------------------------------------------------------------------------------------------------------------------------- Will print the top 5 alignments (based on backbone shifts) for each pairing of chains, as measured by a combination of score and contiguity. Some relevant parameters: HELIX min length: 5 STRAND min length: 3 shift-tolerance = -10 permissible-violations = 4 max-breaks = NIL retain-m = 100 best-n = 100 anglethresh = 0.5 septhresh = 5 min_length = 4 rmsd-tol = 9.9999999999999E12 Legend: score1 [score2] pairings L2ERR {Xbad/Xsig:Xtot} Breaks (score2 is the score from protein2's perspective, not the minimum of the two perspectives as in some earlier printouts.) Recall that "SIMILARITY" refers to similarities over all alignments not just the top ones. ------------------------------------------------------------------------------------------------------------------------- [293, 205]: Comparing 1b5l and 1au1_A, based on their crossing files. There are 6 (6 H + 0 S) secondary structure elements in 1b5l, of which 6 satisfy the size requirements. There are 8 (8 H + 0 S) secondary structure elements in 1au1_A, of which 7 satisfy the size requirements. 1.00045 [ 1.16695] ((1 . 1) (2 . 3) (3 . 4) (4 . 6) (5 . 7) (6 . 8)) 3.305 {0/5:15} B:0 SIMILARITY (1/min{score1}): 0.9995 [and 1/min{score2}: 0.8569] [293, 293]: Comparing 1b5l and 1b5l, based on their crossing files. There are 6 (6 H + 0 S) secondary structure elements in 1b5l, of which 6 satisfy the size requirements. There are 6 (6 H + 0 S) secondary structure elements in 1b5l, of which 6 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6)) 0.000 {0/6:15} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [293, 379]: Comparing 1b5l and 1bgc, based on their crossing files. There are 6 (6 H + 0 S) secondary structure elements in 1b5l, of which 6 satisfy the size requirements. There are 7 (7 H + 0 S) secondary structure elements in 1bgc, of which 6 satisfy the size requirements. 1.50825 [ 1.50825] ((1 . 1) (3 . 5) (4 . 6) (5 . 7)) 9.261 {0/0:6} B:0 10.00056 [10.00056] ((1 . 1) (2 . 3) (3 . 5) (4 . 6) (6 . 7)) 10.261 {4/4:10} B:0 1.53013 [ 1.53013] ((3 . 5) (4 . 6) (5 . 7) (6 . 1)) 12.875 {0/0:6} B:1 SIMILARITY (1/min{score1}): 0.6630 [and 1/min{score2}: 0.6630] [293, 774]: Comparing 1b5l and 1d9c_A, based on their crossing files. There are 6 (6 H + 0 S) secondary structure elements in 1b5l, of which 6 satisfy the size requirements. There are 7 (7 H + 0 S) secondary structure elements in 1d9c_A, of which 7 satisfy the size requirements. 5.01011 [ 5.01867] ((1 . 1) (2 . 2) (3 . 3) (4 . 4)) 4.819 {1/2:6} B:0 5.01035 [ 5.01891] ((1 . 1) (2 . 2) (3 . 3) (5 . 6)) 9.579 {1/2:6} B:0 SIMILARITY (1/min{score1}): 0.1996 [and 1/min{score2}: 0.1993] [293, 1125]: Comparing 1b5l and 1eer_A, based on their crossing files. There are 6 (6 H + 0 S) secondary structure elements in 1b5l, of which 6 satisfy the size requirements. There are 10 (8 H + 2 S) secondary structure elements in 1eer_A, of which 9 satisfy the size requirements. 1.50019 [ 2.25006] ((1 . 2) (3 . 5) (4 . 6) (6 . 9)) 3.608 {0/1:6} B:0 1.50479 [ 2.25143] ((1 . 