Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    456:477 457:476 458:475
	Energy of Broken Structure: -110.2
	Energy of Pseudo-Helices:   -6.7
	Pseudoknot Energy Penalty:  6.9
	Total Free Energy:          -110.0
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -3.7
		Stack = -3.3  for stack of 28-507
		Stack = -2.4  for stack of 29-506
		Stack = -2.2  for stack of 30-505
	Helix total = -7.9
	Internal/bulge = 1.7  for closure of 31-504	Size = 1 BP stack across bulge = -2.1
		Stack = -0.9  for stack of 33-503
		Stack = -2.2  for stack of 34-502
		Stack = -2.4  for stack of 35-501
		Stack = -3.4  for stack of 36-500
		Stack = -2.1  for stack of 37-499
	Helix total = -11.0
	Multiloop = 2.2  for closure of 38-498
		Stack = -3.4  for stack of 451-496
		Stack = -2.1  for stack of 452-495
		Stack = -2.2  for stack of 453-494
		Stack = -3.3  for stack of 454-493
	Helix total = -11.0
	Internal/bulge = 4.4  for closure of 455-492	Size = 6
		Stack = -2.1  for stack of 462-491
		Stack = -2.4  for stack of 463-490
		Stack = -2.1  for stack of 464-489
		Stack = -2.1  for stack of 465-488
	Helix total = -8.7
	Hairpin = 6.1  for closure of 466-487
		Stack = -2.4  for stack of 416-443
		Stack = -2.1  for stack of 417-442
		Stack = -2.1  for stack of 418-441
		Stack = -2.4  for stack of 419-440
	Helix total = -9.0
	Internal/bulge = 1.4  for closure of 420-439	Size = 7
	Helix total = 0.0
	Hairpin = 5.3  for closure of 424-434
		Stack = -3.4  for stack of 380-410
		Stack = -2.1  for stack of 381-409
		Stack = -2.1  for stack of 382-408
	Helix total = -7.6
	Internal/bulge = 1.2  for closure of 383-407	Size = 11
		Stack = -1.5  for stack of 390-401
		Stack = -2.5  for stack of 391-400
		Stack = -3.3  for stack of 392-399
	Helix total = -7.3
	Hairpin = 4.6  for closure of 393-398
		Stack = -3.4  for stack of 40-377
		Stack = -2.4  for stack of 41-376
		Stack = -3.3  for stack of 42-375
		Stack = -3.4  for stack of 43-374
		Stack = -2.1  for stack of 44-373
	Helix total = -14.6
	Internal/bulge = 2.3  for closure of 45-372	Size = 1 BP stack across bulge = -1.1
		Stack = -2.1  for stack of 46-370
	Helix total = -2.1
	Multiloop = 5.2  for closure of 47-369
	Helix total = 0.0
	Internal/bulge = 1.6  for closure of 343-367	Size = 1 BP stack across bulge = -1.3
		Stack = -1.5  for stack of 345-366
		Stack = -2.4  for stack of 346-365
	Helix total = -3.9
	Internal/bulge = 3.0  for closure of 347-364	Size = 4
	Helix total = 0.0
	Internal/bulge = 3.3  for closure of 351-362	Size = 2
		Stack = -3.4  for stack of 354-361
	Helix total = -3.4
	Hairpin = 3.3  for closure of 355-360
	Helix total = 0.0
	Internal/bulge = 3.8  for closure of 48-337	Size = 5
		Stack = -2.1  for stack of 53-335
		Stack = -2.2  for stack of 54-334
	Helix total = -4.3
	Internal/bulge = 1.7  for closure of 55-333	Size = 1 BP stack across bulge = -2.1
		Stack = -2.1  for stack of 57-332
		Stack = -3.4  for stack of 58-331
	Helix total = -5.5
	Multiloop = -0.3  for closure of 59-330
		Stack = -2.1  for stack of 315-326
		Stack = -2.4  for stack of 316-325
		Stack = -3.3  for stack of 317-324
	Helix total = -7.8
	Hairpin = 2.8  for closure of 318-323
		Stack = -2.1  for stack of 292-313
		Stack = -2.1  for stack of 293-312
		Stack = -3.3  for stack of 294-311
