------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [2462, 295]: Comparing 1id0_A and 1b63_A, based on their crossing files. There are 12 (5 H + 7 S) secondary structure elements in 1id0_A, of which 10 satisfy the size requirements. There are 30 (15 H + 15 S) secondary structure elements in 1b63_A, of which 16 satisfy the size requirements. 2.50031 [ 4.00008] ((5 . 2) (6 . 3) (7 . 5) (12 . 9)) 5.988 {0/0:6} B:0 2.50087 [ 4.00021] ((2 . 6) (6 . 9) (7 . 10) (10 . 14)) 7.729 {0/0:6} B:0 2.50161 [ 4.00039] ((2 . 6) (6 . 9) (7 . 10) (10 . 13)) 9.008 {0/0:6} B:0 2.97452 [ 4.14511] ((2 . 1) (10 . 8) (11 . 11) (12 . 12)) 10.080 {1/4:6} B:0 5.07639 [ 5.44811] ((2 . 2) (3 . 3) (5 . 6) (11 . 11)) 5.778 {2/4:6} B:0 SIMILARITY (1/min{score1}): 0.4997 [and 1/min{score2}: 0.4204] [2462, 485]: Comparing 1id0_A and 1bxd_A, based on their crossing files. There are 12 (5 H + 7 S) secondary structure elements in 1id0_A, of which 10 satisfy the size requirements. There are 11 (4 H + 7 S) secondary structure elements in 1bxd_A, of which 11 satisfy the size requirements. 1.00489 [ 1.10368] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (10 . 9) (11 . 10) (12 . 11)) 2.757 {1/27:45} B:0 1.11128 [ 1.22235] ((1 . 1) (2 . 2) (3 . 3) (5 . 5) (6 . 6) (7 . 7) (10 . 9) (11 . 10) (12 . 11)) 2.782 {0/19:36} B:0 1.12249 [ 1.23081] ((2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (10 . 9) (11 . 10) (12 . 11)) 2.751 {1/20:36} B:0 2.00311 [ 2.20234] ((1 . 1) (2 . 2) (4 . 3) (5 . 5) (10 . 9)) 8.993 {0/6:10} B:0 2.11926 [ 2.29200] ((1 . 1) (2 . 2) (5 . 5) (10 . 9) (11 . 11)) 4.529 {1/7:10} B:0 SIMILARITY (1/min{score1}): 0.9951 [and 1/min{score2}: 0.9061] [2462, 494]: Comparing 1id0_A and 1byq_A, based on their crossing files. There are 12 (5 H + 7 S) secondary structure elements in 1id0_A, of which 10 satisfy the size requirements. There are 16 (8 H + 8 S) secondary structure elements in 1byq_A, of which 16 satisfy the size requirements. 2.00045 [ 3.20011] ((5 . 3) (6 . 4) (7 . 5) (11 . 10) (12 . 11)) 5.553 {0/2:10} B:0 2.50040 [ 4.00010] ((2 . 3) (3 . 4) (11 . 12) (12 . 13)) 6.365 {0/2:6} B:0 2.50053 [ 4.00013] ((2 . 6) (5 . 9) (6 . 10) (7 . 11)) 6.827 {0/2:6} B:0 2.50078 [ 4.00019] ((2 . 6) (6 . 10) (7 . 11) (10 . 14)) 7.521 {0/0:6} B:0 2.50348 [ 4.00085] ((2 . 9) (3 . 11) (4 . 12) (6 . 13)) 10.934 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.7518 [and 1/min{score2}: 0.4948] [2462, 1166]: Comparing 1id0_A and 1ei1_A, based on their crossing files. There are 12 (5 H + 7 S) secondary structure elements in 1id0_A, of which 10 satisfy the size requirements. There are 29 (13 H + 16 S) secondary structure elements in 1ei1_A, of which 13 satisfy the size requirements. 