------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [3358, 168]: Comparing 1kmv_A and 1aoe_A, based on their crossing files. There are 16 (5 H + 11 S) secondary structure elements in 1kmv_A, of which 13 satisfy the size requirements. There are 20 (8 H + 12 S) secondary structure elements in 1aoe_A, of which 16 satisfy the size requirements. 1.00016 [ 1.23085] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 7) (8 . 9) (9 . 10) (10 . 11) (11 . 12) (12 . 13) (15 . 19) (16 . 20)) 1.412 {1/65:78} B:0 2.17879 [ 2.67320] ((1 . 2) (3 . 3) (4 . 4) (5 . 5) (15 . 19) (16 . 20)) 5.608 {1/12:15} B:0 2.62191 [ 3.21184] ((2 . 7) (3 . 10) (5 . 12) (7 . 13) (8 . 17)) 6.964 {1/9:10} B:0 2.62344 [ 3.21267] ((2 . 7) (5 . 12) (7 . 13) (10 . 17) (12 . 20)) 9.898 {1/9:10} B:0 2.63743 [ 3.22032] ((2 . 7) (5 . 12) (7 . 13) (8 . 17) (12 . 20)) 11.285 {1/8:10} B:0 SIMILARITY (1/min{score1}): 0.9998 [and 1/min{score2}: 0.8124] [3358, 710]: Comparing 1kmv_A and 1cz3_A, based on their crossing files. There are 16 (5 H + 11 S) secondary structure elements in 1kmv_A, of which 13 satisfy the size requirements. There are 15 (4 H + 11 S) secondary structure elements in 1cz3_A, of which 14 satisfy the size requirements. 1.08386 [ 1.16709] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 6) (8 . 7) (9 . 8) (10 . 9) (11 . 10) (12 . 11) (16 . 15)) 3.045 {1/52:66} B:0 1.62506 [ 1.75005] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 7) (9 . 8) (11 . 10)) 2.833 {0/25:28} B:0 2.60006 [ 2.80005] ((7 . 4) (8 . 6) (10 . 9) (12 . 11) (16 . 15)) 4.134 {0/8:10} B:0 2.60036 [ 2.80029] ((1 . 4) (2 . 6) (3 . 8) (5 . 10) (7 . 11)) 6.403 {0/7:10} B:0 2.60102 [ 2.80081] ((1 . 4) (2 . 6) (5 . 10) (7 . 11) (10 . 14)) 8.271 {0/9:10} B:0 SIMILARITY (1/min{score1}): 0.9226 [and 1/min{score2}: 0.8568] [3358, 818]: Comparing 1kmv_A and 1df7_A, based on their crossing files. There are 16 (5 H + 11 S) secondary structure elements in 1kmv_A, of which 13 satisfy the size requirements. There are 16 (5 H + 11 S) secondary structure elements in 1df7_A, of which 13 satisfy the size requirements. 1.10304 [ 1.10304] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (16 . 16)) 2.194 {3/53:66} B:0 1.18223 [ 1.18223] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 7) (8 . 8) (10 . 10) (11 . 11) (12 . 12) (16 . 16)) 2.073 {1/45:55} B:0 1.86108 [ 1.86108] ((2 . 1) (3 . 3) (4 . 4) (5 . 5) (7 . 7) (8 . 8) (11 . 11)) 4.462 {1/18:21} B:0 1.86347 [ 1.86347] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 7) (8 . 10)) 5.088 {1/16:21} B:0 2.16669 [ 2.16669] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 8)) 2.815 {0/12:15} B:0 SIMILARITY (1/min{score1}): 0.9066 [and 1/min{score2}: 0.9066] [3358, 2724]: Comparing 1kmv_A and 1j3k_A, based on their crossing files. There are 16 (5 H + 11 S) secondary structure elements in 1kmv_A, of which 13 satisfy the size requirements. There are 21 (10 H + 11 S) secondary structure elements in 1j3k_A, of which 16 satisfy the size requirements. 1.01452 [ 1.23865] ((1 . 2) (2 . 5) (3 . 6) (4 . 8) (5 . 9) (7 . 11) (8 . 13) (9 . 14) (10 . 15) (11 . 16) (12 . 17) (15 . 20) (16 . 21)) 2.748 {3/61:78} B:0 1.08814 [ 1.33592] ((1 . 2) (2 . 5) (3 . 6) (4 . 8) (5 . 9) (7 . 11) (8 . 13) (9 . 14) (10 . 15) (11 . 16) (12 . 17) (16 . 21)) 2.806 {2/51:66} B:0 1.62873 [ 2.00200] ((4 . 8) (5 . 9) (8 . 11) (9 . 14) (10 . 15) (11 . 16) (12 . 