack of 117-156
	Helix total = -0.5
	Internal/bulge = 1.3  for closure of 118-155	Size = 6
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 122-151	Size = 2
		Stack = -2.5  for stack of 124-149
		Stack = -2.1  for stack of 125-148
		Stack = -1.3  for stack of 126-147
	Helix total = -5.9
	Internal/bulge = 1.0  for closure of 127-146	Size = 4
		Stack = -3.4  for stack of 130-143
		Stack = -3.3  for stack of 131-142
		Stack = -1.4  for stack of 132-141
	Helix total = -8.1
	Hairpin = 5.2  for closure of 133-140
		Stack = -2.4  for stack of 49-68
		Stack = -2.4  for stack of 50-67
		Stack = -2.1  for stack of 51-66
		Stack = -3.3  for stack of 52-65
	Helix total = -10.2
	Hairpin = 5.0  for closure of 53-64


	Total energy = -76.5