2.50021 [ 3.25010] ((5 . 5) (6 . 6) (7 . 7) (12 . 11)) 5.423 {0/0:6} B:0 2.50047 [ 3.25021] ((2 . 8) (6 . 11) (7 . 12) (10 . 16)) 6.623 {0/0:6} B:0 2.50090 [ 3.25041] ((2 . 5) (3 . 6) (4 . 7) (11 . 14)) 7.801 {0/3:6} B:0 3.57081 [ 3.91567] ((2 . 8) (6 . 12) (11 . 17) (12 . 18)) 7.944 {1/3:6} B:0 3.57088 [ 3.91572] ((5 . 8) (10 . 10) (11 . 12) (12 . 15)) 8.328 {1/3:6} B:0 SIMILARITY (1/min{score1}): 0.5601 [and 1/min{score2}: 0.5108] [2462, 1859]: Comparing 1id0_A and 1gkz_A, based on their crossing files. There are 12 (5 H + 7 S) secondary structure elements in 1id0_A, of which 10 satisfy the size requirements. There are 19 (9 H + 10 S) secondary structure elements in 1gkz_A, of which 9 satisfy the size requirements. 1.12503 [ 1.01891] ((2 . 11) (3 . 12) (4 . 13) (5 . 14) (6 . 15) (7 . 16) (10 . 17) (11 . 18) (12 . 19)) 2.895 {1/19:36} B:0 1.32960 [ 1.22957] ((2 . 11) (3 . 12) (5 . 14) (6 . 15) (7 . 16) (10 . 17) (11 . 18) (12 . 19)) 2.702 {1/11:28} B:0 2.00011 [ 1.80015] ((2 . 11) (3 . 12) (5 . 14) (7 . 15) (10 . 17)) 3.901 {0/3:10} B:0 2.50013 [ 2.25018] ((2 . 11) (5 . 14) (6 . 16) (10 . 17)) 4.799 {0/2:6} B:0 2.50041 [ 2.25056] ((2 . 11) (4 . 12) (5 . 14) (10 . 17)) 6.392 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.8889 [and 1/min{score2}: 0.9814] [2462, 2124]: Comparing 1id0_A and 1h7s_A, based on their crossing files. There are 12 (5 H + 7 S) secondary structure elements in 1id0_A, of which 10 satisfy the size requirements. There are 30 (13 H + 17 S) secondary structure elements in 1h7s_A, of which 15 satisfy the size requirements. 2.00102 [ 3.00030] ((5 . 2) (6 . 3) (7 . 5) (10 . 9) (12 . 12)) 6.807 {0/2:10} B:0 2.50009 [ 3.75003] ((5 . 2) (10 . 9) (11 . 12) (12 . 13)) 4.369 {0/3:6} B:0 2.50085 [ 3.75025] ((2 . 2) (3 . 3) (7 . 10) (11 . 13)) 7.689 {0/0:6} B:0 2.50112 [ 3.75033] ((3 . 8) (7 . 13) (11 . 16) (12 . 17)) 8.232 {0/2:6} B:0 2.50193 [ 3.75057] ((1 . 5) (3 . 8) (11 . 16) (12 . 17)) 9.429 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.5226 [and 1/min{score2}: 0.4550] [2462, 2403]: Comparing 1id0_A and 1i58_A, based on their crossing files. There are 12 (5 H + 7 S) secondary structure elements in 1id0_A, of which 10 satisfy the size requirements. There are 16 (9 H + 7 S) secondary structure elements in 1i58_A, of which 16 satisfy the size requirements. 1.00055 [ 1.60013] ((1 . 1) (2 . 2) (3 . 4) (4 . 5) (5 . 6) (6 . 8) (7 . 9) (10 . 14) (11 . 15) (12 . 16)) 3.468 {0/20:45} B:0 1.02341 [ 1.60589] ((1 . 