------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [230, 230]: Comparing 1axc_A and 1axc_A, based on their crossing files. There are 24 (5 H + 19 S) secondary structure elements in 1axc_A, of which 12 satisfy the size requirements. There are 24 (5 H + 19 S) secondary structure elements in 1axc_A, of which 12 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (13 . 13)) 0.000 {0/52:66} B:0 3.00035 [ 3.00035] ((1 . 1) (2 . 2) (7 . 8) (9 . 9)) 7.073 {0/5:6} B:0 3.00035 [ 3.00035] ((1 . 1) (2 . 2) (8 . 7) (9 . 9)) 7.073 {0/5:6} B:0 3.00042 [ 3.00042] ((3 . 4) (4 . 5) (10 . 11) (11 . 12)) 7.395 {0/4:6} B:0 3.00042 [ 3.00042] ((4 . 3) (5 . 4) (11 . 10) (12 . 11)) 7.395 {0/4:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [230, 231]: Comparing 1axc_A and 1axc_A, based on their crossing files. There are 24 (5 H + 19 S) secondary structure elements in 1axc_A, of which 12 satisfy the size requirements. There are 24 (5 H + 19 S) secondary structure elements in 1axc_A, of which 11 satisfy the size requirements. 1.20003 [ 1.10004] ((1 . 14) (2 . 15) (3 . 16) (4 . 17) (5 . 18) (8 . 20) (9 . 21) (10 . 22) (11 . 23) (12 . 24)) 1.929 {0/32:45} B:0 3.00022 [ 2.75028] ((5 . 20) (8 . 22) (10 . 23) (11 . 24)) 6.272 {0/4:6} B:0 3.00028 [ 2.75036] ((5 . 14) (8 . 16) (10 . 17) (11 . 18)) 6.643 {0/4:6} B:0 3.00045 [ 2.75059] ((3 . 17) (4 . 18) (10 . 23) (11 . 24)) 7.523 {0/4:6} B:0 3.00047 [ 2.75061] ((4 . 16) (5 . 17) (11 . 22) (12 . 23)) 7.598 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.8333 [and 1/min{score2}: 0.9091] [230, 309]: Comparing 1axc_A and 1b77_A, based on their crossing files. There are 24 (5 H + 19 S) secondary structure elements in 1axc_A, of which 12 satisfy the size requirements. There are 21 (5 H + 16 S) secondary structure elements in 1b77_A, of which 9 satisfy the size requirements. 1.33349 [ 1.00038] ((2 . 1) (3 . 2) (4 . 3) (5 . 4) (8 . 5) (9 . 6) (10 . 7) (11 . 8) (12 . 9)) 3.152 {0/25:36} B:0 3.00007 [ 2.25018] ((2 . 1) (5 . 2) (9 . 6) (12 . 9)) 4.788 {0/2:6} B:0 3.00022 [ 2.25052] ((9 . 1) (10 . 3) (11 . 4) (12 . 5)) 6.265 {0/1:6} B:0 3.00023 [ 2.25054] ((8 . 4) (10 . 5) (11 . 7) (12 . 8)) 6.325 {0/4:6} B:0 3.00084 [ 2.25199] ((3 . 4) (4 . 5) (7 . 7) (10 . 9)) 8.782 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.7499 [and 1/min{score2}: 0.9996] [230, 310]: Comparing 1axc_A and 1b77_A, based on their crossing files. There are 24 (5 H + 19 S) secondary structure elements in 1axc_A, of which 12 satisfy the size requirements. There are 21 (5 H + 16 S) secondary structure elements in 1b77_A, of which 9 satisfy the size requirements. 1.33370 [ 1.00088] ((1 . 11) (2 . 12) (3 . 13) (4 . 14) (5 . 15) (8 . 16) (10 . 18) (11 . 19) (12 . 20)) 3.894 {0/27:36} B:0 1.50017 [ 1.12539] ((1 . 11) (2 . 12) (3 . 13) (4 . 14) (8 . 16) (10 . 18) (11 . 19) (12 . 20)) 3.476 {0/21:28} B:0 2.00038 [ 1.50091] ((1 . 13) (3 . 14) (8 . 15) (10 . 16) (11 . 18) (12 . 19)) 5.327 {0/9:15} B:0 3.00005 [ 2.25012] ((8 . 15) (10 . 16) (11 . 18) (12 . 19)) 4.330 {0/4:6} B:0 3.00020 [ 2.25048] ((4 . 