------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [4246, 908]: Comparing 1nh0_A and 1dpj_A, based on their crossing files. There are 11 (1 H + 10 S) secondary structure elements in 1nh0_A, of which 8 satisfy the size requirements. There are 38 (11 H + 27 S) secondary structure elements in 1dpj_A, of which 32 satisfy the size requirements. 2.00026 [ 8.00000] ((2 . 4) (3 . 5) (6 . 8) (10 . 12)) 4.841 {0/6:6} B:0 2.00066 [ 8.00001] ((2 . 32) (3 . 33) (5 . 37) (6 . 38)) 6.094 {0/2:6} B:0 2.00180 [ 8.00003] ((2 . 4) (3 . 5) (6 . 8) (8 . 9)) 7.844 {0/6:6} B:0 2.00246 [ 8.00004] ((2 . 22) (3 . 23) (5 . 25) (6 . 28)) 8.475 {0/4:6} B:0 2.00503 [ 8.00008] ((2 . 8) (3 . 9) (6 . 13) (11 . 19)) 10.144 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.4999 [and 1/min{score2}: 0.2298] [4246, 1541]: Comparing 1nh0_A and 1fkn_A, based on their crossing files. There are 11 (1 H + 10 S) secondary structure elements in 1nh0_A, of which 8 satisfy the size requirements. There are 37 (12 H + 25 S) secondary structure elements in 1fkn_A, of which 30 satisfy the size requirements. 2.00056 [ 7.50001] ((2 . 6) (3 . 7) (7 . 9) (10 . 11)) 5.844 {0/5:6} B:0 2.00074 [ 7.50001] ((2 . 29) (3 . 30) (5 . 34) (6 . 35)) 6.285 {0/3:6} B:0 2.00136 [ 7.50003] ((2 . 20) (3 . 21) (8 . 26) (11 . 29)) 7.313 {0/4:6} B:0 2.00140 [ 7.50003] ((2 . 24) (7 . 30) (10 . 33) (11 . 35)) 7.362 {0/3:6} B:0 2.00366 [ 7.50007] ((2 . 16) (5 . 20) (6 . 21) (11 . 24)) 9.368 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.8398 [and 1/min{score2}: 0.2333] [4246, 1559]: Comparing 1nh0_A and 1fmb, based on their crossing files. There are 11 (1 H + 10 S) secondary structure elements in 1nh0_A, of which 8 satisfy the size requirements. There are 11 (2 H + 9 S) secondary structure elements in 1fmb, of which 9 satisfy the size requirements. 1.38169 [ 1.53463] ((2 . 1) (3 . 2) (5 . 6) (7 . 8) (8 . 9) (10 . 11)) 3.276 {1/12:15} B:0 1.42742 [ 1.50850] ((2 . 1) (3 . 2) (5 . 6) (6 . 7) (7 . 8) (8 . 9) (10 . 11)) 4.067 {2/16:21} B:0 2.00054 [ 2.25038] ((2 . 1) (7 . 2) (8 . 3) (11 . 6)) 5.793 {0/5:6} B:0 2.00056 [ 2.25039] ((2 . 1) (3 . 2) (5 . 3) (10 . 11)) 5.844 {0/5:6} B:0 2.72446 [ 2.83640] ((7 . 1) (8 . 2) (10 . 4) (11 . 6)) 6.853 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.7238 [and 1/min{score2}: 0.6629] [4246, 2272]: Comparing 1nh0_A and 1hrn_A, based on their crossing files. There are 11 (1 H + 10 S) secondary structure elements in 1nh0_A, of which 8 satisfy the size requirements. There are 37 (11 H + 26 S) secondary structure elements in 1hrn_A, of which 30 satisfy the size requirements. 1.16295 [ 4.28611] ((2 . 2) (3 . 3) (5 . 7) (6 . 8) (7 . 9) (8 . 10) (10 . 15)) 3.868 {1/17:21} B:0 1.69180 [ 6.00190] ((2 . 3) (3 . 4) (6 . 7) (8 . 9) (10 . 11)) 9.305 {1/9:10} B:0 2.00222 [ 7.50004] ((5 . 19) (7 . 22) (8 . 23) (11 . 27)) 8.265 {0/5:6} B:0 2.20863 [ 7.50462] ((3 . 7) (5 . 9) (6 . 10) (8 . 12)) 8.491 {1/6:6} B:0 2.37881 [ 7.50948] ((2 . 7) (3 . 8) (7 . 12) (10 . 15)) 6.120 {1/5:6} B:0 SIMILARITY (1/min{score1}): 0.8599 [and 1/min{score2}: 0.2507] [4246, 2751]: Comparing 1nh0_A and 1j71_A, based on their crossing files. There are 11 (1 H + 10 S) secondary structure elements in 1nh0_A, of which 8 satisfy the size requirements. There are 37 (7 H + 30 S) secondary structure elements in 1j71_A, of which 33 satisfy the size requirements. 