------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [4374, 2013]: Comparing 1ns5_A and 1gz0_A, based on their crossing files. There are 11 (5 H + 6 S) secondary structure elements in 1ns5_A, of which 10 satisfy the size requirements. There are 23 (12 H + 11 S) secondary structure elements in 1gz0_A, of which 12 satisfy the size requirements. 1.28215 [ 1.51897] ((1 . 10) (2 . 11) (3 . 12) (5 . 17) (8 . 20) (9 . 21) (10 . 22) (11 . 23)) 2.634 {1/14:28} B:0 1.66676 [ 2.00005] ((1 . 10) (2 . 11) (3 . 12) (8 . 17) (9 . 21) (11 . 23)) 3.254 {0/4:15} B:0 1.83049 [ 1.89382] ((1 . 10) (2 . 11) (3 . 12) (4 . 16) (5 . 17) (8 . 20) (9 . 21) (10 . 22) (11 . 23)) 4.200 {3/17:36} B:0 2.00008 [ 2.40005] ((1 . 10) (2 . 11) (3 . 15) (5 . 17) (11 . 23)) 3.651 {0/5:10} B:0 2.00194 [ 2.40112] ((1 . 10) (3 . 12) (4 . 13) (5 . 15) (11 . 21)) 7.985 {0/4:10} B:0 SIMILARITY (1/min{score1}): 0.7927 [and 1/min{score2}: 0.7257] [4374, 2556]: Comparing 1ns5_A and 1ipa_A, based on their crossing files. There are 11 (5 H + 6 S) secondary structure elements in 1ns5_A, of which 10 satisfy the size requirements. There are 23 (12 H + 11 S) secondary structure elements in 1ipa_A, of which 12 satisfy the size requirements. 1.25004 [ 1.50003] ((1 . 11) (2 . 12) (3 . 13) (5 . 18) (8 . 20) (9 . 21) (10 . 22) (11 . 23)) 2.185 {0/12:28} B:0 1.47138 [ 1.58576] ((1 . 11) (2 . 12) (3 . 13) (4 . 17) (5 . 18) (8 . 20) (9 . 21) (10 . 22) (11 . 23)) 3.525 {2/15:36} B:0 1.66673 [ 2.00004] ((1 . 11) (2 . 12) (3 . 13) (8 . 18) (9 . 21) (11 . 23)) 2.941 {0/3:15} B:0 1.66692 [ 2.00014] ((1 . 11) (2 . 12) (3 . 13) (5 . 18) (8 . 22) (11 . 23)) 4.168 {0/6:15} B:0 1.68420 [ 1.80722] ((1 . 11) (2 . 12) (3 . 13) (4 . 17) (5 . 18) (8 . 20) (10 . 22) (11 . 23)) 3.587 {2/13:28} B:0 SIMILARITY (1/min{score1}): 0.8814 [and 1/min{score2}: 0.7423] [4374, 3162]: Comparing 1ns5_A and 1k3r_A, based on their crossing files. There are 11 (5 H + 6 S) secondary structure elements in 1ns5_A, of which 10 satisfy the size requirements. There are 18 (7 H + 11 S) secondary structure elements in 1k3r_A, of which 13 satisfy the size requirements. 1.11944 [ 1.44826] ((1 . 1) (2 . 2) (3 . 3) (4 . 13) (5 . 14) (7 . 15) (8 . 16) (10 . 17) (11 . 18)) 3.903 {1/22:36} B:0 1.25039 [ 1.62518] ((1 . 1) (2 . 2) (3 . 3) (4 . 13) (5 . 14) (8 . 16) (10 . 17) (11 . 18)) 3.750 {0/15:28} B:0 2.11933 [ 2.65744] ((3 . 12) (4 . 13) (5 . 14) (7 . 15) (11 . 18)) 4.970 {1/7:10} B:0 2.50025 [ 3.25011] ((5 . 1) (7 . 2) (8 . 3) (11 . 6)) 5.653 {0/4:6} B:0 2.50071 [ 3.25033] ((1 . 3) (4 . 6) (10 . 12) (11 . 