2) (3 . 5) (4 . 6) (6 . 10)) 8.080 {0/1:6} B:0 6.00241 [ 6.01212] ((1 . 2) (2 . 4) (3 . 5) (4 . 6) (6 . 9)) 4.939 {3/5:10} B:0 1.25000 [ 1.81556] ((1 . 2) (3 . 5) (4 . 6) (5 . 10) (6 . 9)) 12.460 {0/1:10} B:1 SIMILARITY (1/min{score1}): 0.8000 [and 1/min{score2}: 0.5508] [293, 1258]: Comparing 1b5l and 1ete_A, based on their crossing files. There are 6 (6 H + 0 S) secondary structure elements in 1b5l, of which 6 satisfy the size requirements. There are 7 (5 H + 2 S) secondary structure elements in 1ete_A, of which 6 satisfy the size requirements. 1.51754 [ 1.51754] ((1 . 1) (3 . 3) (4 . 4) (5 . 6)) 11.210 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.6590 [and 1/min{score2}: 0.6590] [293, 1278]: Comparing 1b5l and 1evs_A, based on their crossing files. There are 6 (6 H + 0 S) secondary structure elements in 1b5l, of which 6 satisfy the size requirements. There are 8 (8 H + 0 S) secondary structure elements in 1evs_A, of which 8 satisfy the size requirements. 1.50248 [ 2.00105] ((1 . 2) (3 . 5) (4 . 7) (6 . 8)) 6.846 {0/0:6} B:0 1.50599 [ 2.00254] ((2 . 4) (3 . 5) (4 . 7) (5 . 8)) 8.544 {0/2:6} B:0 1.51725 [ 2.00736] ((3 . 1) (4 . 2) (5 . 4) (6 . 5)) 11.162 {0/0:6} B:0 6.67096 [ 6.68015] ((1 . 2) (2 . 4) (3 . 5) (6 . 8)) 6.726 {2/3:6} B:0 1.20602 [ 1.60255] ((1 . 7) (3 . 8) (4 . 2) (5 . 4) (6 . 5)) 7.240 {0/1:10} B:1 SIMILARITY (1/min{score1}): 0.8292 [and 1/min{score2}: 0.6240] [293, 1395]: Comparing 1b5l and 1f45_B, based on their crossing files. There are 6 (6 H + 0 S) secondary structure elements in 1b5l, of which 6 satisfy the size requirements. There are 6 (6 H + 0 S) secondary structure elements in 1f45_B, of which 6 satisfy the size requirements. 1.20038 [ 1.20038] ((1 . 1) (2 . 2) (3 . 4) (4 . 5) (6 . 6)) 3.620 {0/3:10} B:0 1.50956 [ 1.50956] ((1 . 1) (2 . 2) (4 . 4) (6 . 6)) 9.613 {0/1:6} B:0 1.51106 [ 1.51106] ((1 . 1) (3 . 4) (4 . 5) (5 . 6)) 9.973 {0/1:6} B:0 4.00816 [ 4.00816] ((1 . 1) (2 . 3) (3 . 4) (4 . 5) (6 . 6)) 6.076 {2/5:10} B:0 SIMILARITY (1/min{score1}): 0.8331 [and 1/min{score2}: 0.8331] [293, 1417]: Comparing 1b5l and 1f6f_A, based on their crossing files. There are 6 (6 H + 0 S) secondary structure elements in 1b5l, of which 6 satisfy the size requirements. There are 9 (9 H + 0 S) secondary structure elements in 1f6f_A, of which 7 satisfy the size requirements. 1.20511 [ 1.40322] ((1 . 2) (3 . 6) (4 . 7) (5 . 8) (6 . 9)) 6.946 {0/1:10} B:0 1.20867 [ 1.40549] ((1 . 2) (3 . 5) (4 . 7) (5 . 8) (6 . 9)) 7.938 {0/1:10} B:0 5.00211 [ 5.00382] ((1 . 2) (2 . 5) (3 . 6) (4 . 7) (5 . 8) (6 . 9)) 7.830 {2/4:15} B:0 5.01065 [ 5.01921] ((1 . 5) (2 . 6) (3 . 7) (5 . 9)) 11.639 {1/2:6} B:0 10.00131 [10.00239] ((2 . 6) (3 . 7) (5 . 2) (6 . 5)) 10.364 {1/1:6} B:1 SIMILARITY (1/min{score1}): 0.8298 [and 1/min{score2}: 0.7126] [293, 2294]: Comparing 1b5l and 1hul_A, based on their crossing files. There are 6 (6 H + 0 S) secondary structure elements in 1b5l, of which 6 satisfy the size requirements. There are 8 (6 H + 2 S) secondary structure elements in 1hul_A, of which 7 satisfy the size requirements. 1.52480 [ 1.76579] ((1 . 