Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    53:74 54:73 55:72 56:71 57:70 160:199 162:197 163:196
	    164:195 165:194 166:193 167:192 213:238 214:237 215:236 242:279
	    243:278 244:277 245:276 246:275 249:273 256:268
	Energy of Broken Structure: -54.6
	Energy of Pseudo-Helices:   -33.8
	Pseudoknot Energy Penalty:  30.6
	Total Free Energy:          -57.8
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-357
		Stack = -1.5  for stack of 2-356
		Stack = -2.1  for stack of 3-355
		Stack = -3.3  for stack of 4-354
		Stack = -2.2  for stack of 5-353
		Stack = -2.1  for stack of 6-352
	Helix total = -14.5
	Multiloop = 6.7  for closure of 7-351
		Stack = -2.1  for stack of 334-350
		Stack = -3.4  for stack of 335-349
		Stack = -2.1  for stack of 336-348
		Stack = -2.1  for stack of 337-347
	Helix total = -9.7
	Hairpin = 5.0  for closure of 338-346
		Stack = -2.1  for stack of 20-330
		Stack = -0.6  for stack of 21-329
		Stack = -0.5  for stack of 22-328
		Stack = -1.3  for stack of 23-327
		Stack = -0.6  for stack of 24-326
		Stack = -1.4  for stack of 25-325
		Stack = -1.3  for stack of 26-324
		Stack = -0.6  for stack of 27-323
		Stack = -1.4  for stack of 28-322
		Stack = -1.0  for stack of 29-321
		Stack = -2.1  for stack of 30-320
		Stack = -2.4  for stack of 31-319
	Helix total = -15.3
	Internal/bulge = 1.9  for closure of 32-318	Size = 2
		Stack = -2.4  for stack of 34-316
		Stack = -2.1  for stack of 35-315
	Helix total = -4.5
	Internal/bulge = 1.9  for closure of 36-314	Size = 2
		Stack = -2.1  for stack of 38-312
		Stack = -3.4  for stack of 39-311
	Helix total = -5.5
	Internal/bulge = 2.9  for closure of 40-310	Size = 7
		Stack = -2.1  for stack of 43-304
		Stack = -1.1  for stack of 44-303
		Stack = -2.1  for stack of 45-302
		Stack = -3.4  for stack of 46-301
	Helix total = -8.7
	Multiloop = 5.0  for closure of 47-300
		Stack = -2.1  for stack of 260-294
		Stack = -2.4  for stack of 261-293
		Stack = -0.9  for stack of 262-292
		Stack = -2.1  for stack of 263-291
		Stack = -2.2  for stack of 264-290
		Stack = -2.1  for stack of 265-289
		Stack = -2.4  for stack of 266-288
	Helix total = -14.2
	Hairpin = 6.7  for closure of 267-287
		Stack = -1.3  for stack of 201-227
		Stack = -1.1  for stack of 202-226
		Stack = -0.9  for stack of 203-225
		Stack = -1.3  for stack of 204-224
	Helix total = -4.6
	Internal/bulge = 1.9  for closure of 205-223	Size = 2
		Stack = -2.1  for stack of 207-221
		Stack = -2.4  for stack of 208-220
	Helix total = -4.5
	Internal/bulge = 1.9  for closure of 209-219	Size = 2
	Helix total = 0.0
	Hairpin = 5.5  for closure of 211-217
		Stack = -3.3  for stack of 146-183
		Stack = -2.1  for stack of 147-182
		Stack = -1.4  for stack of 148-181
		Stack = -3.4  for stack of 149-180
	Helix total = -10.2
	Internal/bulge = 1.2  for closure of 150-179	Size = 2
		Stack = -0.9  for stack of 152-177
		Stack = -0.9  for stack of 153-176
	Helix total = -1.8
	Internal/bulge = 1.9  for closure of 154-175	Size = 2
	Helix total = 0.0
	Hairpin = 6.8  for closure of 156-173
		Stack = -3.4  for stack of 119-145
		Stack = -2.1  for stack of 120-144
	Helix total = -5.5
	Internal/bulge = 2.6  for closure of 121-143	Size = 3
		Stack = -0.6  for stack of 124-141
		Stack = -2.5  for stack of 125-140
		Stack = -2.1  for stack of 126-139
		Stack = -2.1  for stack of 127-138
	Helix total = -7.3
	Hairpin = 4.8  for closure of 128-137
		Stack = -2.1  for stack of 48-63
		Stack = -3.4  for stack of 49-62
		Stack = -2.1  for stack of 50-61
		Stack = -0.9  for stack of 51-60
	Helix total = -8.5
	Hairpin = 5.2  for closure of 52-59


	Total energy = -54.6



