Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    601:622 602:621 603:620
	Energy of Broken Structure: -98.7
	Energy of Pseudo-Helices:   -6.7
	Pseudoknot Energy Penalty:  7.2
	Total Free Energy:          -98.2
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -2.8
		Stack = -0.6  for stack of 22-652
	Helix total = -0.6
	Internal/bulge = 1.9  for closure of 23-651	Size = 2
		Stack = -1.1  for stack of 25-649
		Stack = -1.3  for stack of 26-648
		Stack = -1.4  for stack of 27-647
		Stack = -1.4  for stack of 28-646
		Stack = -3.4  for stack of 29-645
		Stack = -2.1  for stack of 30-644
	Helix total = -10.7
	Multiloop = 3.6  for closure of 31-643
		Stack = -0.9  for stack of 595-641
		Stack = -2.1  for stack of 596-640
		Stack = -3.3  for stack of 597-639
		Stack = -2.4  for stack of 598-638
		Stack = -2.1  for stack of 599-637
	Helix total = -10.8
	Internal/bulge = 4.6  for closure of 600-636	Size = 7
		Stack = -2.1  for stack of 608-635
		Stack = -2.1  for stack of 609-634
		Stack = -3.3  for stack of 610-633
	Helix total = -7.5
	Internal/bulge = 0.7  for closure of 611-632	Size = 2
	Helix total = 0.0
	Hairpin = 6.9  for closure of 613-630
		Stack = -2.2  for stack of 565-585
	Helix total = -2.2
	Hairpin = 6.9  for closure of 566-584
		Stack = -2.1  for stack of 527-558
		Stack = -0.9  for stack of 528-557
	Helix total = -3.0
	Internal/bulge = 2.3  for closure of 529-556	Size = 1 BP stack across bulge = -1.1
		Stack = -1.3  for stack of 530-554
		Stack = -2.2  for stack of 531-553
		Stack = -2.1  for stack of 532-552
		Stack = -2.1  for stack of 533-551
		Stack = -3.3  for stack of 534-550
	Helix total = -11.0
	Internal/bulge = 1.1  for closure of 535-549	Size = 3
		Stack = -2.1  for stack of 537-546
		Stack = -2.4  for stack of 538-545
	Helix total = -4.5
	Hairpin = 4.2  for closure of 539-544
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 34-521	Size = 2
		Stack = -2.4  for stack of 36-519
	Helix total = -2.4
	Multiloop = 5.5  for closure of 37-518
	Helix total = 0.0
	Internal/bulge = 2.1  for closure of 487-512	Size = 1 BP stack across bulge = -1.3
		Stack = -2.2  for stack of 489-511
		Stack = -3.3  for stack of 490-510
	Helix total = -5.5
	Internal/bulge = 3.0  for closure of 491-509	Size = 4
		Stack = -1.5  for stack of 495-507
		Stack = -3.3  for stack of 496-506
		Stack = -3.3  for stack of 497-505
		Stack = -2.4  for stack of 498-504
	Helix total = -10.5
	Hairpin = 5.4  for closure of 499-503
	Helix total = 0.0
	Internal/bulge = 4.4  for closure of 41-481	Size = 6
		Stack = -3.4  for stack of 47-479
		Stack = -3.3  for stack of 48-478
	Helix total = -6.7
	Internal/bulge = 1.7  for closure of 49-477	Size = 1 BP stack across bulge = -2.1
		Stack = -2.1  for stack of 51-476
		Stack = -3.4  for stack of 52-475
	Helix total = -5.5
	Multiloop = 0.1  for closure of 53-474
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 459-470	Size = 2
		Stack = -2.4  for stack of 461-468
	Helix total = -2.4
	Hairpin = 3.3  for closure of 462-467
		Stack = -3.3  for stack of 436-457
	Helix total = -3.3
	Internal/bulge = 1.2  for closure of 437-456	Size = 2
		Stack = -2.1  for stack of 439-454
		Stack = -3.4  for stack of 440-453
	Helix total = -5.5
	Hairpin = 5.5  for closure of 441-452
		Stack = -2.1  for stack of 96-434
		Stack = -2.4  for stack of 97-433
	Helix total = -4.5
	Multiloop = 2.6  for closure of 98-432
		Stack = -2.4  for stack of 409-431
		Stack = -3.3  for stack of 410-430
		Stack = -1.5  for stack of 411-429
	Helix total = -7.2
	Internal/bulge = 3.7  for closure of 412-428	Size = 3
		Stack = -2.4  for stack of 413-424
		Stack = -0.9  for stack of 414-423
		Stack = -1.4  for stack of 415-422
	Helix total = -4.7
	Hairpin = 5.4  for closure of 416-421
		Stack = -3.3  for stack of 357-405
		Stack = -2.1  for stack of 358-404
