------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [795, 795]: Comparing 1dcj_A and 1dcj_A, based on their crossing files. There are 6 (2 H + 4 S) secondary structure elements in 1dcj_A, of which 6 satisfy the size requirements. There are 6 (2 H + 4 S) secondary structure elements in 1dcj_A, of which 6 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6)) 0.000 {0/6:15} B:0 1.50262 [ 1.50262] ((1 . 3) (2 . 4) (3 . 5) (5 . 6)) 6.945 {0/0:6} B:0 1.50262 [ 1.50262] ((3 . 1) (4 . 2) (5 . 3) (6 . 5)) 6.945 {0/0:6} B:0 3.34726 [ 3.34726] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 6)) 3.451 {1/3:10} B:0 3.36703 [ 3.36703] ((1 . 1) (2 . 2) (4 . 4) (6 . 5)) 4.342 {1/3:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [795, 1183]: Comparing 1dcj_A and 1ejd_A, based on their crossing files. There are 6 (2 H + 4 S) secondary structure elements in 1dcj_A, of which 6 satisfy the size requirements. There are 39 (15 H + 24 S) secondary structure elements in 1ejd_A, of which 35 satisfy the size requirements. 1.00040 [ 5.83334] ((1 . 2) (2 . 22) (3 . 23) (4 . 25) (5 . 26) (6 . 27)) 3.202 {0/2:15} B:0 1.00079 [ 5.83334] ((1 . 15) (2 . 16) (3 . 17) (4 . 18) (5 . 19) (6 . 20)) 3.792 {0/2:15} B:0 1.20008 [ 7.00000] ((2 . 10) (3 . 11) (4 . 12) (5 . 13) (6 . 14)) 2.424 {0/1:10} B:0 1.20013 [ 7.00000] ((2 . 3) (3 . 4) (4 . 5) (5 . 6) (6 . 7)) 2.791 {0/2:10} B:0 1.20015 [ 7.00000] ((2 . 22) (3 . 23) (4 . 25) (5 . 26) (6 . 27)) 2.894 {0/1:10} B:0 SIMILARITY (1/min{score1}): 0.9996 [and 1/min{score2}: 0.1714] [795, 1744]: Comparing 1dcj_A and 1g6s_A, based on their crossing files. There are 6 (2 H + 4 S) secondary structure elements in 1dcj_A, of which 6 satisfy the size requirements. There are 39 (15 H + 24 S) secondary structure elements in 1g6s_A, of which 37 satisfy the size requirements. 1.00040 [ 6.16667] ((1 . 2) (2 . 22) (3 . 23) (4 . 24) (5 . 25) (6 . 26)) 3.194 {0/1:15} B:0 1.00052 [ 6.16667] ((1 . 27) (2 . 28) (3 . 29) (4 . 31) (5 . 32) (6 . 33)) 3.422 {0/1:15} B:0 1.00053 [ 6.16667] ((1 . 15) (2 . 16) (3 . 17) (4 . 18) (5 . 19) (6 . 20)) 3.430 {0/5:15} B:0 1.00168 [ 6.16667] ((1 . 8) (2 . 9) (3 . 10) (4 . 12) (5 . 13) (6 . 14)) 4.586 {0/4:15} B:0 1.20010 [ 7.40000] ((2 . 22) (3 . 23) (4 . 24) (5 . 25) (6 . 26)) 2.589 {0/1:10} B:0 SIMILARITY (1/min{score1}): 0.9996 [and 1/min{score2}: 0.1622] [795, 2168]: Comparing 1dcj_A and 1hc7_A, based on their crossing files. There are 6 (2 H + 4 S) secondary structure elements in 1dcj_A, of which 6 satisfy the size requirements. There are 37 (14 H + 23 S) secondary structure elements in 1hc7_A, of which 6 satisfy the size requirements. 1.00060 [ 1.00060] ((1 . 32) (2 . 33) (3 . 34) (4 . 35) (5 . 36) (6 . 37)) 3.547 {0/6:15} B:0 1.20010 [ 1.20010] ((1 . 32) (2 . 33) (3 . 34) (5 . 36) (6 . 37)) 2.624 {0/4:10} B:0 1.20033 [ 1.20033] ((1 . 32) (3 . 34) (4 . 35) (5 . 36) (6 . 37)) 3.491 {0/4:10} B:0 1.50102 [ 1.50102] ((2 . 33) (3 . 34) (4 . 35) (6 . 36)) 5.485 {0/1:6} B:0 1.50274 [ 1.50274] ((3 . 32) (4 . 33) (5 . 34) (6 . 36)) 7.019 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.9994 [and 1/min{score2}: 0.9994] [795, 2831]: Comparing 1dcj_A and 1jdq_A, based on their crossing files. There are 6 (2 H + 4 S) secondary structure elements in 1dcj_A, of which 6 satisfy the size requirements. There are 6 (2 H + 4 S) secondary structure elements in 1jdq_A, of which 6 satisfy the size requirements. 