------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [6058, 1849]: Comparing 1un7_A and 1gkp_A, based on their crossing files. There are 38 (15 H + 23 S) secondary structure elements in 1un7_A, of which 10 satisfy the size requirements. There are 41 (18 H + 23 S) secondary structure elements in 1gkp_A, of which 10 satisfy the size requirements. 1.12583 [ 1.12583] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (36 . 35) (37 . 39) (38 . 40)) 2.254 {3/34:45} B:0 1.16234 [ 1.16234] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (6 . 6) (7 . 7) (36 . 35) (37 . 39) (38 . 40)) 1.588 {2/27:36} B:0 5.07639 [ 5.07639] ((1 . 6) (2 . 7) (36 . 35) (38 . 39)) 5.927 {2/4:6} B:0 6.04473 [ 6.04473] ((3 . 2) (5 . 4) (6 . 6) (7 . 7)) 5.916 {3/5:6} B:0 SIMILARITY (1/min{score1}): 0.8882 [and 1/min{score2}: 0.8882] [6058, 1851]: Comparing 1un7_A and 1gkr_A, based on their crossing files. There are 38 (15 H + 23 S) secondary structure elements in 1un7_A, of which 10 satisfy the size requirements. There are 40 (18 H + 22 S) secondary structure elements in 1gkr_A, of which 10 satisfy the size requirements. 1.30676 [ 1.30676] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (36 . 34) (37 . 38) (38 . 39)) 2.037 {4/34:45} B:0 1.34749 [ 1.34749] ((1 . 1) (2 . 2) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (36 . 34) (37 . 38) (38 . 39)) 1.901 {3/26:36} B:0 1.64536 [ 1.64536] ((1 . 1) (2 . 2) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (38 . 34)) 3.889 {2/15:21} B:0 2.72641 [ 2.72641] ((3 . 2) (5 . 4) (6 . 5) (38 . 34)) 10.588 {1/5:6} B:0 4.14518 [ 4.14518] ((3 . 2) (4 . 3) (5 . 4) (38 . 34)) 10.366 {2/5:6} B:0 SIMILARITY (1/min{score1}): 0.7653 [and 1/min{score2}: 0.7653] [6058, 3194]: Comparing 1un7_A and 1k6w_A, based on their crossing files. There are 38 (15 H + 23 S) secondary structure elements in 1un7_A, of which 10 satisfy the size requirements. There are 35 (17 H + 18 S) secondary structure elements in 1k6w_A, of which 11 satisfy the size requirements. 1.25795 [ 1.38099] ((1 . 1) (4 . 2) (5 . 3) (6 . 4) (7 . 5) (36 . 30) (37 . 32) (38 . 33)) 1.867 {1/20:28} B:0 2.50190 [ 2.75143] ((2 . 32) (3 . 33) (4 . 34) (5 . 35)) 9.395 {0/3:6} B:0 2.97404 [ 3.13311] ((1 . 3) (3 . 4) (36 . 32) (37 . 33)) 9.155 {1/4:6} B:0 3.57052 [ 3.66618] ((1 . 5) (6 . 30) (37 . 32) (38 . 33)) 4.827 {1/3:6} B:0 3.57087 [ 3.66650] ((4 . 1) (5 . 2) (6 . 3) (38 . 30)) 8.271 {1/3:6} B:0 SIMILARITY (1/min{score1}): 0.7949 [and 1/min{score2}: 0.7241] [6058, 3268]: Comparing 1un7_A and 1kcx_A, based on their crossing files. There are 38 (15 H + 23 S) secondary structure elements in 1un7_A, of which 10 satisfy the size requirements. There are 40 (18 H + 22 S) secondary structure elements in 1kcx_A, of which 13 satisfy the size requirements. 1.02566 [ 1.31197] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (36 . 34) (37 . 37) (38 . 38)) 1.293 {2/35:45} B:0 2.50139 [ 3.25063] ((2 . 34) (3 . 35) (6 . 37) (7 . 38)) 8.687 {0/2:6} B:0 3.57053 [ 3.91545] ((1 . 34) (2 . 35) (4 . 37) (6 . 38)) 5.033 {1/3:6} B:0 5.07640 [ 5.20962] ((1 . 34) (2 . 35) (5 . 36) (6 . 38)) 6.199 {2/4:6} B:0 6.01844 [ 6.05222] ((1 . 34) (2 . 35) (3 . 36) (4 . 37) (6 . 38)) 4.933 {3/5:10} B:0 SIMILARITY (1/min{score1}): 0.9750 [and 1/min{score2}: 0.7622] [6058, 4467]: Comparing 1un7_A and 1o12_A, based on their crossing files. There are 38 (15 H + 23 S) secondary structure elements in 1un7_A, of which 10 satisfy the size requirements. There are 32 (11 H + 21 S) secondary structure elements in 1o12_A, of which 8 satisfy the size requirements. 1.25003 [ 1.00007] ((2 . 1) (3 . 2) (4 . 3) (5 . 4) (7 . 5) (36 . 30) (37 . 31) (38 . 32)) 2.038 {0/22:28} B:0 1.25021 [ 1.00042] ((1 . 1) (3 . 2) (4 . 