	Helix total = -5.4
	Internal/bulge = 4.1  for closure of 359-403	Size = 10
		Stack = -2.2  for stack of 364-396
		Stack = -2.1  for stack of 365-395
	Helix total = -4.3
	Internal/bulge = 4.6  for closure of 366-394	Size = 4
		Stack = -1.1  for stack of 371-393
		Stack = -2.1  for stack of 372-392
		Stack = -3.3  for stack of 373-391
		Stack = -2.2  for stack of 374-390
		Stack = -1.3  for stack of 375-389
		Stack = -2.1  for stack of 376-388
	Helix total = -12.1
	Hairpin = 5.4  for closure of 377-387
		Stack = -2.1  for stack of 106-355
		Stack = -2.1  for stack of 107-354
	Helix total = -4.2
	Internal/bulge = 1.5  for closure of 108-353	Size = 2
	Helix total = 0.0
	Internal/bulge = 3.8  for closure of 110-351	Size = 6
		Stack = -1.3  for stack of 115-348
	Helix total = -1.3
	Internal/bulge = 3.5  for closure of 116-347	Size = 7
		Stack = -2.1  for stack of 121-343
		Stack = -3.3  for stack of 122-342
	Helix total = -5.4
	Multiloop = 7.3  for closure of 123-341
		Stack = -2.4  for stack of 314-336
		Stack = -2.4  for stack of 315-335
		Stack = -3.4  for stack of 316-334
	Helix total = -8.2
	Internal/bulge = 0.5  for closure of 317-333	Size = 1 BP stack across bulge = -3.3
		Stack = -2.4  for stack of 319-332
		Stack = -3.4  for stack of 320-331
		Stack = -3.3  for stack of 321-330
	Helix total = -9.1
	Hairpin = 4.6  for closure of 322-329
		Stack = -0.9  for stack of 219-302
		Stack = -1.3  for stack of 220-301
		Stack = -1.1  for stack of 221-300
		Stack = -2.4  for stack of 222-299
	Helix total = -5.7
	Internal/bulge = 3.2  for closure of 223-298	Size = 15
		Stack = -2.2  for stack of 232-290
		Stack = -3.3  for stack of 233-289
		Stack = -2.1  for stack of 234-288
		Stack = -0.9  for stack of 235-287
	Helix total = -8.5
	Internal/bulge = 3.0  for closure of 236-286	Size = 3
		Stack = -3.3  for stack of 238-283
		Stack = -2.4  for stack of 239-282
	Helix total = -5.7
	Internal/bulge = 1.0  for closure of 240-281	Size = 9
		Stack = -3.4  for stack of 245-275
		Stack = -3.3  for stack of 246-274
		Stack = -3.3  for stack of 247-273
	Helix total = -10.0
	Internal/bulge = 3.0  for closure of 248-272	Size = 3
		Stack = -1.5  for stack of 250-269
		Stack = -2.1  for stack of 251-268
		Stack = -1.5  for stack of 252-267
		Stack = -3.3  for stack of 253-266
		Stack = -2.4  for stack of 254-265
		Stack = -3.3  for stack of 255-264
		Stack = -3.4  for stack of 256-263
	Helix total = -17.5
	Hairpin = 4.6  for closure of 257-262
		Stack = -2.5  for stack of 185-214
		Stack = -2.4  for stack of 186-213
		Stack = -3.4  for stack of 187-212
	Helix total = -8.3
	Internal/bulge = 0.4  for closure of 188-211	Size = 6
		Stack = -3.3  for stack of 192-207
		Stack = -3.3  for stack of 193-206
		Stack = -3.3  for stack of 194-205
		Stack = -3.3  for stack of 195-204
		Stack = -2.1  for stack of 196-203
	Helix total = -15.3
	Hairpin = 5.5  for closure of 197-202
	Helix total = 0.0
	Internal/bulge = 0.8  for closure of 142-177	Size = 2
		Stack = -2.1  for stack of 144-175
	Helix total = -2.1
	Internal/bulge = 2.2  for closure of 145-174	Size = 11
		Stack = -2.1  for stack of 151-167
	Helix total = -2.1
	Internal/bulge = -0.7  for closure of 152-166	Size = 2
		Stack = -1.0  for stack of 154-164
		Stack = -2.1  for stack of 155-163
	Helix total = -3.1
	Hairpin = 4.1  for closure of 156-162
		Stack = -2.5  for stack of 56-89
	Helix total = -2.5
	Internal/bulge = 4.2  for closure of 57-88	Size = 3
		Stack = -2.1  for stack of 61-87
		Stack = -2.2  for stack of 62-86
	Helix total = -4.3
	Hairpin = 6.8  for closure of 63-85
		Stack = -2.1  for stack of 4-20
		Stack = -2.1  for stack of 5-19
		Stack = -3.3  for stack of 6-18
		Stack = -2.5  for stack of 7-17
	Helix total = -10.0
	Hairpin = 5.1  for closure of 8-16


	Total energy = -98.7



