Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    509:530 510:529 511:528
	Energy of Broken Structure: -216.8
	Energy of Pseudo-Helices:   -6.7
	Pseudoknot Energy Penalty:  7.7
	Total Free Energy:          -215.8
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -3.7
		Stack = -3.3  for stack of 27-560
		Stack = -3.3  for stack of 28-559
		Stack = -2.2  for stack of 29-558
	Helix total = -8.8
	Internal/bulge = 2.5  for closure of 30-557	Size = 1 BP stack across bulge = -1.3
		Stack = -0.9  for stack of 32-556
		Stack = -2.2  for stack of 33-555
		Stack = -2.4  for stack of 34-554
		Stack = -3.4  for stack of 35-553
		Stack = -2.1  for stack of 36-552
	Helix total = -11.0
	Multiloop = 1.6  for closure of 37-551
		Stack = -3.4  for stack of 504-549
		Stack = -3.3  for stack of 505-548
		Stack = -3.3  for stack of 506-547
		Stack = -3.3  for stack of 507-546
	Helix total = -13.3
	Internal/bulge = 4.4  for closure of 508-545	Size = 6
		Stack = -2.1  for stack of 515-544
		Stack = -1.3  for stack of 516-543
		Stack = -2.2  for stack of 517-542
		Stack = -2.4  for stack of 518-541
		Stack = -2.2  for stack of 519-540
		Stack = -1.0  for stack of 520-539
	Helix total = -11.2
	Hairpin = 6.9  for closure of 521-538
		Stack = -2.4  for stack of 446-496
		Stack = -3.3  for stack of 447-495
		Stack = -3.3  for stack of 448-494
		Stack = -3.3  for stack of 449-493
	Helix total = -12.3
	Internal/bulge = 0.7  for closure of 450-492	Size = 7
	Helix total = 0.0
	Internal/bulge = 1.5  for closure of 454-487	Size = 10
		Stack = -3.3  for stack of 460-481
		Stack = -2.2  for stack of 461-480
		Stack = -1.3  for stack of 462-479
		Stack = -2.1  for stack of 463-478
		Stack = -3.3  for stack of 464-477
		Stack = -3.3  for stack of 465-476
	Helix total = -15.5
	Hairpin = 4.2  for closure of 466-475
		Stack = -3.4  for stack of 410-440
		Stack = -2.4  for stack of 411-439
		Stack = -3.3  for stack of 412-438
	Helix total = -9.1
	Internal/bulge = 1.9  for closure of 413-437	Size = 11
		Stack = -2.5  for stack of 420-431
		Stack = -3.3  for stack of 421-430
		Stack = -3.3  for stack of 422-429
	Helix total = -9.1
	Hairpin = 3.7  for closure of 423-428
		Stack = -3.4  for stack of 39-407
		Stack = -2.4  for stack of 40-406
		Stack = -3.3  for stack of 41-405
		Stack = -3.4  for stack of 42-404
		Stack = -2.4  for stack of 43-403
	Helix total = -14.9
	Internal/bulge = 1.3  for closure of 44-402	Size = 1 BP stack across bulge = -2.5
		Stack = -1.4  for stack of 45-400
	Helix total = -1.4
	Multiloop = 5.0  for closure of 46-399
	Helix total = 0.0
	Internal/bulge = 1.3  for closure of 371-397	Size = 1 BP stack across bulge = -2.1
		Stack = -3.3  for stack of 373-396
		Stack = -2.4  for stack of 374-395
	Helix total = -5.7
	Internal/bulge = 3.7  for closure of 375-394	Size = 4
		Stack = 0.3  for stack of 379-392
		Stack = -2.1  for stack of 380-391
		Stack = -3.3  for stack of 381-390
		Stack = -3.3  for stack of 382-389
	Helix total = -8.4
	Hairpin = 3.1  for closure of 383-388
	Helix total = 0.0
	Internal/bulge = 3.8  for closure of 47-365	Size = 5
		Stack = -2.1  for stack of 52-363
		Stack = -2.2  for stack of 53-362
	Helix total = -4.3
	Internal/bulge = 1.7  for closure of 54-361	Size = 1 BP stack across bulge = -2.1
		Stack = -2.1  for stack of 56-360
		Stack = -3.4  for stack of 57-359
	Helix total = -5.5
	Multiloop = -0.3  for closure of 58-358
		Stack = -2.1  for stack of 343-354
		Stack = -2.4  for stack of 344-353
		Stack = -3.3  for stack of 345-352
	Helix total = -7.8
	Hairpin = 2.8  for closure of 346-351
		Stack = -3.3  for stack of 320-341
		Stack = -3.3  for stack of 321-340
		Stack = -3.3  for stack of 322-339
		Stack = -3.4  for stack of 323-338
	Helix total = -13.3