1) (3 . 5) (4 . 6) (5 . 8)) 12.246 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.6558 [and 1/min{score2}: 0.5663] [293, 2295]: Comparing 1b5l and 1huw, based on their crossing files. There are 6 (6 H + 0 S) secondary structure elements in 1b5l, of which 6 satisfy the size requirements. There are 7 (7 H + 0 S) secondary structure elements in 1huw, of which 7 satisfy the size requirements. 1.50988 [ 1.75625] ((1 . 1) (3 . 4) (4 . 6) (5 . 7)) 9.693 {0/1:6} B:0 1.21490 [ 1.40946] ((1 . 1) (3 . 4) (4 . 6) (5 . 3) (6 . 7)) 9.106 {0/1:10} B:1 SIMILARITY (1/min{score1}): 0.8231 [and 1/min{score2}: 0.7095] [293, 2347]: Comparing 1b5l and 1hzi_A, based on their crossing files. There are 6 (6 H + 0 S) secondary structure elements in 1b5l, of which 6 satisfy the size requirements. There are 7 (5 H + 2 S) secondary structure elements in 1hzi_A, of which 6 satisfy the size requirements. 1.50099 [ 1.50099] ((1 . 1) (3 . 4) (4 . 5) (6 . 7)) 5.436 {0/1:6} B:0 1.52125 [ 1.52125] ((1 . 1) (3 . 4) (4 . 5) (5 . 7)) 11.771 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.6662 [and 1/min{score2}: 0.6662] [293, 2519]: Comparing 1b5l and 1ijz_A, based on their crossing files. There are 6 (6 H + 0 S) secondary structure elements in 1b5l, of which 6 satisfy the size requirements. There are 6 (4 H + 2 S) secondary structure elements in 1ijz_A, of which 6 satisfy the size requirements. 1.51132 [ 1.51132] ((1 . 1) (3 . 3) (4 . 4) (5 . 6)) 10.033 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.6617 [and 1/min{score2}: 0.6617] [293, 3698]: Comparing 1b5l and 1lqs_L, based on their crossing files. There are 6 (6 H + 0 S) secondary structure elements in 1b5l, of which 6 satisfy the size requirements. There are 9 (9 H + 0 S) secondary structure elements in 1lqs_L, of which 7 satisfy the size requirements. 1.53492 [ 1.77234] ((1 . 2) (3 . 3) (4 . 5) (5 . 7)) 13.374 {0/1:6} B:0 1.62889 [ 1.83573] ((1 . 2) (3 . 4) (4 . 5) (6 . 9)) 18.973 {0/1:6} B:0 5.01019 [ 5.01875] ((1 . 2) (2 . 3) (3 . 4) (4 . 5)) 7.551 {2/4:6} B:0 1.50967 [ 1.75611] ((1 . 2) (3 . 4) (4 . 5) (6 . 3)) 9.640 {0/1:6} B:1 SIMILARITY (1/min{score1}): 0.6624 [and 1/min{score2}: 0.5694] [293, 3830]: Comparing 1b5l and 1m48_A, based on their crossing files. There are 6 (6 H + 0 S) secondary structure elements in 1b5l, of which 6 satisfy the size requirements. There are 6 (6 H + 0 S) secondary structure elements in 1m48_A, of which 6 satisfy the size requirements. 1.51940 [ 1.51940] ((1 . 1) (3 . 4) (4 . 5) (5 . 6)) 11.502 {0/1:6} B:0 3.36779 [ 3.36779] ((1 . 1) (2 . 2) (3 . 4) (4 . 5)) 9.459 {1/3:6} B:0 5.01068 [ 5.01068] ((1 . 1) (2 . 2) (3 . 3) (4 . 5)) 11.807 {2/4:6} B:0 SIMILARITY (1/min{score1}): 0.6582 [and 1/min{score2}: 0.6582] [293, 3834]: Comparing 1b5l and 1m4r_A, based on their crossing files. There are 6 (6 H + 0 S) secondary structure elements in 1b5l, of which 6 satisfy the size requirements. There are 8 (8 H + 0 S) secondary structure elements in 1m4r_A, of which 7 satisfy the size requirements. 1.20368 [ 1.40232] ((1 . 2) (3 . 4) (4 . 5) (5 . 6) (6 . 7)) 6.396 {0/1:10} B:0 1.20524 [ 1.40331] ((1 . 