------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [2244, 555]: Comparing 1hn0_A and 1cb8_A, based on their crossing files. There are 80 (28 H + 52 S) secondary structure elements in 1hn0_A, of which 11 satisfy the size requirements. There are 57 (22 H + 35 S) secondary structure elements in 1cb8_A, of which 10 satisfy the size requirements. 1.57148 [ 1.42864] ((69 . 47) (70 . 48) (71 . 49) (73 . 51) (74 . 52) (75 . 53) (76 . 54)) 2.674 {0/9:21} B:0 1.83371 [ 1.66716] ((69 . 48) (70 . 49) (71 . 50) (73 . 52) (75 . 54) (76 . 55)) 4.956 {0/5:15} B:0 1.83406 [ 1.66763] ((69 . 48) (70 . 49) (71 . 50) (74 . 53) (75 . 54) (76 . 55)) 5.853 {0/7:15} B:0 2.20037 [ 2.00049] ((73 . 48) (76 . 51) (78 . 53) (79 . 54) (80 . 55)) 5.657 {0/4:10} B:0 2.20039 [ 2.00052] ((70 . 47) (71 . 48) (75 . 52) (76 . 53) (78 . 55)) 5.757 {0/6:10} B:0 SIMILARITY (1/min{score1}): 0.8180 [and 1/min{score2}: 0.8997] [2244, 1364]: Comparing 1hn0_A and 1f1s_A, based on their crossing files. There are 80 (28 H + 52 S) secondary structure elements in 1hn0_A, of which 11 satisfy the size requirements. There are 68 (27 H + 41 S) secondary structure elements in 1f1s_A, of which 8 satisfy the size requirements. 1.57157 [ 1.14322] ((69 . 61) (70 . 62) (71 . 63) (73 . 65) (74 . 66) (75 . 67) (76 . 68)) 3.463 {0/7:21} B:0 1.83354 [ 1.33386] ((74 . 61) (75 . 62) (76 . 63) (77 . 64) (78 . 65) (79 . 66)) 4.258 {0/2:15} B:0 2.20020 [ 1.60052] ((69 . 62) (70 . 63) (73 . 66) (74 . 67) (75 . 68)) 4.855 {0/3:10} B:0 2.75009 [ 2.00024] ((77 . 61) (78 . 62) (79 . 63) (80 . 64)) 4.713 {0/0:6} B:0 2.75015 [ 2.00038] ((69 . 65) (70 . 66) (71 . 67) (73 . 68)) 5.303 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.6363 [and 1/min{score2}: 0.8747] [2244, 2244]: Comparing 1hn0_A and 1hn0_A, based on their crossing files. There are 80 (28 H + 52 S) secondary structure elements in 1hn0_A, of which 11 satisfy the size requirements. There are 80 (28 H + 52 S) secondary structure elements in 1hn0_A, of which 11 satisfy the size requirements. 1.00000 [ 1.00000] ((69 . 69) (70 . 70) (71 . 71) (73 . 73) (74 . 74) (75 . 75) (76 . 76) (77 . 77) (78 . 78) (79 . 79) (80 . 80)) 0.000 {0/38:55} B:0 1.87346 [ 1.87346] ((70 . 69) (71 . 70) (74 . 73) (76 . 75) (78 . 77) (80 . 79)) 6.156 {1/10:15} B:0 1.87346 [ 1.87346] ((69 . 70) (70 . 71) (73 . 74) (75 . 76) (77 . 78) (79 . 80)) 6.156 {1/10:15} B:0 1.87363 [ 1.87363] ((70 . 69) (71 . 70) (75 . 74) (76 . 75) (78 . 77) (80 . 79)) 6.450 {1/10:15} B:0 1.87363 [ 1.87363] ((69 . 70) (70 . 71) (74 . 75) (75 . 76) (77 . 78) (79 . 