------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [4771, 3299]: Comparing 1os1_A and 1khb_A, based on their crossing files. There are 49 (21 H + 28 S) secondary structure elements in 1os1_A, of which 23 satisfy the size requirements. There are 55 (23 H + 32 S) secondary structure elements in 1khb_A, of which 25 satisfy the size requirements. 1.05899 [ 1.13398] ((20 . 26) (21 . 27) (22 . 28) (23 . 29) (24 . 30) (25 . 31) (26 . 32) (27 . 33) (28 . 34) (29 . 35) (32 . 40) (34 . 42) (35 . 43) (36 . 44) (37 . 45) (38 . 46) (41 . 48) (42 . 49) (43 . 50) (44 . 51) (45 . 52) (48 . 54) (49 . 55)) 3.615 {14/197:253} B:0 1.48353 [ 1.51849] ((20 . 26) (21 . 27) (22 . 28) (23 . 29) (24 . 30) (25 . 31) (26 . 32) (27 . 33) (28 . 34) (29 . 35) (32 . 40) (34 . 42) (35 . 43) (36 . 44) (38 . 45) (41 . 48) (42 . 49) (43 . 50) (44 . 51) (45 . 52) (48 . 53) (49 . 55)) 5.023 {25/181:231} B:0 1.79380 [ 1.82954] ((20 . 26) (21 . 27) (22 . 28) (23 . 29) (24 . 30) (27 . 33) (32 . 35) (34 . 42) (35 . 43) (36 . 44) (37 . 45) (38 . 46) (41 . 48) (42 . 49) (43 . 50) (44 . 51) (45 . 52) (48 . 54) (49 . 55)) 4.148 {22/130:171} B:0 1.90901 [ 1.92578] ((20 . 26) (21 . 27) (22 . 28) (23 . 29) (24 . 30) (25 . 31) (26 . 32) (27 . 33) (28 . 34) (29 . 35) (32 . 40) (34 . 42) (35 . 43) (36 . 44) (37 . 45) (38 . 46) (41 . 48) (42 . 49) (43 . 50) (44 . 51) (45 . 52) (48 . 55)) 3.974 {33/177:231} B:0 3.28678 [ 3.57226] ((23 . 29) (27 . 33) (28 . 34) (29 . 35) (38 . 43) (41 . 48) (43 . 50)) 6.757 {1/17:21} B:0 SIMILARITY (1/min{score1}): 0.9443 [and 1/min{score2}: 0.8819] [4771, 3369]: Comparing 1os1_A and 1knx_A, based on their crossing files. There are 49 (21 H + 28 S) secondary structure elements in 1os1_A, of which 23 satisfy the size requirements. There are 27 (13 H + 14 S) secondary structure elements in 1knx_A, of which 15 satisfy the size requirements. 1.94539 [ 1.34462] ((20 . 12) (21 . 13) (22 . 14) (23 . 15) (24 . 16) (25 . 17) (26 . 18) (27 . 19) (32 . 20) (34 . 23) (42 . 25) (43 . 26)) 4.203 {4/42:66} B:0 4.60006 [ 3.00023] ((20 . 16) (21 . 17) (22 . 18) (26 . 23) (27 . 24)) 6.377 {0/9:10} B:0 4.69742 [ 3.31079] ((20 . 16) (21 . 17) (22 . 18) (26 . 23) (29 . 25)) 8.735 {2/8:10} B:0 4.76251 [ 3.48617] ((20 . 12) (21 . 13) (22 . 14) (24 . 16) (27 . 18)) 8.120 {2/7:10} B:0 5.75003 [ 3.75012] ((21 . 13) (24 . 14) (29 . 19) (34 . 25)) 6.355 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.5140 [and 1/min{score2}: 0.7437] [4771, 3377]: Comparing 1os1_A and 1ko7_A, based on their crossing files. There are 49 (21 H + 28 S) secondary structure elements in 1os1_A, of which 23 satisfy the size requirements. There are 31 (14 H + 17 S) secondary structure elements in 1ko7_A, of which 17 satisfy the size requirements. 1.92262 [ 1.43125] ((20 . 14) (21 . 15) (22 . 16) (23 . 17) (24 . 18) (25 . 19) (26 . 20) (27 . 22) (32 . 23) (34 . 27) (42 . 29) (43 . 30)) 3.568 {3/47:66} B:0 2.09957 [ 1.56660] ((20 . 14) (21 . 15) (22 . 16) (23 . 17) (24 . 18) (25 . 19) (26 . 20) (27 . 22) (32 . 23) (34 . 27) (43 . 30)) 3.510 {3/40:55} B:0 5.75004 [ 4.25009] ((35 . 15) (41 . 21) (44 . 28) (45 . 29)) 6.473 {0/5:6} B:0 5.75006 [ 4.25015] ((27 . 14) (32 . 19) (34 . 23) (36 . 24)) 7.411 {0/4:6} B:0 5.75006 [ 4.25016] ((37 . 16) (41 . 21) (42 . 22) (48 . 30)) 7.488 {0/6:6} B:0 SIMILARITY (1/min{score1}): 0.5201 [and 1/min{score2}: 0.6987] [4771, 4771]: Comparing 1os1_A and 1os1_A, based on their crossing files. There are 49 (21 H + 28 S) secondary structure elements in 1os1_A, of which 23 satisfy the size requirements. There are 49 (21 H + 28 S) secondary structure elements in 1os1_A, of which 23 satisfy the size requirements. 1.00000 [ 1.00000] ((20 . 20) (21 . 21) (22 . 22) (23 . 23) (24 . 24) (25 . 25) (26 . 26) (27 . 27) (28 . 28) (29 . 29) (32 . 32) (34 . 34) (35 . 35) (36 . 36) (37 . 37) (38 . 38) (41 . 41) (42 . 42) (43 . 43) (44 . 44) (45 . 45) (48 . 48) (49 . 49)) 0.000 {0/213:253} B:0 4.60028 [ 4.60028] ((21 . 24) (22 . 25) (36 . 41) (38 . 42) (48 . 49)) 9.191 {0/8:10} B:0 4.60028 [ 4.60028] ((24 . 21) (25 . 22) (41 . 36) (42 . 38) (49 . 48)) 9.191 {0/8:10} B:0 5.75004 [ 5.75004] ((38 . 22) (43 . 28) (44 . 29) (45 . 32)) 6.796 {0/2:6} B:0 5.75004 [ 5.75004] ((22 . 38) (28 . 43) (29 . 44) (32 . 45)) 6.796 {0/2:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] -------------------------------------------------------------------------------------------------------------------------