------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [4679, 1030]: Comparing 1ojr_A and 1e4c_P, based on their crossing files. There are 23 (14 H + 9 S) secondary structure elements in 1ojr_A, of which 20 satisfy the size requirements. There are 16 (9 H + 7 S) secondary structure elements in 1e4c_P, of which 13 satisfy the size requirements. 1.53856 [ 1.00035] ((2 . 1) (3 . 2) (7 . 3) (10 . 6) (12 . 7) (13 . 8) (14 . 9) (16 . 10) (18 . 12) (19 . 13) (20 . 14) (21 . 15) (22 . 16)) 2.545 {1/60:78} B:0 2.29502 [ 2.15091] ((2 . 1) (3 . 2) (11 . 6) (12 . 7) (13 . 8) (14 . 9) (16 . 10) (18 . 12) (19 . 13) (20 . 14) (21 . 15) (22 . 16)) 3.417 {11/52:66} B:0 3.33570 [ 2.17524] ((12 . 7) (13 . 8) (14 . 9) (17 . 13) (21 . 15) (22 . 16)) 2.582 {1/13:15} B:0 4.00001 [ 2.60003] ((10 . 6) (12 . 7) (13 . 8) (14 . 9) (17 . 13)) 3.391 {0/9:10} B:0 4.00013 [ 2.60048] ((2 . 1) (5 . 6) (7 . 8) (12 . 12) (13 . 13)) 6.869 {0/8:10} B:0 SIMILARITY (1/min{score1}): 0.6500 [and 1/min{score2}: 0.9996] [4679, 3123]: Comparing 1ojr_A and 1k0w_A, based on their crossing files. There are 23 (14 H + 9 S) secondary structure elements in 1ojr_A, of which 20 satisfy the size requirements. There are 16 (9 H + 7 S) secondary structure elements in 1k0w_A, of which 15 satisfy the size requirements. 1.42870 [ 1.07174] ((2 . 1) (3 . 2) (7 . 3) (10 . 5) (11 . 6) (12 . 7) (13 . 8) (14 . 9) (16 . 10) (18 . 12) (19 . 13) (20 . 14) (21 . 15) (22 . 16)) 2.962 {1/73:91} B:0 1.53858 [ 1.15412] ((2 . 1) (3 . 2) (7 . 3) (10 . 5) (11 . 6) (12 . 7) (13 . 8) (14 . 9) (16 . 10) (18 . 12) (19 . 13) (20 . 14) (21 . 15)) 2.868 {1/62:78} B:0 1.53859 [ 1.15414] ((2 . 1) (3 . 2) (7 . 3) (10 . 5) (11 . 6) (12 . 7) (13 . 8) (16 . 10) (18 . 12) (19 . 13) (20 . 14) (21 . 15) (22 . 16)) 2.915 {1/61:78} B:0 4.00044 [ 3.00105] ((2 . 1) (3 . 2) (14 . 11) (15 . 12) (17 . 13)) 9.295 {0/9:10} B:0 5.00002 [ 3.75005] ((18 . 1) (19 . 2) (20 . 3) (23 . 9)) 5.063 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.6999 [and 1/min{score2}: 0.9331] [4679, 4679]: Comparing 1ojr_A and 1ojr_A, based on their crossing files. There are 23 (14 H + 9 S) secondary structure elements in 1ojr_A, of which 20 satisfy the size requirements. There are 23 (14 H + 9 S) secondary structure elements in 1ojr_A, of which 20 satisfy the size requirements. 1.00000 [ 1.00000] ((2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (10 . 10) (11 . 11) (12 . 12) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (17 . 17) (18 . 18) (19 . 19) (20 . 20) (21 . 21) (22 . 22) (23 . 23)) 0.000 {0/167:190} B:0 2.22260 [ 2.22260] ((2 . 2) (4 . 4) (6 . 6) (12 . 12) (13 . 13) (19 . 17) (21 . 21) (22 . 22) (23 . 23)) 1.650 {1/28:36} B:0 4.00000 [ 4.00000] ((2 . 2) (12 . 12) (13 . 13) (17 . 19) (21 . 21)) 2.086 {0/6:10} B:0 4.00674 [ 4.00674] ((7 . 10) (10 . 11) (14 . 15) (19 . 20) (22 . 23)) 10.784 {1/9:10} B:0 4.09289 [ 4.09289] ((10 . 7) (11 . 10) (14 . 12) (20 . 19) (23 . 22)) 11.124 {2/9:10} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [4679, 5133]: Comparing 1ojr_A and 1pvt_A, based on their crossing files. There are 23 (14 H + 9 S) secondary structure elements in 1ojr_A, of which 20 satisfy the size requirements. There are 19 (10 H + 9 S) secondary structure elements in 1pvt_A, of which 17 satisfy the size requirements. 1.25025 [ 1.06291] ((2 . 1) (3 . 2) (5 . 3) (7 . 4) (10 . 7) (11 . 8) (12 . 9) (13 . 10) (14 . 11) (15 . 13) (16 . 14) (17 . 15) (18 . 16) (19 . 17) (20 . 18) (21 . 19)) 2.213 {2/100:120} B:0 1.33339 [ 1.13342] ((2 . 1) (3 . 2) (5 . 3) (7 . 4) (10 . 7) (11 . 8) (12 . 9) (13 . 10) (14 . 11) (16 . 14) (17 . 15) (18 . 16) (19 . 17) (20 . 18) (21 . 19)) 2.125 {1/86:105} B:0 2.50001 [ 2.12502] ((2 . 1) (3 . 2) (5 . 3) (7 . 4) (12 . 9) (13 . 10) (17 . 17) (21 . 19)) 2.583 {0/20:28} B:0 3.37055 [ 2.89305] ((12 . 9) (13 . 10) (16 . 13) (17 . 15) (18 . 16) (21 . 19)) 4.322 {2/13:15} B:0 4.00008 [ 3.40013] ((7 . 2) (10 . 4) (11 . 7) (15 . 11) (20 . 17)) 6.073 {0/6:10} B:0 SIMILARITY (1/min{score1}): 0.7998 [and 1/min{score2}: 0.9408] -------------------------------------------------------------------------------------------------------------------------