Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    258:309 260:308 261:307 262:306 263:305 264:304
	Energy of Broken Structure: -108.7
	Energy of Pseudo-Helices:   -8.0
	Pseudoknot Energy Penalty:  8.0
	Total Free Energy:          -108.7
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -8.3
		Stack = -2.2  for stack of 310-402
	Helix total = -2.2
	Multiloop = 5.1  for closure of 311-401
		Stack = -0.9  for stack of 367-393
		Stack = -2.1  for stack of 368-392
		Stack = -2.2  for stack of 369-391
		Stack = -1.3  for stack of 370-390
		Stack = -0.9  for stack of 371-389
		Stack = -2.1  for stack of 372-388
		Stack = -2.2  for stack of 373-387
	Helix total = -11.7
	Hairpin = 5.1  for closure of 374-386
		Stack = -3.3  for stack of 328-366
		Stack = -2.1  for stack of 329-365
		Stack = -1.3  for stack of 330-364
		Stack = -1.1  for stack of 331-363
	Helix total = -7.8
	Internal/bulge = 1.9  for closure of 332-362	Size = 2
		Stack = -2.1  for stack of 334-360
	Helix total = -2.1
	Internal/bulge = 2.1  for closure of 335-359	Size = 11
		Stack = -2.1  for stack of 341-352
		Stack = -3.4  for stack of 342-351
		Stack = -3.3  for stack of 343-350
	Helix total = -8.8
	Hairpin = 3.3  for closure of 344-349
		Stack = -2.1  for stack of 314-327
		Stack = -2.1  for stack of 315-326
		Stack = -3.4  for stack of 316-325
		Stack = -2.1  for stack of 317-324
	Helix total = -9.7
	Hairpin = 4.1  for closure of 318-323
		Stack = -3.4  for stack of 276-295
		Stack = -2.1  for stack of 277-294
		Stack = -0.9  for stack of 278-293
		Stack = -2.1  for stack of 279-292
		Stack = -3.4  for stack of 280-291
		Stack = -2.1  for stack of 281-290
		Stack = -1.1  for stack of 282-289
	Helix total = -15.1
	Hairpin = 4.1  for closure of 283-288
		Stack = -2.1  for stack of 89-274
		Stack = -2.2  for stack of 90-273
		Stack = -2.1  for stack of 91-272
		Stack = -2.1  for stack of 92-271
	Helix total = -8.5
	Internal/bulge = 0.9  for closure of 93-270	Size = 1 BP stack across bulge = -2.5
		Stack = -1.5  for stack of 95-269
	Helix total = -1.5
	Multiloop = 8.8  for closure of 96-268
		Stack = -2.5  for stack of 216-254
	Helix total = -2.5
	Internal/bulge = 1.9  for closure of 217-253	Size = 7
		Stack = -2.1  for stack of 222-249
		Stack = -2.4  for stack of 223-248
		Stack = -3.3  for stack of 224-247
	Helix total = -7.8
	Internal/bulge = 3.0  for closure of 225-246	Size = 5
		Stack = -2.1  for stack of 229-243
		Stack = -3.3  for stack of 230-242
		Stack = -3.4  for stack of 231-241
		Stack = -2.1  for stack of 232-240
	Helix total = -10.9
	Hairpin = 4.2  for closure of 233-239
		Stack = -2.1  for stack of 101-215
		Stack = -3.4  for stack of 102-214
		Stack = -2.4  for stack of 103-213
		Stack = -3.3  for stack of 104-212
		Stack = -1.5  for stack of 105-211
	Helix total = -12.7
	Internal/bulge = 3.4  for closure of 106-210	Size = 7
		Stack = -3.3  for stack of 111-206
		Stack = -3.3  for stack of 112-205
	Helix total = -6.6
	Multiloop = 5.1  for closure of 113-204
		Stack = -2.1  for stack of 195-201
	Helix total = -2.1
	Hairpin = 5.4  for closure of 196-200
		Stack = -2.1  for stack of 119-193
		Stack = -0.9  for stack of 120-192
		Stack = -0.9  for stack of 121-191
		Stack = -2.1  for stack of 122-190
		Stack = -3.4  for stack of 123-189
		Stack = -2.1  for stack of 124-188
	Helix total = -11.5
	Internal/bulge = 2.5  for closure of 125-187	Size = 1 BP stack across bulge = -1.3
	Helix total = 0.0
	Internal/bulge = 4.6  for closure of 126-185	Size = 4
		Stack = -2.2  for stack of 127-180
		Stack = -3.3  for stack of 128-179
	Helix total = -5.5
	Multiloop = 5.4  for closure of 129-178
		Stack = -3.3  for stack of 156-173
		Stack = -2.1  for stack of 157-172
	Helix total = -5.4
	Internal/bulge = 1.3  for closure of 158-171	Size = 1 BP stack across bulge = -2.1
		Stack = -3.3  for stack of 159-169
		Stack = -2.2  for stack of 160-168
	Helix total = -5.5
	Hairpin = 4.2  for closure of 161-167
		Stack = -2.5  for stack of 132-153
		Stack = -2.1  for stack of 133-152
		Stack = 0.3  for stack of 134-151
		Stack = -1.4  for stack of 135-150
		Stack = -2.4  for stack of 136-149
		Stack = -3.3  for stack of 137-148
		Stack = -2.1  for stack of 138-147
		Stack = -1.0  for stack of 139-146
	Helix total = -14.5
	Hairpin = 4.4  for closure of 140-145
		Stack = -2.5  for stack of 58-86
		Stack = -1.0  for stack of 59-85
		Stack = -1.4  for stack of 60-84
	Helix total = -4.9
	Internal/bulge = 1.9  for closure of 61-83	Size = 2
		Stack = -1.0  for stack of 63-81
		Stack = -2.1  for stack of 64-80
		Stack = -3.3  for stack of 65-79
		Stack = -2.2  for stack of 66-78
		Stack = -2.1  for stack of 67-77
	Helix total = -10.7
	Hairpin = 4.4  for closure of 68-76
		Stack = -2.1  for stack of 35-56
		Stack = -2.5  for stack of 36-55
		Stack = -1.5  for stack of 37-54
		Stack = -1.4  for stack of 38-53
		Stack = -1.3  for stack of 39-52
		Stack = -0.9  for stack of 40-51
		Stack = -2.1  for stack of 41-50
		Stack = -3.3  for stack of 42-49
	Helix total = -15.1
	Hairpin = 3.1  for closure of 43-48
		Stack = -2.1  for stack of 1-31
		Stack = -3.3  for stack of 2-30
		Stack = -3.4  for stack of 3-29
		Stack = -2.4  for stack of 4-28
		Stack = -2.5  for stack of 5-27
		Stack = -0.6  for stack of 6-26
	Helix total = -14.3
	Hairpin = 6.8  for closure of 7-25


	Total energy = -108.7



