Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    54:77 55:76 56:75 57:74 58:73 147:205 148:204 149:203
	    150:202 151:201 152:200 153:199 221:249 222:248 223:247 224:246
	    268:306 269:305 270:304 271:303 272:301 273:300 274:299
	Energy of Broken Structure: -98.2
	Energy of Pseudo-Helices:   -39.6
	Pseudoknot Energy Penalty:  31.7
	Total Free Energy:          -106.1
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-366
		Stack = -1.5  for stack of 2-365
		Stack = -2.1  for stack of 3-364
		Stack = -3.3  for stack of 4-363
		Stack = -3.4  for stack of 5-362
		Stack = -2.4  for stack of 6-361
	Helix total = -16.0
	Multiloop = 5.1  for closure of 7-360
		Stack = -3.4  for stack of 343-359
		Stack = -2.4  for stack of 344-358
		Stack = -3.3  for stack of 345-357
		Stack = -3.3  for stack of 346-356
	Helix total = -12.4
	Hairpin = 4.4  for closure of 347-355
		Stack = -2.1  for stack of 20-339
		Stack = -2.1  for stack of 21-338
		Stack = -1.5  for stack of 22-337
		Stack = -0.5  for stack of 23-336
		Stack = -2.1  for stack of 24-335
		Stack = -2.5  for stack of 25-334
	Helix total = -10.8
	Internal/bulge = 1.2  for closure of 26-333	Size = 2
		Stack = -2.2  for stack of 28-331
	Helix total = -2.2
	Internal/bulge = 2.2  for closure of 29-330	Size = 5
		Stack = -2.5  for stack of 33-327
		Stack = -2.4  for stack of 34-326
		Stack = -1.5  for stack of 35-325
		Stack = -2.5  for stack of 36-324
		Stack = -2.1  for stack of 37-323
		Stack = -1.0  for stack of 38-322
		Stack = -2.1  for stack of 39-321
	Helix total = -14.1
	Internal/bulge = 2.9  for closure of 40-320	Size = 7
		Stack = -2.1  for stack of 43-314
		Stack = -1.1  for stack of 44-313
		Stack = -2.1  for stack of 45-312
		Stack = -2.2  for stack of 46-311
	Helix total = -7.5
	Multiloop = 4.6  for closure of 47-310
		Stack = -3.3  for stack of 254-287
		Stack = -2.4  for stack of 255-286
		Stack = -2.2  for stack of 256-285
	Helix total = -7.9
	Internal/bulge = 2.4  for closure of 257-284	Size = 7
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 262-280	Size = 3
		Stack = -3.4  for stack of 264-277
		Stack = -2.4  for stack of 265-276
	Helix total = -5.8
	Hairpin = 4.5  for closure of 266-275
		Stack = -2.5  for stack of 209-235
		Stack = -3.3  for stack of 210-234
		Stack = -2.1  for stack of 211-233
		Stack = -2.1  for stack of 212-232
	Helix total = -10.0
	Internal/bulge = 0.5  for closure of 213-231	Size = 2
		Stack = -3.3  for stack of 215-229
		Stack = -2.4  for stack of 216-228
	Helix total = -5.7
	Hairpin = 3.9  for closure of 217-227
		Stack = -3.3  for stack of 133-191
		Stack = -2.1  for stack of 134-190
		Stack = -2.4  for stack of 135-189
		Stack = -2.1  for stack of 136-188
		Stack = -2.1  for stack of 137-187
	Helix total = -12.0
	Multiloop = 0.8  for closure of 138-186
		Stack = -2.4  for stack of 171-184
		Stack = -3.3  for stack of 172-183
		Stack = -2.2  for stack of 173-182
		Stack = -1.3  for stack of 174-181
	Helix total = -9.2
	Hairpin = 4.4  for closure of 175-180
		Stack = -2.2  for stack of 161-170
		Stack = -2.4  for stack of 162-169
	Helix total = -4.6
	Hairpin = 3.3  for closure of 163-168
		Stack = -2.1  for stack of 140-159
		Stack = -1.3  for stack of 141-158
		Stack = -2.1  for stack of 142-157
		Stack = -2.5  for stack of 143-156
		Stack = -0.5  for stack of 144-155
	Helix total = -8.5
	Hairpin = 5.3  for closure of 145-154
		Stack = -1.4  for stack of 112-131
		Stack = -3.3  for stack of 113-130
		Stack = -3.4  for stack of 114-129
	Helix total = -8.1
	Internal/bulge = 0.5  for closure of 115-128	Size = 2
		Stack = -3.4  for stack of 117-126
		Stack = -3.3  for stack of 118-125
	Helix total = -6.7
	Hairpin = 3.6  for closure of 119-124
		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 = -3.3  for stack of 51-62
	Helix total = -10.2
	Hairpin = 4.4  for closure of 52-61


	Total energy = -98.2



