------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [2127, 502]: Comparing 1h7w_A and 1c0p_A, based on their crossing files. There are 81 (45 H + 36 S) secondary structure elements in 1h7w_A, of which 11 satisfy the size requirements. There are 28 (12 H + 16 S) secondary structure elements in 1c0p_A, of which 15 satisfy the size requirements. 1.37509 [ 1.87503] ((14 . 1) (15 . 2) (16 . 3) (18 . 12) (19 . 13) (21 . 15) (39 . 27) (41 . 28)) 2.772 {0/14:28} B:0 1.57144 [ 2.14286] ((14 . 1) (15 . 2) (16 . 3) (18 . 12) (19 . 13) (21 . 15) (41 . 28)) 1.947 {0/10:21} B:0 2.20099 [ 3.00039] ((14 . 1) (15 . 2) (16 . 3) (18 . 5) (41 . 28)) 7.256 {0/4:10} B:0 2.75109 [ 3.75043] ((18 . 12) (19 . 13) (21 . 15) (38 . 28)) 8.786 {0/3:6} B:0 2.75962 [ 3.75381] ((15 . 8) (18 . 12) (19 . 13) (38 . 28)) 15.155 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.7272 [and 1/min{score2}: 0.5333] [2127, 609]: Comparing 1h7w_A and 1cjc_A, based on their crossing files. There are 81 (45 H + 36 S) secondary structure elements in 1h7w_A, of which 11 satisfy the size requirements. There are 40 (21 H + 19 S) secondary structure elements in 1cjc_A, of which 14 satisfy the size requirements. 1.19455 [ 1.44944] ((14 . 1) (15 . 2) (16 . 3) (17 . 4) (18 . 5) (19 . 6) (20 . 7) (21 . 8) (39 . 35) (41 . 37)) 2.142 {2/23:45} B:0 1.23263 [ 1.56064] ((14 . 1) (15 . 2) (16 . 3) (17 . 4) (18 . 5) (19 . 6) (21 . 8) (39 . 35) (41 . 37)) 2.018 {1/19:36} B:0 2.75082 [ 3.50040] ((15 . 7) (16 . 8) (39 . 35) (41 . 37)) 8.175 {0/3:6} B:0 2.75181 [ 3.50088] ((16 . 1) (17 . 2) (18 . 4) (21 . 6)) 9.964 {0/2:6} B:0 3.66736 [ 4.06764] ((14 . 3) (15 . 4) (18 . 7) (19 . 8)) 11.216 {1/3:6} B:0 SIMILARITY (1/min{score1}): 0.8371 [and 1/min{score2}: 0.6899] [2127, 2127]: Comparing 1h7w_A and 1h7w_A, based on their crossing files. There are 81 (45 H + 36 S) secondary structure elements in 1h7w_A, of which 11 satisfy the size requirements. There are 81 (45 H + 36 S) secondary structure elements in 1h7w_A, of which 11 satisfy the size requirements. 1.00000 [ 1.00000] ((14 . 14) (15 . 15) (16 . 16) (17 . 17) (18 . 18) (19 . 19) (20 . 20) (21 . 21) (38 . 38) (39 . 39) (41 . 41)) 0.000 {0/33:55} B:0 2.75036 [ 2.75036] ((16 . 14) (18 . 20) (19 . 21) (20 . 41)) 6.639 {0/1:6} B:0 2.75036 [ 2.75036] ((14 . 16) (20 . 18) (21 . 19) (41 . 20)) 6.639 {0/1:6} B:0 2.75277 [ 2.75277] ((14 . 16) (18 . 20) (19 . 21) (41 . 41)) 11.086 {0/1:6} B:0 2.75277 [ 2.75277] ((16 . 14) (20 . 18) (21 . 19) (41 . 41)) 11.086 {0/1:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [2127, 2432]: Comparing 1h7w_A and 1i8t_A, based on their crossing files. There are 81 (45 H + 36 S) secondary structure elements in 1h7w_A, of which 11 satisfy the size requirements. There are 32 (16 H + 16 S) secondary structure elements in 1i8t_A, of which 23 satisfy the size requirements. 1.24965 [ 2.55865] ((14 . 1) (15 . 2) (16 . 3) (18 . 18) (19 . 19) (21 . 22) (38 . 30) (39 . 31) (41 . 32)) 5.009 {1/15:36} B:0 1.39948 [ 2.87775] ((14 . 1) (15 . 2) (16 . 3) (18 . 18) (19 . 19) (21 . 22) (39 . 31) (41 . 32)) 2.933 {1/14:28} B:0 1.42718 [ 2.58380] ((14 . 1) (15 . 2) (16 . 3) (18 . 18) (19 . 19) (20 . 21) (21 . 22) (39 . 31) (41 . 32)) 3.140 {2/17:36} B:0 2.75015 [ 5.75002] ((16 . 1) (18 . 2) (19 . 3) (38 . 21)) 5.390 {0/0:6} B:0 2.75017 [ 5.75002] ((14 . 1) (15 . 2) (16 . 3) (18 . 