1) (2 . 3) (3 . 4) (4 . 5) (5 . 6) (6 . 8) (7 . 9) (10 . 14) (11 . 15) (12 . 16)) 3.265 {1/18:45} B:0 2.00468 [ 3.20115] ((2 . 3) (3 . 5) (5 . 6) (6 . 8) (7 . 9)) 9.963 {0/1:10} B:0 2.50018 [ 4.00004] ((2 . 6) (10 . 14) (11 . 15) (12 . 16)) 5.230 {0/1:6} B:0 2.50031 [ 4.00008] ((2 . 3) (6 . 8) (7 . 9) (10 . 12)) 5.960 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.9994 [and 1/min{score2}: 0.6249] [2462, 2462]: Comparing 1id0_A and 1id0_A, based on their crossing files. There are 12 (5 H + 7 S) secondary structure elements in 1id0_A, of which 10 satisfy the size requirements. There are 12 (5 H + 7 S) secondary structure elements in 1id0_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) (10 . 10) (11 . 11) (12 . 12)) 0.000 {0/27:45} B:0 2.00171 [ 2.00171] ((1 . 1) (2 . 2) (3 . 4) (5 . 5) (10 . 10)) 7.741 {0/6:10} B:0 2.00171 [ 2.00171] ((1 . 1) (2 . 2) (4 . 3) (5 . 5) (10 . 10)) 7.741 {0/6:10} B:0 6.69940 [ 6.69940] ((1 . 4) (2 . 5) (3 . 6) (7 . 11)) 5.586 {2/3:6} B:0 6.69940 [ 6.69940] ((4 . 1) (5 . 2) (6 . 3) (11 . 7)) 5.586 {2/3:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [2462, 2968]: Comparing 1id0_A and 1jm6_A, based on their crossing files. There are 12 (5 H + 7 S) secondary structure elements in 1id0_A, of which 10 satisfy the size requirements. There are 20 (13 H + 7 S) secondary structure elements in 1jm6_A, of which 9 satisfy the size requirements. 1.11143 [ 1.00043] ((2 . 10) (3 . 11) (4 . 12) (5 . 13) (6 . 14) (7 . 15) (10 . 18) (11 . 19) (12 . 20)) 3.265 {0/19:36} B:0 2.50010 [ 2.25014] ((2 . 10) (5 . 13) (6 . 15) (10 . 18)) 4.495 {0/2:6} B:0 2.50030 [ 2.25041] ((2 . 10) (4 . 11) (5 . 13) (10 . 18)) 5.932 {0/3:6} B:0 2.50184 [ 2.25252] ((2 . 13) (3 . 15) (5 . 18) (7 . 19)) 9.319 {0/1:6} B:0 2.07293 [ 2.04896] ((1 . 11) (2 . 10) (4 . 14) (5 . 13) (7 . 15) (10 . 18) (11 . 19) (12 . 20)) 6.249 {2/10:28} B:2 SIMILARITY (1/min{score1}): 0.8997 [and 1/min{score2}: 0.9996] [2462, 3504]: Comparing 1id0_A and 1l0o_A, based on their crossing files. There are 12 (5 H + 7 S) secondary structure elements in 1id0_A, of which 10 satisfy the size requirements. There are 12 (6 H + 6 S) secondary structure elements in 1l0o_A, of which 10 satisfy the size requirements. 1.66748 [ 1.66748] ((5 . 3) (6 . 5) (7 . 6) (10 . 9) (11 . 10) (12 . 12)) 5.614 {0/2:15} B:0 2.00036 [ 2.00036] ((5 . 3) (7 . 5) (10 . 9) (11 . 10) (12 . 11)) 5.243 {0/1:10} B:0 6.66875 [ 6.66875] ((1 . 1) (2 . 2) (5 . 3) (6 . 5) (7 . 6) (10 . 9) (11 . 10) (12 . 11)) 6.781 {4/6:28} B:0 6.66876 [ 6.66876] ((1 . 1) (2 . 2) (4 . 5) (5 . 3) (7 . 6) (10 . 