Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    48:68 49:67 50:66 51:65 52:64 165:199 166:198 167:197
	    168:196 169:195 170:194 217:247 218:246 219:245 220:244 221:243
	    222:242 267:307 268:306 269:305 270:304 271:303 272:302 275:299
	Energy of Broken Structure: -129.0
	Energy of Pseudo-Helices:   -43.6
	Pseudoknot Energy Penalty:  36.5
	Total Free Energy:          -136.1
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-367
		Stack = -1.5  for stack of 2-366
		Stack = -2.1  for stack of 3-365
		Stack = -2.4  for stack of 4-364
		Stack = -1.1  for stack of 5-363
		Stack = -2.1  for stack of 6-362
	Helix total = -12.5
	Multiloop = 5.0  for closure of 7-361
		Stack = -3.3  for stack of 344-360
		Stack = -3.3  for stack of 345-359
		Stack = -3.3  for stack of 346-358
		Stack = -3.3  for stack of 347-357
	Helix total = -13.2
	Hairpin = 4.4  for closure of 348-356
		Stack = -2.4  for stack of 19-340
		Stack = -2.4  for stack of 20-339
		Stack = -2.2  for stack of 21-338
		Stack = -2.4  for stack of 22-337
		Stack = -3.3  for stack of 23-336
		Stack = -2.5  for stack of 24-335
		Stack = -1.5  for stack of 25-334
		Stack = -2.4  for stack of 26-333
		Stack = -2.5  for stack of 27-332
		Stack = -1.0  for stack of 28-331
	Helix total = -22.6
	Internal/bulge = 1.8  for closure of 29-330	Size = 7
		Stack = -2.1  for stack of 34-326
		Stack = -2.1  for stack of 35-325
		Stack = -3.3  for stack of 36-324
		Stack = -2.4  for stack of 37-323
	Helix total = -9.9
	Internal/bulge = 2.4  for closure of 38-322	Size = 10
		Stack = -2.4  for stack of 43-315
		Stack = -3.3  for stack of 44-314
		Stack = -3.3  for stack of 45-313
		Stack = -2.2  for stack of 46-312
	Helix total = -11.2
	Multiloop = 4.4  for closure of 47-311
		Stack = -2.1  for stack of 250-288
		Stack = -3.4  for stack of 251-287
		Stack = -3.3  for stack of 252-286
		Stack = -3.3  for stack of 253-285
	Helix total = -12.1
	Internal/bulge = 2.8  for closure of 254-284	Size = 2
		Stack = -2.4  for stack of 257-283
		Stack = -3.3  for stack of 258-282
		Stack = -3.4  for stack of 259-281
		Stack = -2.4  for stack of 260-280
	Helix total = -11.5
	Internal/bulge = 2.3  for closure of 261-279	Size = 3
		Stack = -2.1  for stack of 264-277
	Helix total = -2.1
	Hairpin = 6.3  for closure of 265-276
		Stack = -2.1  for stack of 205-233
		Stack = -1.4  for stack of 206-232
		Stack = -2.4  for stack of 207-231
		Stack = -2.1  for stack of 208-230
		Stack = -2.4  for stack of 209-229
		Stack = -2.1  for stack of 210-228
		Stack = -3.4  for stack of 211-227
		Stack = -3.3  for stack of 212-226
		Stack = -3.3  for stack of 213-225
	Helix total = -22.5
	Hairpin = 4.1  for closure of 214-224
		Stack = -2.4  for stack of 149-186
		Stack = -2.5  for stack of 150-185
		Stack = -1.5  for stack of 151-184
		Stack = -2.1  for stack of 152-183
		Stack = -2.1  for stack of 153-182
	Helix total = -10.6
	Internal/bulge = 2.3  for closure of 154-181	Size = 4
		Stack = -3.3  for stack of 156-177
		Stack = -2.4  for stack of 157-176
		Stack = -3.3  for stack of 158-175
		Stack = -3.3  for stack of 159-174
		Stack = -3.3  for stack of 160-173
	Helix total = -15.6
	Hairpin = 5.2  for closure of 161-172
		Stack = -2.4  for stack of 113-148
		Stack = -2.2  for stack of 114-147
		Stack = -2.1  for stack of 115-146
		Stack = -0.9  for stack of 116-145
		Stack = -2.4  for stack of 117-144
		Stack = -2.4  for stack of 118-143
	Helix total = -12.4
	Internal/bulge = 2.6  for closure of 119-142	Size = 5
		Stack = -2.1  for stack of 122-138
		Stack = -2.4  for stack of 123-137
		Stack = -2.4  for stack of 124-136
		Stack = -3.4  for stack of 125-135
	Helix total = -10.3
	Hairpin = 5.0  for closure of 126-134
		Stack = -1.4  for stack of 54-83
		Stack = -3.4  for stack of 55-82
		Stack = -2.4  for stack of 56-81
		Stack = -3.4  for stack of 57-80
		Stack = -2.1  for stack of 58-79
		Stack = -2.1  for stack of 59-78
	Helix total = -14.8
	Hairpin = 5.4  for closure of 60-77


	Total energy = -129.0



