------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [2335, 1951]: Comparing 1hyo_A and 1gtt_A, based on their crossing files. There are 42 (16 H + 26 S) secondary structure elements in 1hyo_A, of which 20 satisfy the size requirements. There are 45 (16 H + 29 S) secondary structure elements in 1gtt_A, of which 13 satisfy the size requirements. 1.66765 [ 1.08689] ((12 . 1) (13 . 2) (15 . 4) (21 . 9) (22 . 10) (23 . 11) (33 . 14) (34 . 15) (35 . 17) (36 . 18) (41 . 20) (42 . 21)) 3.347 {2/56:66} B:0 1.81837 [ 1.18249] ((12 . 1) (15 . 4) (21 . 9) (22 . 10) (23 . 11) (33 . 14) (34 . 15) (35 . 17) (36 . 18) (41 . 20) (42 . 21)) 3.383 {1/45:55} B:0 1.81962 [ 1.18701] ((12 . 1) (13 . 2) (21 . 9) (22 . 10) (23 . 11) (33 . 14) (34 . 15) (35 . 17) (36 . 18) (41 . 20) (42 . 21)) 3.267 {2/47:55} B:0 3.33340 [ 2.16690] ((12 . 1) (16 . 4) (21 . 9) (22 . 10) (23 . 11) (34 . 20)) 5.005 {0/13:15} B:0 4.00001 [ 2.60003] ((13 . 2) (21 . 9) (22 . 10) (23 . 11) (34 . 20)) 3.368 {0/9:10} B:0 SIMILARITY (1/min{score1}): 0.5996 [and 1/min{score2}: 0.9201] [2335, 1952]: Comparing 1hyo_A and 1gtt_A, based on their crossing files. There are 42 (16 H + 26 S) secondary structure elements in 1hyo_A, of which 20 satisfy the size requirements. There are 45 (16 H + 29 S) secondary structure elements in 1gtt_A, of which 12 satisfy the size requirements. 1.81822 [ 1.09109] ((12 . 23) (15 . 24) (21 . 29) (22 . 30) (23 . 31) (33 . 38) (34 . 39) (35 . 41) (36 . 42) (41 . 43) (42 . 44)) 2.810 {0/43:55} B:0 3.34978 [ 2.07264] ((12 . 29) (15 . 31) (21 . 38) (23 . 39) (25 . 41) (36 . 43)) 5.399 {1/8:15} B:0 4.00001 [ 2.40005] ((16 . 24) (21 . 29) (22 . 30) (23 . 31) (34 . 43)) 3.729 {0/7:10} B:0 4.00007 [ 2.40032] ((21 . 24) (33 . 38) (34 . 39) (35 . 41) (36 . 42)) 5.846 {0/9:10} B:0 5.00007 [ 3.00031] ((12 . 31) (18 . 38) (19 . 39) (23 . 42)) 6.822 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.5500 [and 1/min{score2}: 0.9165] [2335, 2335]: Comparing 1hyo_A and 1hyo_A, based on their crossing files. There are 42 (16 H + 26 S) secondary structure elements in 1hyo_A, of which 20 satisfy the size requirements. There are 42 (16 H + 26 S) secondary structure elements in 1hyo_A, of which 20 satisfy the size requirements. 1.00000 [ 1.00000] ((12 . 12) (13 . 13) (15 . 15) (16 . 16) (18 . 18) (19 . 19) (21 . 21) (22 . 22) (23 . 23) (25 . 25) (26 . 26) (27 . 27) (29 . 29) (33 . 33) (34 . 34) (35 . 35) (36 . 36) (38 . 38) (41 . 41) (42 . 42)) 0.000 {0/168:190} B:0 4.14481 [ 4.14481] ((25 . 35) (27 . 36) (29 . 38) (33 . 41) (34 . 42)) 8.285 {2/8:10} B:0 4.14481 [ 4.14481] ((35 . 25) (36 . 27) (38 . 29) (41 . 33) (42 . 34)) 8.285 {2/8:10} B:0 4.41358 [ 4.41358] ((12 . 12) (13 . 13) (33 . 34) (35 . 35) (38 . 38)) 3.760 {3/9:10} B:0 4.41358 [ 4.41358] ((12 . 12) (13 . 13) (34 . 33) (35 . 35) (38 . 38)) 3.760 {3/9:10} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [2335, 4363]: Comparing 1hyo_A and 1nr9_A, based on their crossing files. There are 42 (16 H + 26 S) secondary structure elements in 1hyo_A, of which 20 satisfy the size requirements. There are 22 (8 H + 14 S) secondary structure elements in 1nr9_A, of which 16 satisfy the size requirements. 1.42901 [ 1.14372] ((12 . 1) (15 . 2) (16 . 4) (21 . 6) (22 . 7) (23 . 8) (25 . 9) (27 . 11) (33 . 15) (34 . 16) (35 . 18) (36 . 19) (41 . 21) (42 . 22)) 2.700 {2/78:91} B:0 1.53855 [ 1.23094] ((12 . 1) (16 . 4) (21 . 6) (22 . 7) (23 . 8) (25 . 9) (27 . 11) (33 . 15) (34 . 16) (35 . 18) (36 . 19) (41 . 21) (42 . 22)) 2.644 {1/67:78} B:0 1.82972 [ 1.67656] ((12 . 1) (15 . 2) (16 . 4) (21 . 6) (22 . 7) (23 . 8) (26 . 9) (33 . 15) (34 . 16) (35 . 18) (36 . 19) (41 . 21) (42 . 22)) 4.080 {10/65:78} B:0 3.33342 [ 2.66684] ((16 . 2) (21 . 6) (22 . 7) (23 . 8) (25 . 9) (27 . 11)) 5.422 {0/11:15} B:0 3.34367 [ 2.68672] ((12 . 6) (15 . 8) (21 . 15) (23 . 16) (25 . 18) (36 . 21)) 5.482 {1/9:15} B:0 SIMILARITY (1/min{score1}): 0.6998 [and 1/min{score2}: 0.8743] -------------------------------------------------------------------------------------------------------------------------