9) (11 . 10) (12 . 11)) 7.174 {4/6:28} B:1 8.57240 [ 8.57240] ((2 . 2) (3 . 1) (5 . 3) (6 . 5) (7 . 6) (10 . 9) (11 . 10) (12 . 11)) 4.710 {6/7:28} B:1 SIMILARITY (1/min{score1}): 0.5997 [and 1/min{score2}: 0.5997] [2462, 4034]: Comparing 1id0_A and 1mu5_A, based on their crossing files. There are 12 (5 H + 7 S) secondary structure elements in 1id0_A, of which 10 satisfy the size requirements. There are 33 (18 H + 15 S) secondary structure elements in 1mu5_A, of which 14 satisfy the size requirements. 2.00084 [ 2.80031] ((2 . 3) (3 . 5) (7 . 9) (11 . 12) (12 . 13)) 6.473 {0/3:10} B:0 2.50032 [ 3.50012] ((2 . 7) (6 . 9) (7 . 10) (11 . 13)) 6.024 {0/0:6} B:0 2.50070 [ 3.50026] ((2 . 7) (10 . 14) (11 . 15) (12 . 16)) 7.331 {0/2:6} B:0 3.57244 [ 4.06808] ((2 . 1) (6 . 6) (10 . 8) (11 . 10)) 12.379 {1/3:6} B:0 5.03197 [ 5.11890] ((2 . 1) (5 . 3) (6 . 5) (7 . 6) (10 . 8)) 9.800 {1/2:10} B:0 SIMILARITY (1/min{score1}): 0.5997 [and 1/min{score2}: 0.4285] [2462, 5126]: Comparing 1id0_A and 1pvg_A, based on their crossing files. There are 12 (5 H + 7 S) secondary structure elements in 1id0_A, of which 10 satisfy the size requirements. There are 32 (14 H + 18 S) secondary structure elements in 1pvg_A, of which 15 satisfy the size requirements. 2.50018 [ 3.75005] ((2 . 12) (3 . 13) (6 . 17) (10 . 19)) 5.183 {0/0:6} B:0 2.50062 [ 3.75018] ((2 . 10) (6 . 13) (7 . 14) (10 . 19)) 7.103 {0/0:6} B:0 2.50076 [ 3.75023] ((2 . 10) (6 . 16) (7 . 17) (11 . 20)) 7.479 {0/3:6} B:0 2.50087 [ 3.75026] ((1 . 5) (2 . 7) (11 . 13) (12 . 14)) 7.722 {0/2:6} B:0 2.50183 [ 3.75054] ((2 . 10) (6 . 13) (7 . 14) (10 . 18)) 9.302 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.6119 [and 1/min{score2}: 0.5234] [2462, 5746]: Comparing 1id0_A and 1s14_A, based on their crossing files. There are 12 (5 H + 7 S) secondary structure elements in 1id0_A, of which 10 satisfy the size requirements. There are 14 (5 H + 9 S) secondary structure elements in 1s14_A, of which 13 satisfy the size requirements. 2.00136 [ 2.60062] ((5 . 1) (6 . 2) (7 . 3) (10 . 5) (12 . 8)) 7.303 {0/1:10} B:0 2.00140 [ 2.60064] ((5 . 1) (6 . 2) (7 . 3) (10 . 5) (12 . 9)) 7.367 {0/1:10} B:0 2.50022 [ 3.25010] ((3 . 3) (10 . 12) (11 . 13) (12 . 14)) 5.468 {0/1:6} B:0 2.50090 [ 3.25041] ((2 . 4) (5 . 5) (6 . 9) (7 . 10)) 7.795 {0/2:6} B:0 2.50090 [ 3.25041] ((2 . 4) (5 . 5) (6 . 8) (7 . 10)) 7.797 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.6724 [and 1/min{score2}: 0.5707] -------------------------------------------------------------------------------------------------------------------------