		Stack = -3.3  for stack of 295-310
	Helix total = -10.8
	Hairpin = 5.4  for closure of 296-309
		Stack = -2.2  for stack of 99-290
		Stack = -2.1  for stack of 100-289
	Helix total = -4.3
	Multiloop = 4.4  for closure of 101-288
		Stack = -3.4  for stack of 265-287
		Stack = -2.1  for stack of 266-286
		Stack = -2.1  for stack of 267-285
	Helix total = -7.6
	Internal/bulge = 3.7  for closure of 268-284	Size = 3
		Stack = -1.4  for stack of 269-280
		Stack = -2.4  for stack of 270-279
		Stack = -2.1  for stack of 271-278
	Helix total = -5.9
	Hairpin = 4.7  for closure of 272-277
		Stack = -2.1  for stack of 215-262
		Stack = -2.1  for stack of 216-261
	Helix total = -4.2
	Internal/bulge = 2.9  for closure of 217-260	Size = 10
		Stack = -3.4  for stack of 222-253
		Stack = -2.1  for stack of 223-252
	Helix total = -5.5
	Internal/bulge = 3.8  for closure of 224-251	Size = 2
		Stack = -0.9  for stack of 227-250
		Stack = -2.1  for stack of 228-249
		Stack = -3.3  for stack of 229-248
	Helix total = -6.3
	Internal/bulge = 1.2  for closure of 230-247	Size = 2
		Stack = -2.1  for stack of 232-245
		Stack = -3.3  for stack of 233-244
	Helix total = -5.4
	Hairpin = 3.3  for closure of 234-243
		Stack = -2.5  for stack of 108-214
		Stack = -2.4  for stack of 109-213
		Stack = -2.5  for stack of 110-212
		Stack = -1.0  for stack of 111-211
		Stack = -0.9  for stack of 112-210
		Stack = -2.1  for stack of 113-209
	Helix total = -11.4
	Internal/bulge = 1.1  for closure of 114-208	Size = 3
		Stack = -3.3  for stack of 117-206
	Helix total = -3.3
	Internal/bulge = 2.6  for closure of 118-205	Size = 5
		Stack = -2.1  for stack of 122-202
		Stack = -1.3  for stack of 123-201
		Stack = -1.1  for stack of 124-200
		Stack = -2.4  for stack of 125-199
		Stack = -2.4  for stack of 126-198
		Stack = -3.3  for stack of 127-197
	Helix total = -12.6
	Multiloop = 3.5  for closure of 128-196
		Stack = -3.3  for stack of 184-194
		Stack = -2.2  for stack of 185-193
	Helix total = -5.5
	Hairpin = 4.2  for closure of 186-192
		Stack = -2.5  for stack of 170-179
		Stack = -2.1  for stack of 171-178
	Helix total = -4.6
	Hairpin = 4.1  for closure of 172-177
		Stack = -3.3  for stack of 130-164
		Stack = -3.3  for stack of 131-163
		Stack = -3.3  for stack of 132-162
	Helix total = -9.9
	Internal/bulge = 2.2  for closure of 133-161	Size = 11
		Stack = -2.1  for stack of 139-154
	Helix total = -2.1
	Internal/bulge = 1.2  for closure of 140-153	Size = 2
		Stack = 0.3  for stack of 142-151
		Stack = -2.1  for stack of 143-150
	Helix total = -1.8
	Hairpin = 3.1  for closure of 144-149
		Stack = -2.5  for stack of 62-92
		Stack = -1.5  for stack of 63-91
	Helix total = -4.0
	Internal/bulge = 3.3  for closure of 64-90	Size = 2
		Stack = -2.2  for stack of 67-89
	Helix total = -2.2
	Internal/bulge = 1.1  for closure of 68-88	Size = 5
		Stack = -2.5  for stack of 71-84
		Stack = -2.1  for stack of 72-83
		Stack = -0.9  for stack of 73-82
		Stack = -0.9  for stack of 74-81
	Helix total = -6.4
	Hairpin = 4.4  for closure of 75-80
		Stack = -2.4  for stack of 10-26
		Stack = -2.1  for stack of 11-25
		Stack = -2.5  for stack of 12-24
		Stack = -0.5  for stack of 13-23
	Helix total = -7.5
	Hairpin = 5.1  for closure of 14-22


	Total energy = -110.2