80)) 6.450 {1/10:15} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [2244, 2690]: Comparing 1hn0_A and 1j0m_A, based on their crossing files. There are 80 (28 H + 52 S) secondary structure elements in 1hn0_A, of which 11 satisfy the size requirements. There are 58 (23 H + 35 S) secondary structure elements in 1j0m_A, of which 12 satisfy the size requirements. 1.00008 [ 1.09097] ((69 . 47) (70 . 48) (71 . 49) (73 . 51) (74 . 52) (75 . 53) (76 . 54) (77 . 55) (78 . 56) (79 . 57) (80 . 58)) 2.162 {0/33:55} B:0 1.83371 [ 2.00029] ((69 . 48) (70 . 49) (71 . 50) (75 . 54) (76 . 55) (79 . 58)) 4.975 {0/9:15} B:0 1.83380 [ 2.00036] ((70 . 47) (71 . 48) (75 . 52) (76 . 53) (78 . 55) (80 . 57)) 5.243 {0/9:15} B:0 2.20039 [ 2.40030] ((69 . 48) (70 . 49) (71 . 50) (74 . 53) (75 . 54)) 5.739 {0/3:10} B:0 2.20073 [ 2.40056] ((74 . 49) (76 . 53) (78 . 55) (79 . 56) (80 . 57)) 6.720 {0/4:10} B:0 SIMILARITY (1/min{score1}): 0.9999 [and 1/min{score2}: 0.9166] [2244, 4154]: Comparing 1hn0_A and 1n7o_A, based on their crossing files. There are 80 (28 H + 52 S) secondary structure elements in 1hn0_A, of which 11 satisfy the size requirements. There are 59 (26 H + 33 S) secondary structure elements in 1n7o_A, of which 7 satisfy the size requirements. 1.83336 [ 1.16675] ((69 . 51) (70 . 52) (71 . 53) (73 . 55) (74 . 56) (75 . 57)) 2.449 {0/4:15} B:0 2.75009 [ 1.75033] ((70 . 51) (71 . 52) (75 . 56) (76 . 57)) 4.652 {0/2:6} B:0 2.75013 [ 1.75051] ((69 . 52) (70 . 53) (71 . 54) (74 . 57)) 5.179 {0/1:6} B:0 2.75022 [ 1.75085] ((76 . 52) (78 . 54) (79 . 55) (80 . 56)) 5.886 {0/1:6} B:0 2.75031 [ 1.75120] ((70 . 51) (71 . 52) (73 . 53) (75 . 56)) 6.409 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.6362 [and 1/min{score2}: 0.9983] [2244, 5712]: Comparing 1hn0_A and 1rwh_A, based on their crossing files. There are 80 (28 H + 52 S) secondary structure elements in 1hn0_A, of which 11 satisfy the size requirements. There are 60 (22 H + 38 S) secondary structure elements in 1rwh_A, of which 12 satisfy the size requirements. 1.00131 [ 1.09192] ((69 . 49) (70 . 50) (71 . 51) (73 . 53) (74 . 54) (75 . 55) (76 . 56) (77 . 57) (78 . 58) (79 . 59) (80 . 60)) 2.326 {1/38:55} B:0 1.83381 [ 2.00037] ((69 . 50) (70 . 51) (71 . 52) (73 . 54) (75 . 56) (79 . 60)) 5.267 {0/7:15} B:0 1.83489 [ 2.00120] ((70 . 50) (73 . 51) (74 . 52) (76 . 56) (79 . 59) (80 . 60)) 7.084 {0/8:15} B:0 2.20017 [ 2.40013] ((69 . 54) (70 . 55) (71 . 56) (73 . 58) (74 . 59)) 4.660 {0/3:10} B:0 2.20056 [ 2.40043] ((69 . 50) (70 . 51) (71 . 52) (74 . 55) (75 . 56)) 6.300 {0/3:10} B:0 SIMILARITY (1/min{score1}): 0.9987 [and 1/min{score2}: 0.9158] -------------------------------------------------------------------------------------------------------------------------