13)) 7.356 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.8933 [and 1/min{score2}: 0.6905] [4374, 4073]: Comparing 1ns5_A and 1mxi_A, based on their crossing files. There are 11 (5 H + 6 S) secondary structure elements in 1ns5_A, of which 10 satisfy the size requirements. There are 14 (8 H + 6 S) secondary structure elements in 1mxi_A, of which 10 satisfy the size requirements. 1.36235 [ 1.36235] ((1 . 1) (2 . 2) (3 . 3) (4 . 7) (5 . 8) (8 . 10) (9 . 11) (11 . 14)) 3.827 {1/10:28} B:0 1.42860 [ 1.42860] ((1 . 1) (2 . 2) (3 . 3) (5 . 8) (8 . 10) (9 . 11) (11 . 14)) 2.247 {0/7:21} B:0 1.42877 [ 1.42877] ((1 . 1) (2 . 2) (3 . 3) (4 . 7) (5 . 8) (8 . 10) (11 . 14)) 3.497 {0/7:21} B:0 1.42901 [ 1.42901] ((1 . 1) (2 . 2) (3 . 6) (4 . 7) (5 . 8) (8 . 10) (11 . 14)) 4.271 {0/8:21} B:0 1.67314 [ 1.67314] ((1 . 3) (3 . 6) (4 . 7) (5 . 8) (7 . 11) (11 . 14)) 9.430 {0/8:15} B:0 SIMILARITY (1/min{score1}): 0.7643 [and 1/min{score2}: 0.7643] [4374, 4374]: Comparing 1ns5_A and 1ns5_A, based on their crossing files. There are 11 (5 H + 6 S) secondary structure elements in 1ns5_A, of which 10 satisfy the size requirements. There are 11 (5 H + 6 S) secondary structure elements in 1ns5_A, of which 10 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)) 0.000 {0/28:45} B:0 2.50058 [ 2.50058] ((2 . 4) (3 . 5) (5 . 10) (7 . 11)) 6.989 {0/4:6} B:0 2.50058 [ 2.50058] ((4 . 2) (5 . 3) (10 . 5) (11 . 7)) 6.989 {0/4:6} B:0 2.50081 [ 2.50081] ((1 . 3) (2 . 4) (3 . 5) (5 . 8)) 7.588 {0/2:6} B:0 2.50081 [ 2.50081] ((3 . 1) (4 . 2) (5 . 3) (8 . 5)) 7.588 {0/2:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [4374, 4510]: Comparing 1ns5_A and 1o6d_A, based on their crossing files. There are 11 (5 H + 6 S) secondary structure elements in 1ns5_A, of which 10 satisfy the size requirements. There are 11 (5 H + 6 S) secondary structure elements in 1o6d_A, of which 11 satisfy the size requirements. 1.01057 [ 1.10798] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11)) 2.030 {1/22:45} B:0 1.15582 [ 1.25644] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (8 . 8) (9 . 9) (10 . 10) (11 . 11)) 2.004 {1/14:36} B:0 2.50013 [ 2.75010] ((1 . 8) (2 . 9) (3 . 10) (4 . 11)) 4.822 {0/2:6} B:0 2.50063 [ 2.75047] ((4 . 2) (5 . 3) (10 . 5) (11 . 7)) 7.117 {0/3:6} B:0 2.50074 [ 2.75055] ((1 . 5) (3 . 8) (5 . 10) (7 . 11)) 7.410 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.9895 [and 1/min{score2}: 0.9025] [4374, 4824]: Comparing 1ns5_A and 1oy5_A, based on their crossing files. There are 11 (5 H + 6 S) secondary structure elements in 1ns5_A, of which 10 satisfy the size requirements. There are 20 (11 H + 9 S) secondary structure elements in 1oy5_A, of which 12 satisfy the size requirements. 