17) (16 . 21)) 3.246 {1/20:28} B:0 1.85722 [ 2.28575] ((3 . 6) (7 . 8) (8 . 11) (9 . 14) (11 . 16) (12 . 17) (16 . 21)) 3.321 {0/14:21} B:0 2.16682 [ 2.66675] ((1 . 5) (4 . 8) (5 . 9) (7 . 11) (8 . 13) (12 . 17)) 4.478 {0/11:15} B:0 SIMILARITY (1/min{score1}): 0.9857 [and 1/min{score2}: 0.8073] [3358, 3067]: Comparing 1kmv_A and 1juv_A, based on their crossing files. There are 16 (5 H + 11 S) secondary structure elements in 1kmv_A, of which 13 satisfy the size requirements. There are 17 (5 H + 12 S) secondary structure elements in 1juv_A, of which 17 satisfy the size requirements. 1.10601 [ 1.42702] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 6) (8 . 7) (10 . 11) (11 . 12) (12 . 13) (15 . 16) (16 . 17)) 4.820 {3/52:66} B:0 1.30096 [ 1.70043] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 6) (8 . 7) (11 . 12) (12 . 13) (16 . 17)) 3.578 {1/36:45} B:0 1.54834 [ 1.66426] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 6) (8 . 7) (9 . 8) (10 . 11) (11 . 12) (12 . 13) (15 . 16) (16 . 17)) 4.893 {9/61:78} B:0 2.16672 [ 2.83336] ((3 . 3) (5 . 5) (7 . 7) (11 . 12) (12 . 13) (16 . 17)) 3.465 {0/11:15} B:0 2.60008 [ 3.40004] ((3 . 3) (4 . 6) (7 . 7) (11 . 12) (12 . 13)) 4.406 {0/8:10} B:0 SIMILARITY (1/min{score1}): 0.9041 [and 1/min{score2}: 0.7008] [3358, 3358]: Comparing 1kmv_A and 1kmv_A, based on their crossing files. There are 16 (5 H + 11 S) secondary structure elements in 1kmv_A, of which 13 satisfy the size requirements. There are 16 (5 H + 11 S) secondary structure elements in 1kmv_A, of which 13 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) (15 . 15) (16 . 16)) 0.000 {0/66:78} B:0 1.08333 [ 1.08333] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (16 . 16)) 0.000 {0/55:66} B:0 1.54826 [ 1.54826] ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (16 . 15)) 4.155 {6/43:55} B:0 1.54826 [ 1.54826] ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (15 . 16)) 4.155 {6/43:55} B:0 1.62502 [ 1.62502] ((3 . 3) (4 . 4) (5 . 5) (8 . 7) (9 . 9) (10 . 10) (11 . 11) (12 . 12)) 2.038 {0/22:28} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [3358, 5504]: Comparing 1kmv_A and 1qzf_A, based on their crossing files. There are 16 (5 H + 11 S) secondary structure elements in 1kmv_A, of which 13 satisfy the size requirements. There are 40 (19 H + 21 S) secondary structure elements in 1qzf_A, of which 14 satisfy the size requirements. 1.00255 [ 1.07896] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 6) (8 . 7) (9 . 8) (10 . 9) (11 . 10) (12 . 11) (15 . 14) (16 . 15)) 1.453 {2/63:78} B:0 1.62750 [ 1.75200] ((3 . 3) (4 . 4) (5 . 5) (7 . 7) (9 . 8) (10 . 9) (11 . 10) (12 . 11)) 2.172 {1/22:28} B:0 1.85718 [ 2.00003] ((7 . 4) (8 . 6) (9 . 8) (10 . 9) (11 . 10) (12 . 11) (16 . 15)) 2.899 {0/14:21} B:0 2.60022 [ 2.80018] ((1 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 7)) 5.669 {0/7:10} B:0 2.60030 [ 2.80024] ((1 . 4) (2 . 6) (3 . 8) (7 . 11) (8 . 13)) 6.120 {0/7:10} B:0 SIMILARITY (1/min{score1}): 0.9975 [and 1/min{score2}: 0.9268] [3358, 5601]: Comparing 1kmv_A and 1ra9, based on their crossing files. There are 16 (5 H + 11 S) secondary structure elements in 1kmv_A, of which 13 satisfy the size requirements. There are 16 (6 H + 10 S) secondary structure elements in 1ra9, of which 13 satisfy the size requirements. 1.10171 [ 1.10171] ((1 . 1) (2 . 3) (3 . 4) (4 . 