	Hairpin = 5.3  for closure of 324-337
		Stack = -2.2  for stack of 110-318
		Stack = -2.1  for stack of 111-317
	Helix total = -4.3
	Multiloop = 1.8  for closure of 112-316
		Stack = -3.4  for stack of 293-315
		Stack = -3.3  for stack of 294-314
		Stack = -2.4  for stack of 295-313
	Helix total = -9.1
	Internal/bulge = 3.7  for closure of 296-312	Size = 3
		Stack = -2.5  for stack of 297-308
		Stack = -3.3  for stack of 298-307
		Stack = -2.1  for stack of 299-306
	Helix total = -7.9
	Hairpin = 4.7  for closure of 300-305
		Stack = -3.3  for stack of 244-290
		Stack = -3.3  for stack of 245-289
	Helix total = -6.6
	Internal/bulge = 2.7  for closure of 246-288	Size = 10
		Stack = -3.3  for stack of 251-281
		Stack = -2.5  for stack of 252-280
	Helix total = -5.8
	Internal/bulge = 3.8  for closure of 253-279	Size = 2
		Stack = -0.9  for stack of 256-278
		Stack = -2.1  for stack of 257-277
		Stack = -3.3  for stack of 258-276
		Stack = -2.2  for stack of 259-275
		Stack = -2.1  for stack of 260-274
		Stack = -3.3  for stack of 261-273
		Stack = -3.3  for stack of 262-272
	Helix total = -17.2
	Hairpin = 3.8  for closure of 263-271
		Stack = -2.4  for stack of 120-242
		Stack = -2.5  for stack of 121-241
		Stack = -1.4  for stack of 122-240
		Stack = -3.3  for stack of 123-239
		Stack = -3.3  for stack of 124-238
		Stack = -2.5  for stack of 125-237
	Helix total = -15.4
	Internal/bulge = 3.3  for closure of 126-236	Size = 2
		Stack = -3.3  for stack of 129-235
	Helix total = -3.3
	Internal/bulge = 2.6  for closure of 130-234	Size = 5
		Stack = -3.3  for stack of 134-231
		Stack = -2.1  for stack of 135-230
		Stack = -2.4  for stack of 136-229
		Stack = -3.3  for stack of 137-228
		Stack = -2.4  for stack of 138-227
		Stack = -3.3  for stack of 139-226
	Helix total = -16.8
	Multiloop = 2.3  for closure of 140-225
		Stack = -3.3  for stack of 210-223
		Stack = -3.3  for stack of 211-222
		Stack = -3.3  for stack of 212-221
		Stack = -3.4  for stack of 213-220
	Helix total = -13.3
	Hairpin = 4.1  for closure of 214-219
		Stack = -2.1  for stack of 182-205
		Stack = -2.4  for stack of 183-204
		Stack = -3.3  for stack of 184-203
		Stack = -2.1  for stack of 185-202
		Stack = -1.4  for stack of 186-201
		Stack = -1.5  for stack of 187-200
		Stack = -2.1  for stack of 188-199
		Stack = -0.9  for stack of 189-198
		Stack = -2.2  for stack of 190-197
	Helix total = -18.0
	Hairpin = 3.3  for closure of 191-196
		Stack = -3.3  for stack of 142-176
		Stack = -3.3  for stack of 143-175
		Stack = -3.3  for stack of 144-174
	Helix total = -9.9
	Internal/bulge = 2.2  for closure of 145-173	Size = 11
		Stack = -3.3  for stack of 151-166
		Stack = -2.1  for stack of 152-165
		Stack = -2.1  for stack of 153-164
		Stack = -3.3  for stack of 154-163
		Stack = -3.3  for stack of 155-162
	Helix total = -14.1
	Hairpin = 3.1  for closure of 156-161
		Stack = -2.5  for stack of 61-103
		Stack = -1.5  for stack of 62-102
	Helix total = -4.0
	Internal/bulge = 2.8  for closure of 63-101	Size = 2
		Stack = -3.4  for stack of 66-100
	Helix total = -3.4
	Internal/bulge = 0.5  for closure of 67-99	Size = 2
		Stack = -3.3  for stack of 69-97
		Stack = -3.3  for stack of 70-96
	Helix total = -6.6
	Internal/bulge = 1.2  for closure of 71-95	Size = 2
	Helix total = 0.0
	Internal/bulge = 2.1  for closure of 73-93	Size = 5
		Stack = -2.1  for stack of 76-89
		Stack = -2.4  for stack of 77-88
		Stack = -3.3  for stack of 78-87
		Stack = -3.3  for stack of 79-86
	Helix total = -11.1
	Hairpin = 3.7  for closure of 80-85
		Stack = -1.5  for stack of 9-25
		Stack = -2.1  for stack of 10-24
		Stack = -2.5  for stack of 11-23
		Stack = -0.5  for stack of 12-22
	Helix total = -6.6
	Hairpin = 5.1  for closure of 13-21


	Total energy = -216.8