1.14586 [ 1.35392] ((1 . 1) (2 . 2) (3 . 4) (4 . 8) (5 . 9) (7 . 10) (8 . 11) (9 . 12) (11 . 14)) 3.493 {1/15:36} B:0 1.29272 [ 1.52537] ((1 . 1) (3 . 4) (4 . 8) (5 . 9) (7 . 10) (8 . 11) (9 . 12) (11 . 14)) 2.949 {1/13:28} B:0 1.48684 [ 1.65533] ((1 . 1) (2 . 3) (3 . 4) (4 . 8) (5 . 9) (8 . 11) (9 . 12) (11 . 14)) 4.125 {1/8:28} B:0 1.54454 [ 1.78546] ((1 . 4) (4 . 8) (5 . 9) (7 . 10) (8 . 11) (9 . 12) (11 . 14)) 3.405 {1/9:21} B:0 1.54472 [ 1.64543] ((1 . 1) (2 . 3) (3 . 4) (4 . 8) (5 . 9) (7 . 10) (8 . 11) (9 . 12) (11 . 14)) 4.194 {2/14:36} B:0 SIMILARITY (1/min{score1}): 0.8727 [and 1/min{score2}: 0.7386] [4374, 5949]: Comparing 1ns5_A and 1ual_A, based on their crossing files. There are 11 (5 H + 6 S) secondary structure elements in 1ns5_A, of which 10 satisfy the size requirements. There are 21 (11 H + 10 S) secondary structure elements in 1ual_A, of which 15 satisfy the size requirements. 1.00937 [ 1.50281] ((1 . 1) (2 . 2) (3 . 4) (4 . 8) (5 . 9) (7 . 11) (8 . 12) (9 . 13) (10 . 14) (11 . 15)) 3.495 {1/23:45} B:0 1.42870 [ 2.14290] ((1 . 4) (4 . 8) (5 . 9) (7 . 11) (8 . 12) (10 . 14) (11 . 15)) 3.154 {0/13:21} B:0 2.00085 [ 3.00025] ((1 . 4) (4 . 8) (5 . 10) (7 . 11) (11 . 15)) 6.493 {0/6:10} B:0 2.00492 [ 3.00146] ((1 . 1) (2 . 2) (3 . 4) (7 . 8) (11 . 15)) 10.087 {0/2:10} B:0 2.37894 [ 3.13852] ((1 . 9) (2 . 11) (3 . 12) (4 . 13) (5 . 14)) 6.560 {1/5:10} B:0 SIMILARITY (1/min{score1}): 0.9907 [and 1/min{score2}: 0.6654] [4374, 6158]: Comparing 1ns5_A and 1v2x_A, based on their crossing files. There are 11 (5 H + 6 S) secondary structure elements in 1ns5_A, of which 10 satisfy the size requirements. There are 16 (9 H + 7 S) secondary structure elements in 1v2x_A, of which 12 satisfy the size requirements. 1.28255 [ 1.51921] ((1 . 2) (2 . 3) (3 . 4) (4 . 8) (5 . 9) (8 . 12) (10 . 14) (11 . 15)) 4.044 {1/14:28} B:0 1.41154 [ 1.53875] ((1 . 2) (2 . 3) (3 . 4) (4 . 8) (5 . 9) (8 . 12) (9 . 13) (10 . 14) (11 . 15)) 4.095 {2/16:36} B:0 1.66672 [ 2.00003] ((1 . 2) (2 . 3) (3 . 4) (8 . 9) (9 . 13) (11 . 15)) 2.878 {0/3:15} B:0 1.66701 [ 2.00020] ((1 . 2) (2 . 3) (3 . 7) (4 . 8) (5 . 9) (11 . 15)) 4.513 {0/7:15} B:0 2.00088 [ 2.40051] ((3 . 2) (4 . 3) (5 . 4) (7 . 8) (11 . 13)) 6.553 {0/1:10} B:0 SIMILARITY (1/min{score1}): 0.8985 [and 1/min{score2}: 0.7494] [4374, 6227]: Comparing 1ns5_A and 1vh0_A, based on their crossing files. There are 11 (5 H + 6 S) secondary structure elements in 1ns5_A, of which 10 satisfy the size requirements. There are 11 (5 H + 6 S) secondary structure elements in 1vh0_A, of which 10 satisfy the size requirements. 