3) (5 . 4) (7 . 5) (36 . 30) (37 . 31) (38 . 32)) 3.236 {0/22:28} B:0 2.50174 [ 2.00339] ((3 . 1) (5 . 3) (36 . 31) (37 . 32)) 9.185 {0/5:6} B:0 2.72409 [ 2.37848] ((3 . 2) (4 . 3) (5 . 4) (36 . 32)) 3.924 {1/5:6} B:0 2.97310 [ 2.72415] ((5 . 1) (36 . 30) (37 . 31) (38 . 32)) 4.882 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.8000 [and 1/min{score2}: 0.9999] [6058, 4734]: Comparing 1un7_A and 1onw_A, based on their crossing files. There are 38 (15 H + 23 S) secondary structure elements in 1un7_A, of which 10 satisfy the size requirements. There are 34 (15 H + 19 S) secondary structure elements in 1onw_A, of which 10 satisfy the size requirements. 1.00149 [ 1.00149] ((1 . 2) (2 . 3) (3 . 4) (4 . 5) (5 . 6) (6 . 7) (7 . 8) (36 . 31) (37 . 32) (38 . 33)) 0.629 {1/36:45} B:0 2.50020 [ 2.50020] ((4 . 3) (5 . 4) (36 . 32) (37 . 33)) 5.351 {0/4:6} B:0 2.97303 [ 2.97303] ((5 . 2) (36 . 31) (37 . 32) (38 . 33)) 2.776 {1/4:6} B:0 5.07642 [ 5.07642] ((6 . 3) (7 . 4) (37 . 31) (38 . 32)) 6.679 {2/4:6} B:0 5.07643 [ 5.07643] ((1 . 4) (2 . 5) (3 . 6) (5 . 7)) 7.040 {2/4:6} B:0 SIMILARITY (1/min{score1}): 0.9985 [and 1/min{score2}: 0.9985] [6058, 4865]: Comparing 1un7_A and 1p1m_A, based on their crossing files. There are 38 (15 H + 23 S) secondary structure elements in 1un7_A, of which 10 satisfy the size requirements. There are 34 (18 H + 16 S) secondary structure elements in 1p1m_A, of which 9 satisfy the size requirements. 1.42863 [ 1.28579] ((1 . 1) (4 . 2) (5 . 3) (7 . 5) (36 . 29) (37 . 32) (38 . 33)) 2.545 {0/16:21} B:0 1.42882 [ 1.28605] ((2 . 1) (4 . 2) (5 . 3) (7 . 5) (36 . 29) (37 . 32) (38 . 33)) 3.705 {0/15:21} B:0 2.97317 [ 2.83621] ((1 . 1) (2 . 2) (3 . 3) (36 . 5)) 5.700 {1/4:6} B:0 2.97320 [ 2.83625] ((1 . 1) (2 . 2) (3 . 3) (36 . 33)) 5.985 {1/4:6} B:0 2.97363 [ 2.83674] ((2 . 2) (4 . 3) (36 . 32) (37 . 33)) 8.048 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.7000 [and 1/min{score2}: 0.7777] [6058, 6058]: Comparing 1un7_A and 1un7_A, based on their crossing files. There are 38 (15 H + 23 S) secondary structure elements in 1un7_A, of which 10 satisfy the size requirements. There are 38 (15 H + 23 S) secondary structure elements in 1un7_A, of which 10 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (36 . 36) (37 . 37) (38 . 38)) 0.000 {0/37:45} B:0 6.69940 [ 6.69940] ((4 . 1) (5 . 2) (6 . 4) (7 . 5)) 5.950 {2/3:6} B:0 6.69940 [ 6.69940] ((1 . 4) (2 . 5) (4 . 6) (5 . 7)) 5.950 {2/3:6} B:0 6.00283 [ 6.00283] ((1 . 37) (2 . 5) (4 . 36) (5 . 7) (6 . 38) (7 . 4) (36 . 1) (37 . 6)) 4.230 {12/20:28} B:4 7.00179 [ 7.00179] ((1 . 37) (2 . 5) (4 . 36) (5 . 7) (6 . 38) (7 . 4) (36 . 1) (38 . 6)) 5.828 {14/20:28} B:4 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [6058, 6619]: Comparing 1un7_A and 4ubp_C, based on their crossing files. There are 38 (15 H + 23 S) secondary structure elements in 1un7_A, of which 10 satisfy the size requirements. There are 47 (21 H + 26 S) secondary structure elements in 4ubp_C, of which 16 satisfy the size requirements. 1.02568 [ 1.60648] ((1 . 5) (2 . 6) (3 . 7) (4 . 8) (5 . 9) (6 . 10) (7 . 11) (36 . 33) (37 . 35) (38 . 36)) 1.703 {2/35:45} B:0 1.11455 [ 1.77862] ((1 . 5) (2 . 6) (4 . 8) (5 . 9) (6 . 10) (7 . 11) (36 . 33) (37 . 35) (38 . 36)) 1.652 {1/27:36} B:0 2.50010 [ 4.00002] ((2 . 8) (36 . 35) (37 . 36) (38 . 37)) 4.518 {0/2:6} B:0 2.72639 [ 4.06179] ((3 . 6) (5 . 8) (6 . 9) (37 . 33)) 10.561 {1/5:6} B:0 2.81783 [ 3.20791] ((3 . 9) (6 . 10) (7 . 11) (36 . 33) (37 . 35) (38 . 36)) 4.500 {3/11:15} B:0 SIMILARITY (1/min{score1}): 0.9750 [and 1/min{score2}: 0.6225] -------------------------------------------------------------------------------------------------------------------------