1.01096 [ 4.12516] ((2 . 2) (3 . 3) (5 . 9) (6 . 10) (7 . 11) (8 . 13) (10 . 16) (11 . 17)) 4.903 {1/23:28} B:0 1.37043 [ 5.50055] ((2 . 2) (3 . 3) (5 . 5) (6 . 10) (7 . 11) (8 . 13)) 5.737 {1/13:15} B:0 1.45369 [ 4.13729] ((2 . 2) (3 . 3) (5 . 9) (6 . 10) (7 . 11) (8 . 12) (10 . 16) (11 . 17)) 4.773 {3/22:28} B:0 1.94382 [ 6.60671] ((2 . 21) (3 . 22) (5 . 25) (6 . 26) (7 . 27)) 4.614 {1/6:10} B:0 2.00030 [ 8.25000] ((2 . 3) (3 . 4) (6 . 8) (8 . 10)) 5.016 {0/6:6} B:0 SIMILARITY (1/min{score1}): 0.9892 [and 1/min{score2}: 0.2424] [4246, 3611]: Comparing 1nh0_A and 1lf2_A, based on their crossing files. There are 11 (1 H + 10 S) secondary structure elements in 1nh0_A, of which 8 satisfy the size requirements. There are 36 (10 H + 26 S) secondary structure elements in 1lf2_A, of which 29 satisfy the size requirements. 1.16331 [ 4.14330] ((2 . 2) (3 . 3) (5 . 7) (6 . 8) (7 . 9) (8 . 10) (10 . 15)) 4.394 {1/17:21} B:0 1.68650 [ 5.80197] ((2 . 20) (3 . 22) (6 . 26) (7 . 27) (8 . 28)) 5.312 {1/9:10} B:0 2.00060 [ 7.25001] ((2 . 3) (3 . 4) (6 . 7) (8 . 8)) 5.960 {0/5:6} B:0 2.00065 [ 7.25001] ((2 . 27) (3 . 28) (7 . 35) (8 . 36)) 6.072 {0/4:6} B:0 2.00068 [ 7.25001] ((2 . 20) (3 . 22) (5 . 25) (6 . 26)) 6.148 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.8596 [and 1/min{score2}: 0.2599] [4246, 4005]: Comparing 1nh0_A and 1mpp, based on their crossing files. There are 11 (1 H + 10 S) secondary structure elements in 1nh0_A, of which 8 satisfy the size requirements. There are 41 (11 H + 30 S) secondary structure elements in 1mpp, of which 35 satisfy the size requirements. 1.02141 [ 4.37526] ((2 . 2) (3 . 3) (5 . 8) (6 . 9) (7 . 10) (8 . 12) (10 . 17) (11 . 24)) 7.400 {1/22:28} B:0 1.16406 [ 5.00026] ((2 . 2) (3 . 3) (5 . 8) (6 . 9) (7 . 10) (8 . 12) (10 . 17)) 5.111 {1/17:21} B:0 1.65895 [ 7.00074] ((2 . 3) (3 . 4) (6 . 7) (7 . 8) (8 . 9)) 6.056 {1/10:10} B:0 2.00027 [ 8.75000] ((5 . 32) (6 . 33) (7 . 35) (8 . 36)) 4.897 {0/2:6} B:0 2.00069 [ 8.75001] ((2 . 8) (3 . 9) (7 . 14) (10 . 17)) 6.163 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.9790 [and 1/min{score2}: 0.2286] [4246, 4246]: Comparing 1nh0_A and 1nh0_A, based on their crossing files. There are 11 (1 H + 10 S) secondary structure elements in 1nh0_A, of which 8 satisfy the size requirements. There are 11 (1 H + 10 S) secondary structure elements in 1nh0_A, of which 8 satisfy the size requirements. 1.00000 [ 1.00000] ((2 . 2) (3 . 3) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (10 . 10) (11 . 11)) 0.000 {0/24:28} B:0 2.38102 [ 2.38102] ((5 . 3) (7 . 6) (8 . 5) (11 . 8)) 9.795 {1/5:6} B:1 2.38102 [ 2.38102] ((3 . 5) (5 . 8) (6 . 7) (8 . 11)) 9.795 {1/5:6} B:1 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [4246, 4378]: Comparing 1nh0_A and 1nso_A, based on their crossing files. There are 11 (1 H + 10 S) secondary structure elements in 1nh0_A, of which 8 satisfy the size requirements. There are 8 (2 H + 6 S) secondary structure elements in 1nso_A, of which 7 satisfy the size requirements. 1.60009 [ 1.40013] ((2 . 1) (3 . 2) (7 . 6) (8 . 7) (10 . 