1.20025 [ 1.20025] ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (6 . 6)) 3.264 {0/3:10} B:0 1.50251 [ 1.50251] ((3 . 1) (4 . 2) (5 . 3) (6 . 5)) 6.866 {0/0:6} B:0 1.50363 [ 1.50363] ((1 . 3) (2 . 4) (3 . 5) (5 . 6)) 7.532 {0/0:6} B:0 2.51591 [ 2.51591] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6)) 3.920 {1/4:15} B:0 3.36712 [ 3.36712] ((1 . 1) (2 . 2) (4 . 4) (5 . 6)) 5.986 {1/3:6} B:0 SIMILARITY (1/min{score1}): 0.8332 [and 1/min{score2}: 0.8332] [795, 2999]: Comparing 1dcj_A and 1jo0_A, based on their crossing files. There are 6 (2 H + 4 S) secondary structure elements in 1dcj_A, of which 6 satisfy the size requirements. There are 7 (3 H + 4 S) secondary structure elements in 1jo0_A, of which 7 satisfy the size requirements. 1.00092 [ 1.16725] ((1 . 2) (2 . 3) (3 . 4) (4 . 5) (5 . 6) (6 . 7)) 3.941 {0/6:15} B:0 1.50204 [ 1.75129] ((1 . 4) (2 . 5) (3 . 6) (5 . 7)) 6.523 {0/0:6} B:0 10.00130 [10.00238] ((2 . 1) (3 . 4) (4 . 5) (6 . 6)) 9.867 {1/1:6} B:0 10.00130 [10.00238] ((2 . 1) (3 . 2) (5 . 4) (6 . 6)) 10.038 {1/1:6} B:0 1.50176 [ 1.75111] ((1 . 2) (2 . 3) (3 . 6) (4 . 5)) 6.283 {0/2:6} B:1 SIMILARITY (1/min{score1}): 0.9991 [and 1/min{score2}: 0.8567] [795, 4256]: Comparing 1dcj_A and 1nh9_A, based on their crossing files. There are 6 (2 H + 4 S) secondary structure elements in 1dcj_A, of which 6 satisfy the size requirements. There are 6 (2 H + 4 S) secondary structure elements in 1nh9_A, of which 6 satisfy the size requirements. 1.00067 [ 1.00067] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6)) 3.643 {0/5:15} B:0 1.50365 [ 1.50365] ((1 . 3) (2 . 4) (3 . 5) (5 . 6)) 7.543 {0/0:6} B:0 3.34730 [ 3.34730] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (6 . 5)) 4.930 {1/3:10} B:0 1.50023 [ 1.50023] ((2 . 2) (3 . 1) (4 . 4) (5 . 3)) 3.785 {0/2:6} B:2 SIMILARITY (1/min{score1}): 0.9993 [and 1/min{score2}: 0.9993] [795, 4274]: Comparing 1dcj_A and 1nj1_A, based on their crossing files. There are 6 (2 H + 4 S) secondary structure elements in 1dcj_A, of which 6 satisfy the size requirements. There are 41 (14 H + 27 S) secondary structure elements in 1nj1_A, of which 6 satisfy the size requirements. 1.00041 [ 1.00041] ((1 . 36) (2 . 37) (3 . 38) (4 . 39) (5 . 40) (6 . 41)) 3.214 {0/6:15} B:0 1.50241 [ 1.50241] ((3 . 36) (4 . 37) (5 . 38) (6 . 40)) 6.798 {0/1:6} B:0 1.50071 [ 1.50071] ((1 . 36) (2 . 37) (3 . 40) (4 . 39)) 5.013 {0/2:6} B:1 1.50164 [ 1.50164] ((2 . 37) (3 . 36) (4 . 39) (5 . 38)) 6.177 {0/2:6} B:2 SIMILARITY (1/min{score1}): 0.9996 [and 1/min{score2}: 0.9996] [795, 4276]: Comparing 1dcj_A and 1nj8_A, based on their crossing files. There are 6 (2 H + 4 S) secondary structure elements in 1dcj_A, of which 6 satisfy the size requirements. There are 36 (15 H + 21 S) secondary structure elements in 1nj8_A, of which 6 satisfy the size requirements. 1.00105 [ 1.00105] ((1 . 30) (2 . 31) (3 . 32) (4 . 34) (5 . 35) (6 . 36)) 4.076 {0/6:15} B:0 1.20010 [ 1.20010] ((1 . 30) (2 . 31) (3 . 32) (5 . 35) (6 . 36)) 2.570 {0/4:10} B:0 1.50101 [ 1.50101] ((2 . 31) (3 . 32) (4 . 34) (6 . 35)) 5.466 {0/1:6} B:0 1.50235 [ 1.50235] ((3 . 30) (4 . 31) (5 . 32) (6 . 35)) 6.754 {0/0:6} B:0 6.00241 [ 6.00241] ((1 . 30) (2 . 31) (3 . 32) (4 . 