1.00642 [ 1.00642] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11)) 2.164 {1/25:45} B:0 1.12037 [ 1.12037] ((1 . 1) (2 . 2) (3 . 3) (5 . 5) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11)) 1.253 {1/21:36} B:0 2.00108 [ 2.00108] ((2 . 4) (3 . 5) (4 . 7) (5 . 8) (8 . 10)) 6.905 {0/2:10} B:0 2.00357 [ 2.00357] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (11 . 9)) 9.307 {0/2:10} B:0 2.00814 [ 2.00814] ((3 . 1) (4 . 2) (7 . 4) (8 . 5) (11 . 7)) 11.449 {0/3:10} B:0 SIMILARITY (1/min{score1}): 0.9936 [and 1/min{score2}: 0.9936] [4374, 6237]: Comparing 1ns5_A and 1vhk_A, based on their crossing files. There are 11 (5 H + 6 S) secondary structure elements in 1ns5_A, of which 10 satisfy the size requirements. There are 19 (8 H + 11 S) secondary structure elements in 1vhk_A, of which 11 satisfy the size requirements. 1.66675 [ 1.83340] ((1 . 10) (5 . 14) (7 . 15) (8 . 16) (10 . 18) (11 . 19)) 3.209 {0/9:15} B:0 1.67469 [ 1.83937] ((1 . 8) (2 . 9) (3 . 10) (4 . 11) (8 . 16) (11 . 19)) 9.950 {0/2:15} B:0 1.67732 [ 1.84136] ((1 . 8) (2 . 9) (3 . 10) (4 . 11) (8 . 14) (11 . 19)) 10.688 {0/3:15} B:0 1.85853 [ 1.87635] ((1 . 8) (2 . 9) (3 . 10) (4 . 13) (5 . 14) (7 . 15) (8 . 16) (9 . 17) (10 . 18) (11 . 19)) 3.685 {4/22:45} B:0 2.00331 [ 2.20249] ((1 . 10) (2 . 11) (5 . 16) (7 . 17) (11 . 19)) 9.131 {0/4:10} B:0 SIMILARITY (1/min{score1}): 0.8883 [and 1/min{score2}: 0.8108] [4374, 6251]: Comparing 1ns5_A and 1vhy_A, based on their crossing files. There are 11 (5 H + 6 S) secondary structure elements in 1ns5_A, of which 10 satisfy the size requirements. There are 21 (8 H + 13 S) secondary structure elements in 1vhy_A, of which 10 satisfy the size requirements. 1.25007 [ 1.25007] ((1 . 8) (2 . 9) (3 . 10) (5 . 15) (8 . 17) (9 . 18) (10 . 19) (11 . 20)) 2.462 {0/13:28} B:0 1.41132 [ 1.41132] ((1 . 8) (2 . 9) (3 . 10) (4 . 14) (5 . 15) (8 . 17) (9 . 18) (10 . 19) (11 . 20)) 3.269 {2/16:36} B:0 1.67359 [ 1.67359] ((1 . 8) (2 . 9) (3 . 10) (4 . 11) (8 . 15) (11 . 20)) 9.588 {0/2:15} B:0 2.00360 [ 2.00360] ((3 . 8) (4 . 9) (5 . 10) (9 . 14) (11 . 18)) 9.325 {0/2:10} B:0 2.00509 [ 2.00509] ((1 . 8) (2 . 9) (3 . 10) (4 . 11) (11 . 18)) 10.174 {0/0:10} B:0 SIMILARITY (1/min{score1}): 0.8000 [and 1/min{score2}: 0.8000] -------------------------------------------------------------------------------------------------------------------------