8)) 3.124 {0/7:10} B:0 SIMILARITY (1/min{score1}): 0.6250 [and 1/min{score2}: 0.7142] [4246, 4618]: Comparing 1nh0_A and 1oew_A, based on their crossing files. There are 11 (1 H + 10 S) secondary structure elements in 1nh0_A, of which 8 satisfy the size requirements. There are 35 (8 H + 27 S) secondary structure elements in 1oew_A, of which 31 satisfy the size requirements. 1.81643 [ 5.18061] ((2 . 20) (3 . 21) (5 . 25) (7 . 26) (8 . 27) (10 . 33)) 5.015 {2/12:15} B:0 1.83786 [ 4.45624] ((2 . 2) (3 . 3) (5 . 8) (6 . 9) (7 . 10) (8 . 11) (11 . 17)) 4.257 {3/17:21} B:0 2.00049 [ 7.75001] ((2 . 8) (3 . 9) (7 . 14) (10 . 16)) 5.660 {0/5:6} B:0 2.00076 [ 7.75001] ((2 . 26) (3 . 27) (7 . 34) (8 . 35)) 6.323 {0/4:6} B:0 2.00121 [ 7.75002] ((2 . 29) (3 . 30) (5 . 34) (6 . 35)) 7.095 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.6981 [and 1/min{score2}: 0.2443] [4246, 6394]: Comparing 1nh0_A and 2apr, based on their crossing files. There are 11 (1 H + 10 S) secondary structure elements in 1nh0_A, of which 8 satisfy the size requirements. There are 38 (10 H + 28 S) secondary structure elements in 2apr, of which 31 satisfy the size requirements. 1.60078 [ 6.20001] ((2 . 21) (3 . 22) (5 . 27) (7 . 29) (8 . 30)) 5.377 {0/7:10} B:0 2.00082 [ 7.75001] ((2 . 29) (3 . 30) (6 . 37) (8 . 38)) 6.435 {0/5:6} B:0 2.00082 [ 7.75001] ((2 . 3) (3 . 4) (6 . 6) (8 . 7)) 6.447 {0/5:6} B:0 2.00092 [ 7.75002] ((2 . 29) (3 . 30) (7 . 37) (8 . 38)) 6.631 {0/5:6} B:0 2.00131 [ 7.75002] ((2 . 32) (3 . 33) (5 . 37) (6 . 38)) 7.237 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.8620 [and 1/min{score2}: 0.2443] [4246, 6525]: Comparing 1nh0_A and 2rsp_A, based on their crossing files. There are 11 (1 H + 10 S) secondary structure elements in 1nh0_A, of which 8 satisfy the size requirements. There are 12 (1 H + 11 S) secondary structure elements in 2rsp_A, of which 12 satisfy the size requirements. 1.37965 [ 1.80239] ((2 . 2) (3 . 3) (6 . 6) (7 . 7) (8 . 8) (10 . 11) (11 . 12)) 3.102 {2/17:21} B:0 2.00059 [ 3.00018] ((5 . 3) (6 . 4) (7 . 5) (8 . 6)) 5.937 {0/6:6} B:0 2.00067 [ 3.00020] ((2 . 2) (3 . 3) (5 . 4) (10 . 11)) 6.112 {0/5:6} B:0 2.72431 [ 3.31033] ((2 . 3) (8 . 10) (10 . 11) (11 . 12)) 6.105 {1/4:6} B:0 2.72561 [ 3.31105] ((2 . 7) (3 . 8) (5 . 10) (6 . 12)) 9.544 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.7248 [and 1/min{score2}: 0.5852] [4246, 6610]: Comparing 1nh0_A and 4fiv, based on their crossing files. There are 11 (1 H + 10 S) secondary structure elements in 1nh0_A, of which 8 satisfy the size requirements. There are 10 (2 H + 8 S) secondary structure elements in 4fiv, of which 8 satisfy the size requirements. 1.15856 [ 1.15856] ((2 . 1) (3 . 2) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (10 . 10)) 2.296 {1/18:21} B:0 2.37852 [ 2.37852] ((2 . 1) (3 . 2) (6 . 5) (10 . 10)) 4.355 {1/5:6} B:0 4.06126 [ 4.06126] ((5 . 1) (6 . 2) (8 . 3) (11 . 6)) 7.431 {2/5:6} B:0 4.06199 [ 4.06199] ((6 . 1) (7 . 2) (8 . 3) (11 . 5)) 11.238 {2/5:6} B:0 5.03193 [ 5.03193] ((3 . 5) (6 . 6) (7 . 8) (10 . 10)) 9.390 {2/4:6} B:0 SIMILARITY (1/min{score1}): 0.8631 [and 1/min{score2}: 0.8631] -------------------------------------------------------------------------------------------------------------------------