13) (8 . 15) (11 . 18) (12 . 19)) 6.161 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.7498 [and 1/min{score2}: 0.9991] [230, 883]: Comparing 1axc_A and 1dml_A, based on their crossing files. There are 24 (5 H + 19 S) secondary structure elements in 1axc_A, of which 12 satisfy the size requirements. There are 25 (4 H + 21 S) secondary structure elements in 1dml_A, of which 12 satisfy the size requirements. 1.09228 [ 1.09228] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 7) (8 . 8) (10 . 11) (11 . 12) (12 . 13) (13 . 14)) 3.916 {1/41:55} B:0 2.47216 [ 2.47216] ((1 . 1) (2 . 2) (8 . 9) (10 . 11) (11 . 12)) 4.880 {1/7:10} B:0 2.52882 [ 2.52882] ((8 . 1) (9 . 2) (10 . 3) (11 . 4) (12 . 5)) 3.282 {1/6:10} B:0 3.00013 [ 3.00013] ((1 . 9) (3 . 11) (4 . 12) (7 . 13)) 5.484 {0/2:6} B:0 3.00018 [ 3.00018] ((1 . 3) (4 . 7) (8 . 11) (11 . 13)) 5.986 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.9155 [and 1/min{score2}: 0.9155] [230, 884]: Comparing 1axc_A and 1dml_A, based on their crossing files. There are 24 (5 H + 19 S) secondary structure elements in 1axc_A, of which 12 satisfy the size requirements. There are 25 (4 H + 21 S) secondary structure elements in 1dml_A, of which 11 satisfy the size requirements. 1.09141 [ 1.00064] ((1 . 15) (2 . 16) (3 . 17) (4 . 18) (5 . 19) (7 . 20) (8 . 21) (9 . 22) (10 . 23) (11 . 24) (12 . 25)) 3.606 {0/39:55} B:0 2.40062 [ 2.20080] ((3 . 18) (4 . 19) (7 . 21) (10 . 24) (11 . 25)) 6.874 {0/5:10} B:0 2.40238 [ 2.20308] ((4 . 17) (5 . 18) (8 . 20) (10 . 21) (13 . 24)) 9.636 {0/7:10} B:0 3.00031 [ 2.75041] ((7 . 15) (8 . 17) (10 . 18) (11 . 19)) 6.861 {0/1:6} B:0 3.00032 [ 2.75041] ((3 . 15) (8 . 20) (10 . 21) (11 . 23)) 6.881 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.9162 [and 1/min{score2}: 0.9994] [230, 2675]: Comparing 1axc_A and 1iz5_A, based on their crossing files. There are 24 (5 H + 19 S) secondary structure elements in 1axc_A, of which 12 satisfy the size requirements. There are 23 (5 H + 18 S) secondary structure elements in 1iz5_A, of which 11 satisfy the size requirements. 1.09092 [ 1.00001] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12)) 1.317 {0/39:55} B:0 3.00028 [ 2.75036] ((5 . 1) (8 . 3) (10 . 4) (11 . 5)) 6.678 {0/5:6} B:0 3.00030 [ 2.75039] ((1 . 5) (3 . 8) (4 . 10) (5 . 11)) 6.811 {0/4:6} B:0 3.00040 [ 2.75051] ((4 . 3) (5 . 4) (11 . 10) (12 . 11)) 7.272 {0/4:6} B:0 3.00055 [ 2.75071] ((4 . 3) (5 . 4) (8 . 5) (11 . 10)) 7.891 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.9167 [and 1/min{score2}: 0.9999] [230, 2676]: Comparing 1axc_A and 1iz5_A, based on their crossing files. There are 24 (5 H + 19 S) secondary structure elements in 1axc_A, of which 12 satisfy the size requirements. There are 23 (5 H + 18 S) secondary structure elements in 1iz5_A, of which 11 satisfy the size requirements. 1.09095 [ 1.00005] ((1 . 13) (2 . 14) (3 . 15) (4 . 16) (5 . 17) (7 . 18) (8 . 19) (9 . 20) (10 . 21) (11 . 22) (12 . 23)) 1.917 {0/40:55} B:0 2.00066 [ 1.83418] ((8 . 13) (9 . 14) (10 . 