Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    53:76 55:74 56:72 57:71 155:190 156:189 157:188 158:187
	    159:186 160:185 207:236 208:235 209:234 210:233 211:232 258:299
	    259:298 260:297 261:296 262:295 263:294 264:293
	Energy of Broken Structure: -77.1
	Energy of Pseudo-Helices:   -35.6
	Pseudoknot Energy Penalty:  32.2
	Total Free Energy:          -80.5
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-360
		Stack = -1.5  for stack of 2-359
		Stack = -2.1  for stack of 3-358
		Stack = -3.3  for stack of 4-357
		Stack = -2.2  for stack of 5-356
		Stack = -2.1  for stack of 6-355
	Helix total = -14.5
	Multiloop = 6.5  for closure of 7-354
		Stack = -2.1  for stack of 337-353
		Stack = -3.3  for stack of 338-352
		Stack = -2.4  for stack of 339-351
		Stack = -2.1  for stack of 340-350
	Helix total = -9.9
	Hairpin = 4.4  for closure of 341-349
		Stack = -2.1  for stack of 20-333
		Stack = -1.1  for stack of 21-332
		Stack = -1.3  for stack of 22-331
		Stack = 0.3  for stack of 23-330
		Stack = -2.5  for stack of 24-329
		Stack = -2.1  for stack of 25-328
		Stack = -0.5  for stack of 26-327
		Stack = -0.5  for stack of 27-326
	Helix total = -9.8
	Internal/bulge = 3.7  for closure of 28-325	Size = 8
		Stack = -2.2  for stack of 33-320
		Stack = -2.1  for stack of 34-319
		Stack = -1.1  for stack of 35-318
		Stack = -2.1  for stack of 36-317
		Stack = -3.4  for stack of 37-316
		Stack = -2.1  for stack of 38-315
		Stack = -2.1  for stack of 39-314
		Stack = -2.5  for stack of 40-313
	Helix total = -17.6
	Internal/bulge = 4.5  for closure of 41-312	Size = 5
		Stack = -2.1  for stack of 43-307
		Stack = -2.2  for stack of 44-306
		Stack = -3.3  for stack of 45-305
		Stack = -2.1  for stack of 46-304
	Helix total = -9.7
	Multiloop = 2.2  for closure of 47-303
		Stack = -3.4  for stack of 239-280
		Stack = -2.1  for stack of 240-279
		Stack = -1.4  for stack of 241-278
		Stack = -3.4  for stack of 242-277
		Stack = -2.4  for stack of 243-276
	Helix total = -12.7
	Internal/bulge = 0.8  for closure of 244-275	Size = 2
		Stack = -2.1  for stack of 246-273
		Stack = -2.2  for stack of 247-272
	Helix total = -4.3
	Internal/bulge = 1.4  for closure of 248-271	Size = 7
		Stack = -3.4  for stack of 253-267
		Stack = -3.3  for stack of 254-266
	Helix total = -6.7
	Hairpin = 4.3  for closure of 255-265
		Stack = -2.2  for stack of 195-221
		Stack = -0.9  for stack of 196-220
		Stack = -1.3  for stack of 197-219
		Stack = -0.9  for stack of 198-218
		Stack = -1.1  for stack of 199-217
		Stack = -2.1  for stack of 200-216
		Stack = -2.5  for stack of 201-215
		Stack = -0.5  for stack of 202-214
	Helix total = -11.5
	Hairpin = 5.5  for closure of 203-213
		Stack = -2.4  for stack of 140-176
		Stack = -1.4  for stack of 141-175
		Stack = -1.5  for stack of 142-174
		Stack = -3.3  for stack of 143-173
	Helix total = -8.6
	Internal/bulge = 3.0  for closure of 144-172	Size = 4
		Stack = -1.5  for stack of 146-168
		Stack = -3.3  for stack of 147-167
		Stack = -2.4  for stack of 148-166
		Stack = -2.4  for stack of 149-165
		Stack = -2.2  for stack of 150-164
		Stack = -2.1  for stack of 151-163
		Stack = -0.5  for stack of 152-162
	Helix total = -14.4
	Hairpin = 5.8  for closure of 153-161
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 113-138	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 115-136	Size = 2
	Helix total = 0.0
	Internal/bulge = 3.3  for closure of 117-134	Size = 2
		Stack = -3.4  for stack of 120-133
	Helix total = -3.4
	Hairpin = 5.5  for closure of 121-132
		Stack = -2.4  for stack of 48-63
		Stack = -3.3  for stack of 49-62
		Stack = -2.4  for stack of 50-61
		Stack = -2.1  for stack of 51-60
	Helix total = -10.2
	Hairpin = 3.2  for closure of 52-59


	Total energy = -77.1