8)) 5.528 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.8002 [and 1/min{score2}: 0.4255] [2127, 3701]: Comparing 1h7w_A and 1lqt_A, based on their crossing files. There are 81 (45 H + 36 S) secondary structure elements in 1h7w_A, of which 11 satisfy the size requirements. There are 39 (19 H + 20 S) secondary structure elements in 1lqt_A, of which 14 satisfy the size requirements. 1.37149 [ 1.55955] ((14 . 1) (15 . 2) (16 . 3) (17 . 4) (18 . 5) (19 . 6) (20 . 7) (21 . 8) (39 . 33) (41 . 35)) 2.290 {3/25:45} B:0 2.75034 [ 3.50016] ((15 . 5) (16 . 6) (39 . 33) (41 . 35)) 6.561 {0/2:6} B:0 2.75072 [ 3.50035] ((15 . 7) (16 . 8) (39 . 33) (41 . 35)) 7.920 {0/2:6} B:0 5.11067 [ 5.27637] ((14 . 3) (16 . 6) (18 . 7) (19 . 8)) 4.945 {1/2:6} B:0 5.11070 [ 5.27640] ((16 . 1) (19 . 3) (20 . 5) (21 . 6)) 6.207 {1/2:6} B:0 SIMILARITY (1/min{score1}): 0.7291 [and 1/min{score2}: 0.6412] [2127, 4558]: Comparing 1h7w_A and 1o94_A, based on their crossing files. There are 81 (45 H + 36 S) secondary structure elements in 1h7w_A, of which 11 satisfy the size requirements. There are 56 (28 H + 28 S) secondary structure elements in 1o94_A, of which 16 satisfy the size requirements. 1.06884 [ 1.47872] ((14 . 30) (15 . 31) (16 . 32) (17 . 33) (18 . 34) (19 . 35) (20 . 36) (21 . 37) (38 . 52) (39 . 54) (41 . 56)) 4.041 {2/27:55} B:0 2.20167 [ 3.20054] ((16 . 30) (18 . 31) (19 . 32) (21 . 35) (41 . 53)) 8.262 {0/2:10} B:0 2.75046 [ 4.00015] ((14 . 32) (15 . 34) (16 . 35) (38 . 56)) 7.079 {0/0:6} B:0 2.75168 [ 4.00055] ((15 . 34) (16 . 35) (19 . 38) (38 . 56)) 9.783 {0/0:6} B:0 2.81222 [ 3.46397] ((16 . 30) (21 . 35) (38 . 52) (39 . 54) (41 . 56)) 7.836 {1/4:10} B:0 SIMILARITY (1/min{score1}): 0.9356 [and 1/min{score2}: 0.6763] [2127, 5094]: Comparing 1h7w_A and 1ps9_A, based on their crossing files. There are 81 (45 H + 36 S) secondary structure elements in 1h7w_A, of which 11 satisfy the size requirements. There are 52 (25 H + 27 S) secondary structure elements in 1ps9_A, of which 13 satisfy the size requirements. 1.11207 [ 1.30737] ((14 . 26) (15 . 27) (16 . 28) (17 . 29) (18 . 30) (19 . 31) (21 . 32) (38 . 49) (39 . 50) (41 . 52)) 3.688 {1/20:45} B:0 1.22251 [ 1.44462] ((14 . 26) (15 . 27) (16 . 28) (18 . 30) (19 . 31) (21 . 32) (38 . 49) (39 . 50) (41 . 52)) 3.439 {0/14:36} B:0 1.23292 [ 1.45097] ((14 . 26) (15 . 27) (16 . 28) (17 . 29) (18 . 30) (19 . 31) (21 . 32) (39 . 50) (41 . 52)) 3.544 {1/19:36} B:0 2.75010 [ 3.25006] ((16 . 26) (38 . 49) (39 . 50) (41 . 52)) 4.855 {0/1:6} B:0 2.75016 [ 3.25010] ((16 . 26) (19 . 28) (39 . 50) (41 . 52)) 5.476 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.8992 [and 1/min{score2}: 0.7649] [2127, 6214]: Comparing 1h7w_A and 1ve9_A, based on their crossing files. There are 81 (45 H + 36 S) secondary structure elements in 1h7w_A, of which 11 satisfy the size requirements. There are 28 (13 H + 15 S) secondary structure elements in 1ve9_A, of which 18 satisfy the size requirements. 1.22228 [ 2.00001] ((14 . 1) (15 . 2) (16 . 3) (18 . 12) (19 . 13) (20 . 14) (21 . 15) (39 . 26) (41 . 28)) 2.272 {0/18:36} B:0 2.20121 [ 3.60028] ((15 . 2) (16 . 3) (18 . 6) (39 . 26) (41 . 28)) 7.618 {0/6:10} B:0 2.30191 [ 3.62467] ((17 . 10) (18 . 12) (19 . 13) (20 . 14) (21 . 15)) 13.364 {1/7:10} B:0 2.81915 [ 3.79629] ((14 . 8) (18 . 12) (19 . 13) (20 . 14) (21 . 15)) 14.509 {1/4:10} B:0 2.82367 [ 3.79814] ((16 . 9) (18 . 12) (19 . 13) (20 . 14) (21 . 15)) 16.318 {1/4:10} B:0 SIMILARITY (1/min{score1}): 0.8181 [and 1/min{score2}: 0.5000] -------------------------------------------------------------------------------------------------------------------------