5) (5 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (16 . 16)) 2.513 {3/54:66} B:0 1.76453 [ 1.76453] ((1 . 1) (2 . 3) (3 . 4) (4 . 5) (5 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (16 . 15)) 3.277 {9/53:66} B:0 1.85721 [ 1.85721] ((7 . 5) (8 . 7) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (16 . 16)) 3.232 {0/15:21} B:0 2.17846 [ 2.17846] ((1 . 1) (2 . 3) (3 . 4) (4 . 5) (5 . 6) (7 . 8)) 3.102 {1/12:15} B:0 2.60048 [ 2.60048] ((5 . 4) (7 . 5) (8 . 7) (12 . 12) (16 . 16)) 6.865 {0/6:10} B:0 SIMILARITY (1/min{score1}): 0.9077 [and 1/min{score2}: 0.9077] [3358, 6211]: Comparing 1kmv_A and 1vdr_A, based on their crossing files. There are 16 (5 H + 11 S) secondary structure elements in 1kmv_A, of which 13 satisfy the size requirements. There are 14 (4 H + 10 S) secondary structure elements in 1vdr_A, of which 12 satisfy the size requirements. 1.46069 [ 1.35386] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 6) (9 . 8) (11 . 10) (12 . 11)) 3.206 {2/30:36} B:0 1.46574 [ 1.36020] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (7 . 6) (9 . 8) (10 . 9) (11 . 10) (12 . 11)) 3.460 {2/28:36} B:0 2.16673 [ 2.00008] ((4 . 4) (7 . 6) (9 . 8) (10 . 9) (11 . 10) (12 . 11)) 3.547 {0/10:15} B:0 2.60008 [ 2.40010] ((7 . 4) (9 . 8) (11 . 10) (12 . 11) (16 . 14)) 4.360 {0/9:10} B:0 2.80285 [ 2.64840] ((7 . 1) (8 . 2) (10 . 4) (11 . 5) (12 . 6)) 5.935 {2/10:10} B:0 SIMILARITY (1/min{score1}): 0.7071 [and 1/min{score2}: 0.7386] [3358, 6563]: Comparing 1kmv_A and 3dfr, based on their crossing files. There are 16 (5 H + 11 S) secondary structure elements in 1kmv_A, of which 13 satisfy the size requirements. There are 16 (6 H + 10 S) secondary structure elements in 3dfr, of which 13 satisfy the size requirements. 1.01495 [ 1.01495] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 6) (8 . 7) (9 . 8) (10 . 9) (11 . 10) (12 . 11) (15 . 14) (16 . 16)) 4.512 {3/62:78} B:0 1.08738 [ 1.08738] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 6) (8 . 7) (9 . 8) (10 . 9) (11 . 10) (12 . 11) (16 . 16)) 2.317 {2/53:66} B:0 1.62680 [ 1.62680] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 7) (9 . 8) (11 . 10)) 2.651 {1/24:28} B:0 1.85723 [ 1.85723] ((7 . 4) (8 . 6) (9 . 8) (10 . 9) (11 . 10) (12 . 11) (16 . 16)) 3.512 {0/15:21} B:0 2.60046 [ 2.60046] ((1 . 4) (2 . 6) (3 . 8) (7 . 11) (8 . 14)) 6.800 {0/7:10} B:0 SIMILARITY (1/min{score1}): 0.9853 [and 1/min{score2}: 0.9853] [3358, 6608]: Comparing 1kmv_A and 4cd2_A, based on their crossing files. There are 16 (5 H + 11 S) secondary structure elements in 1kmv_A, of which 13 satisfy the size requirements. There are 18 (7 H + 11 S) secondary structure elements in 4cd2_A, of which 17 satisfy the size requirements. 1.00005 [ 1.30771] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (15 . 17) (16 . 18)) 1.906 {0/64:78} B:0 1.62505 [ 2.12502] ((3 . 3) (4 . 4) (5 . 5) (8 . 7) (9 . 9) (10 . 10) (11 . 11) (12 . 12)) 2.792 {0/22:28} B:0 1.85720 [ 2.42860] ((4 . 7) (7 . 8) (9 . 9) (10 . 10) (11 . 11) (15 . 17) (16 . 18)) 3.107 {0/16:21} B:0 2.60020 [ 3.40009] ((2 . 1) (3 . 3) (4 . 4) (5 . 5) (8 . 7)) 5.504 {0/7:10} B:0 2.60065 [ 3.40029] ((4 . 7) (7 . 8) (8 . 10) (15 . 17) (16 . 18)) 7.408 {0/9:10} B:0 SIMILARITY (1/min{score1}): 0.9999 [and 1/min{score2}: 0.7647] -------------------------------------------------------------------------------------------------------------------------