15) (11 . 16) (12 . 17) (13 . 18)) 6.089 {0/10:15} B:0 3.00005 [ 2.75007] ((1 . 13) (2 . 14) (9 . 20) (11 . 23)) 4.410 {0/3:6} B:0 3.00036 [ 2.75047] ((3 . 16) (4 . 17) (10 . 22) (11 . 23)) 7.108 {0/4:6} B:0 3.00040 [ 2.75052] ((4 . 15) (5 . 16) (11 . 21) (12 . 22)) 7.290 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.9166 [and 1/min{score2}: 0.9999] [230, 3977]: Comparing 1axc_A and 1mmi_A, based on their crossing files. There are 24 (5 H + 19 S) secondary structure elements in 1axc_A, of which 12 satisfy the size requirements. There are 35 (11 H + 24 S) secondary structure elements in 1mmi_A, of which 10 satisfy the size requirements. 1.20129 [ 1.00223] ((1 . 1) (2 . 2) (3 . 4) (4 . 5) (5 . 6) (8 . 7) (9 . 8) (10 . 9) (11 . 10) (12 . 11)) 2.424 {1/33:45} B:0 3.00021 [ 2.50037] ((1 . 6) (3 . 7) (4 . 9) (5 . 10)) 6.244 {0/4:6} B:0 3.00061 [ 2.50106] ((3 . 5) (4 . 6) (5 . 7) (8 . 9)) 8.112 {0/3:6} B:0 3.00077 [ 2.50132] ((3 . 6) (4 . 7) (7 . 9) (10 . 11)) 8.583 {0/4:6} B:0 3.00087 [ 2.50150] ((5 . 1) (10 . 5) (11 . 6) (12 . 7)) 8.849 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.8324 [and 1/min{score2}: 0.9978] [230, 3978]: Comparing 1axc_A and 1mmi_A, based on their crossing files. There are 24 (5 H + 19 S) secondary structure elements in 1axc_A, of which 12 satisfy the size requirements. There are 35 (11 H + 24 S) secondary structure elements in 1mmi_A, of which 10 satisfy the size requirements. 1.20021 [ 1.00037] ((1 . 13) (2 . 14) (3 . 17) (4 . 18) (5 . 19) (8 . 20) (9 . 21) (10 . 22) (11 . 23) (12 . 24)) 3.135 {0/31:45} B:0 2.91625 [ 2.72512] ((9 . 14) (10 . 17) (11 . 18) (12 . 19) (13 . 20)) 8.687 {1/4:10} B:0 3.00019 [ 2.50034] ((3 . 18) (4 . 19) (10 . 23) (11 . 24)) 6.094 {0/4:6} B:0 3.00042 [ 2.50072] ((3 . 18) (4 . 19) (5 . 20) (8 . 22)) 7.376 {0/2:6} B:0 3.00068 [ 2.50117] ((3 . 19) (4 . 20) (7 . 22) (10 . 24)) 8.327 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.8332 [and 1/min{score2}: 0.9997] [230, 3979]: Comparing 1axc_A and 1mmi_A, based on their crossing files. There are 24 (5 H + 19 S) secondary structure elements in 1axc_A, of which 12 satisfy the size requirements. There are 35 (11 H + 24 S) secondary structure elements in 1mmi_A, of which 10 satisfy the size requirements. 1.20003 [ 1.00005] ((1 . 26) (2 . 27) (3 . 28) (4 . 29) (5 . 30) (8 . 31) (9 . 32) (10 . 33) (11 . 34) (12 . 35)) 1.920 {0/31:45} B:0 3.00016 [ 2.50027] ((8 . 30) (10 . 31) (11 . 33) (12 . 34)) 5.765 {0/4:6} B:0 3.00020 [ 2.50035] ((1 . 30) (3 . 31) (4 . 33) (5 . 34)) 6.172 {0/4:6} B:0 3.00028 [ 2.50049] ((3 . 29) (4 . 30) (10 . 34) (11 . 35)) 6.677 {0/3:6} B:0 3.00034 [ 2.50059] ((3 . 26) (7 . 29) (10 . 31) (13 . 34)) 7.008 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.8333 [and 1/min{score2}: 0.9999] [230, 5047]: Comparing 1axc_A and 1plq, based on their crossing files. There are 24 (5 H + 19 S) secondary structure elements in 1axc_A, of which 12 satisfy the size requirements. There are 24 (6 H + 18 S) secondary structure elements in 1plq, of which 10 satisfy the size requirements. 