34) (5 . 36)) 5.244 {3/5:10} B:0 SIMILARITY (1/min{score1}): 0.9989 [and 1/min{score2}: 0.9989] [795, 5389]: Comparing 1dcj_A and 1qmh_A, based on their crossing files. There are 6 (2 H + 4 S) secondary structure elements in 1dcj_A, of which 6 satisfy the size requirements. There are 25 (10 H + 15 S) secondary structure elements in 1qmh_A, of which 18 satisfy the size requirements. 1.00034 [ 3.00001] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6)) 3.069 {0/2:15} B:0 1.00132 [ 3.00005] ((1 . 7) (2 . 8) (3 . 9) (4 . 10) (5 . 12) (6 . 13)) 4.315 {0/5:15} B:0 1.00293 [ 3.00011] ((1 . 7) (2 . 8) (3 . 9) (4 . 11) (5 . 12) (6 . 13)) 5.272 {0/4:15} B:0 1.20021 [ 3.60001] ((2 . 21) (3 . 22) (4 . 23) (5 . 24) (6 . 25)) 3.126 {0/2:10} B:0 1.50047 [ 4.50002] ((2 . 21) (3 . 22) (4 . 23) (6 . 24)) 4.527 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.9997 [and 1/min{score2}: 0.3333] [795, 5618]: Comparing 1dcj_A and 1rf6_A, based on their crossing files. There are 6 (2 H + 4 S) secondary structure elements in 1dcj_A, of which 6 satisfy the size requirements. There are 39 (16 H + 23 S) secondary structure elements in 1rf6_A, of which 36 satisfy the size requirements. 1.00087 [ 6.00000] ((1 . 2) (2 . 22) (3 . 23) (4 . 24) (5 . 25) (6 . 26)) 3.883 {0/2:15} B:0 1.20014 [ 7.20000] ((2 . 3) (3 . 4) (4 . 5) (5 . 6) (6 . 7)) 2.800 {0/2:10} B:0 1.20029 [ 7.20000] ((2 . 9) (3 . 10) (4 . 12) (5 . 13) (6 . 14)) 3.383 {0/1:10} B:0 1.20031 [ 7.20000] ((2 . 29) (3 . 30) (4 . 32) (5 . 33) (6 . 34)) 3.437 {0/2:10} B:0 1.20040 [ 7.20000] ((2 . 22) (3 . 23) (4 . 24) (5 . 25) (6 . 26)) 3.677 {0/2:10} B:0 SIMILARITY (1/min{score1}): 0.9995 [and 1/min{score2}: 0.1667] [795, 5915]: Comparing 1dcj_A and 1tig, based on their crossing files. There are 6 (2 H + 4 S) secondary structure elements in 1dcj_A, of which 6 satisfy the size requirements. There are 7 (2 H + 5 S) secondary structure elements in 1tig, of which 7 satisfy the size requirements. 1.00102 [ 1.16731] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 6) (6 . 7)) 4.048 {0/6:15} B:0 1.00151 [ 1.16762] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 7)) 4.461 {0/6:15} B:0 10.00127 [10.00235] ((1 . 3) (2 . 4) (3 . 6) (5 . 7)) 7.075 {1/1:6} B:0 1.20120 [ 1.40076] ((1 . 3) (2 . 2) (4 . 4) (5 . 6) (6 . 7)) 4.833 {0/3:10} B:1 5.01017 [ 5.01872] ((1 . 3) (2 . 2) (4 . 4) (5 . 7)) 6.980 {1/2:6} B:1 SIMILARITY (1/min{score1}): 0.9990 [and 1/min{score2}: 0.8567] [795, 5977]: Comparing 1dcj_A and 1udv_A, based on their crossing files. There are 6 (2 H + 4 S) secondary structure elements in 1dcj_A, of which 6 satisfy the size requirements. There are 6 (2 H + 4 S) secondary structure elements in 1udv_A, of which 6 satisfy the size requirements. 1.00070 [ 1.00070] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6)) 3.675 {0/6:15} B:0 1.50058 [ 1.50058] ((1 . 3) (2 . 4) (5 . 5) (6 . 6)) 4.766 {0/1:6} B:0 1.50259 [ 1.50259] ((3 . 1) (4 . 2) (5 . 3) (6 . 5)) 6.924 {0/1:6} B:0 1.50447 [ 1.50447] ((1 . 3) (2 . 4) (3 . 5) (5 . 6)) 7.939 {0/0:6} B:0 3.34729 [ 3.34729] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (6 . 5)) 4.751 {1/3:10} B:0 SIMILARITY (1/min{score1}): 0.9993 [and 1/min{score2}: 0.9993] -------------------------------------------------------------------------------------------------------------------------