2) (3 . 4) (4 . 5) (5 . 6) (6 . 8)) 6.992 {0/1:10} B:0 1.50256 [ 1.75162] ((3 . 4) (4 . 5) (5 . 6) (6 . 7)) 6.904 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.8308 [and 1/min{score2}: 0.7131] [293, 4104]: Comparing 1b5l and 1n1f_A, based on their crossing files. There are 6 (6 H + 0 S) secondary structure elements in 1b5l, of which 6 satisfy the size requirements. There are 9 (9 H + 0 S) secondary structure elements in 1n1f_A, of which 8 satisfy the size requirements. 1.51003 [ 2.00426] ((2 . 2) (3 . 3) (4 . 4) (5 . 6)) 9.731 {0/3:6} B:0 1.52137 [ 2.00915] ((1 . 4) (2 . 6) (3 . 7) (4 . 9)) 11.789 {0/2:6} B:0 2.51682 [ 2.55004] ((1 . 2) (2 . 3) (3 . 4) (4 . 6) (5 . 7) (6 . 9)) 7.984 {1/4:15} B:0 1.20418 [ 1.60177] ((1 . 2) (3 . 4) (4 . 6) (5 . 7) (6 . 3)) 6.603 {0/1:10} B:1 2.51647 [ 2.54970] ((1 . 3) (2 . 2) (3 . 4) (4 . 7) (5 . 6) (6 . 9)) 7.134 {1/4:15} B:2 SIMILARITY (1/min{score1}): 0.8304 [and 1/min{score2}: 0.6243] [293, 5789]: Comparing 1b5l and 1scf_A, based on their crossing files. There are 6 (6 H + 0 S) secondary structure elements in 1b5l, of which 6 satisfy the size requirements. There are 6 (4 H + 2 S) secondary structure elements in 1scf_A, of which 6 satisfy the size requirements. 1.51648 [ 1.51648] ((1 . 1) (3 . 3) (4 . 4) (5 . 6)) 11.034 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.6594 [and 1/min{score2}: 0.6594] [293, 6190]: Comparing 1b5l and 1v7m_V, based on their crossing files. There are 6 (6 H + 0 S) secondary structure elements in 1b5l, of which 6 satisfy the size requirements. There are 9 (7 H + 2 S) secondary structure elements in 1v7m_V, of which 8 satisfy the size requirements. 1.21985 [ 1.60852] ((1 . 1) (3 . 4) (4 . 6) (5 . 8) (6 . 9)) 9.799 {0/0:10} B:0 1.50050 [ 2.00021] ((1 . 1) (3 . 4) (4 . 6) (6 . 8)) 4.589 {0/0:6} B:0 7.50124 [ 7.50389] ((1 . 1) (2 . 3) (3 . 4) (4 . 6) (6 . 8)) 5.613 {3/4:10} B:0 SIMILARITY (1/min{score1}): 0.8198 [and 1/min{score2}: 0.6217] [293, 6461]: Comparing 1b5l and 2gmf_A, based on their crossing files. There are 6 (6 H + 0 S) secondary structure elements in 1b5l, of which 6 satisfy the size requirements. There are 7 (5 H + 2 S) secondary structure elements in 2gmf_A, of which 7 satisfy the size requirements. 5.01045 [ 5.01901] ((1 . 1) (2 . 2) (3 . 4) (4 . 5)) 10.407 {2/4:6} B:0 SIMILARITY (1/min{score1}): 0.1996 [and 1/min{score2}: 0.1992] [293, 6479]: Comparing 1b5l and 2ilk, based on their crossing files. There are 6 (6 H + 0 S) secondary structure elements in 1b5l, of which 6 satisfy the size requirements. There are 10 (10 H + 0 S) secondary structure elements in 2ilk, of which 9 satisfy the size requirements. 1.58382 [ 2.27652] ((1 . 1) (3 . 4) (4 . 6) (6 . 10)) 16.850 {0/1:6} B:0 1.62595 [ 2.29114] ((1 . 1) (3 . 5) (4 . 6) (6 . 10)) 18.850 {0/1:6} B:0 1.50352 [ 2.25105] ((1 . 1) (3 . 4) (4 . 6) (6 . 3)) 7.477 {0/1:6} B:1 10.00135 [10.00649] ((1 . 3) (3 . 5) (4 . 6) (6 . 4)) 12.349 {1/1:6} B:1 SIMILARITY (1/min{score1}): 0.6651 [and 1/min{score2}: 0.4442] -------------------------------------------------------------------------------------------------------------------------