1.20000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12)) 1.010 {0/33:45} B:0 2.40088 [ 2.00151] ((3 . 4) (4 . 5) (5 . 8) (10 . 11) (11 . 12)) 7.509 {0/7:10} B:0 2.40343 [ 2.00591] ((1 . 1) (2 . 2) (8 . 8) (9 . 9) (13 . 12)) 10.563 {0/9:10} B:0 3.00034 [ 2.50059] ((4 . 1) (7 . 3) (10 . 5) (13 . 10)) 7.017 {0/4:6} B:0 3.00071 [ 2.50123] ((3 . 5) (4 . 8) (7 . 10) (10 . 12)) 8.426 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.8333 [and 1/min{score2}: 0.9999] [230, 5048]: Comparing 1axc_A and 1plq, based on their crossing files. There are 24 (5 H + 19 S) secondary structure elements in 1axc_A, of which 12 satisfy the size requirements. There are 24 (6 H + 18 S) secondary structure elements in 1plq, of which 11 satisfy the size requirements. 1.09095 [ 1.00006] ((1 . 13) (2 . 14) (3 . 15) (4 . 16) (5 . 17) (7 . 19) (8 . 20) (9 . 21) (10 . 22) (11 . 23) (12 . 24)) 1.964 {0/39:55} B:0 2.00057 [ 1.83407] ((8 . 13) (9 . 14) (10 . 15) (11 . 16) (12 . 17) (13 . 19)) 5.873 {0/10:15} B:0 3.00023 [ 2.75030] ((5 . 13) (8 . 15) (10 . 16) (11 . 17)) 6.371 {0/4:6} B:0 3.00037 [ 2.75049] ((3 . 16) (4 . 17) (10 . 23) (11 . 24)) 7.175 {0/4:6} B:0 3.00044 [ 2.75057] ((4 . 15) (5 . 16) (8 . 19) (12 . 23)) 7.474 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.9166 [and 1/min{score2}: 0.9999] [230, 5717]: Comparing 1axc_A and 1rwz_A, based on their crossing files. There are 24 (5 H + 19 S) secondary structure elements in 1axc_A, of which 12 satisfy the size requirements. There are 25 (7 H + 18 S) secondary structure elements in 1rwz_A, of which 11 satisfy the size requirements. 1.09093 [ 1.00002] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12)) 1.557 {0/40:55} B:0 2.91563 [ 2.81186] ((1 . 7) (2 . 9) (3 . 10) (4 . 11) (5 . 12)) 6.382 {1/4:10} B:0 3.00005 [ 2.75006] ((1 . 1) (2 . 2) (9 . 9) (11 . 12)) 4.308 {0/3:6} B:0 3.00028 [ 2.75037] ((5 . 1) (8 . 3) (10 . 4) (11 . 5)) 6.683 {0/4:6} B:0 3.00031 [ 2.75040] ((3 . 4) (4 . 5) (10 . 11) (11 . 12)) 6.842 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.9167 [and 1/min{score2}: 0.9999] [230, 5718]: Comparing 1axc_A and 1rwz_A, based on their crossing files. There are 24 (5 H + 19 S) secondary structure elements in 1axc_A, of which 12 satisfy the size requirements. There are 25 (7 H + 18 S) secondary structure elements in 1rwz_A, of which 10 satisfy the size requirements. 1.20002 [ 1.00003] ((1 . 14) (2 . 15) (3 . 16) (4 . 17) (5 . 18) (8 . 21) (9 . 22) (10 . 23) (11 . 24) (12 . 25)) 1.637 {0/34:45} B:0 2.40073 [ 2.00126] ((3 . 17) (4 . 18) (5 . 21) (10 . 24) (11 . 25)) 7.169 {0/7:10} B:0 3.00058 [ 2.50100] ((7 . 14) (10 . 17) (11 . 18) (12 . 21)) 7.995 {0/2:6} B:0 3.00059 [ 2.50102] ((7 . 14) (8 . 16) (10 . 17) (11 . 18)) 8.050 {0/2:6} B:0 3.00073 [ 2.50126] ((3 . 18) (4 . 21) (7 . 23) (10 . 25)) 8.481 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.8333 [and 1/min{score2}: 0.9999] -------------------------------------------------------------------------------------------------------------------------