------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [1495, 69]: Comparing 1ffy_A and 1a8h, based on their crossing files. There are 68 (40 H + 28 S) secondary structure elements in 1ffy_A, of which 16 satisfy the size requirements. There are 35 (21 H + 14 S) secondary structure elements in 1a8h, of which 7 satisfy the size requirements. 3.20019 [ 1.40222] ((46 . 29) (49 . 30) (50 . 31) (53 . 33) (54 . 34)) 6.325 {0/3:10} B:0 4.00142 [ 1.76676] ((49 . 29) (50 . 30) (53 . 31) (54 . 33)) 12.433 {0/1:6} B:0 4.00176 [ 1.77071] ((46 . 30) (49 . 31) (50 . 33) (53 . 35)) 13.119 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.3125 [and 1/min{score2}: 0.7132] [1495, 1430]: Comparing 1ffy_A and 1f7u_A, based on their crossing files. There are 68 (40 H + 28 S) secondary structure elements in 1ffy_A, of which 16 satisfy the size requirements. There are 48 (34 H + 14 S) secondary structure elements in 1f7u_A, of which 6 satisfy the size requirements. 3.20076 [ 1.21409] ((49 . 42) (50 . 45) (52 . 46) (53 . 47) (54 . 48)) 8.978 {0/3:10} B:0 4.00006 [ 1.50110] ((50 . 45) (52 . 46) (53 . 47) (54 . 48)) 5.589 {0/2:6} B:0 4.00010 [ 1.50193] ((46 . 42) (49 . 45) (50 . 47) (53 . 48)) 6.432 {0/3:6} B:0 4.00042 [ 1.50789] ((49 . 42) (52 . 46) (53 . 47) (54 . 48)) 9.159 {0/1:6} B:0 4.00126 [ 1.52339] ((46 . 42) (49 . 45) (52 . 47) (53 . 48)) 12.064 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.3124 [and 1/min{score2}: 0.8237] [1495, 1495]: Comparing 1ffy_A and 1ffy_A, based on their crossing files. There are 68 (40 H + 28 S) secondary structure elements in 1ffy_A, of which 16 satisfy the size requirements. There are 68 (40 H + 28 S) secondary structure elements in 1ffy_A, of which 16 satisfy the size requirements. 1.00000 [ 1.00000] ((46 . 46) (49 . 49) (50 . 50) (52 . 52) (53 . 53) (54 . 54) (56 . 56) (58 . 58) (59 . 59) (60 . 60) (61 . 61) (62 . 62) (63 . 63) (66 . 66) (67 . 67) (68 . 68)) 0.000 {0/106:120} B:0 3.31575 [ 3.31575] ((46 . 46) (49 . 50) (56 . 56) (58 . 61) (68 . 68)) 5.541 {2/10:10} B:0 3.31575 [ 3.31575] ((46 . 46) (50 . 49) (56 . 56) (61 . 58) (68 . 68)) 5.541 {2/10:10} B:0 3.69233 [ 3.69233] ((46 . 46) (49 . 50) (56 . 56) (58 . 58) (68 . 68)) 4.967 {3/10:10} B:0 3.69233 [ 3.69233] ((46 . 46) (50 . 49) (56 . 56) (58 . 58) (68 . 68)) 4.967 {3/10:10} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [1495, 2528]: Comparing 1ffy_A and 1ile, based on their crossing files. There are 68 (40 H + 28 S) secondary structure elements in 1ffy_A, of which 16 satisfy the size requirements. There are 64 (37 H + 27 S) secondary structure elements in 1ile, of which 7 satisfy the size requirements. 2.28603 [ 1.00379] ((46 . 57) (49 . 58) (50 . 59) (52 . 60) (53 . 61) (54 . 62) (56 . 64)) 5.624 {0/15:21} B:0 2.66669 [ 1.16699] ((49 . 58) (50 . 59) (52 . 60) (53 . 61) (54 . 62) (56 . 64)) 3.398 {0/11:15} B:0 4.00051 [ 1.75603] ((49 . 57) (52 . 58) (53 . 59) (59 . 64)) 9.604 {0/4:6} B:0 4.00175 [ 1.77059] ((49 . 57) (50 . 58) (53 . 60) (54 . 61)) 13.099 {0/2:6} B:0 3.88944 [ 3.36248] ((49 . 61) (53 . 57) (54 . 62) (56 . 60) (60 . 64)) 13.674 {2/6:10} B:2 SIMILARITY (1/min{score1}): 0.4374 [and 1/min{score2}: 0.9962] [1495, 2627]: Comparing 1ffy_A and 1ivs_A, based on their crossing files. There are 68 (40 H + 28 S) secondary structure elements in 1ffy_A, of which 16 satisfy the size requirements. There are 68 (34 H + 34 S) secondary structure elements in 1ivs_A, of which 12 satisfy the size requirements. 1.44753 [ 1.22201] ((46 . 52) (49 . 53) (50 . 54) (52 . 55) (53 . 56) (54 . 57) (56 . 59) (58 . 60) (59 . 61) (60 . 62) (62 . 64) (63 . 65)) 3.489 {6/57:66} B:0 1.45464 [ 1.09113] ((46 . 52) (49 . 53) (50 . 54) (52 . 55) (53 . 56) (54 . 57) (56 . 59) (58 . 60) (60 . 62) (62 . 64) (63 . 65)) 2.932 {0/46:55} B:0 3.20005 [ 2.40011] ((46 . 52) (49 . 53) (50 . 54) (56 . 59) (58 . 64)) 4.437 {0/9:10} B:0 3.20037 [ 2.40088] ((52 . 54) (56 . 59) (58 . 60) (59 . 61) (63 . 65)) 7.524 {0/9:10} B:0 3.25749 [ 2.52917] ((46 . 52) (49 . 53) (50 . 54) (53 . 57) (56 . 59)) 6.318 {1/6:10} B:0 SIMILARITY (1/min{score1}): 0.6908 [and 1/min{score2}: 0.9165] [1495, 5000]: Comparing 1ffy_A and 1pfv_A, based on their crossing files. There are 68 (40 H + 28 S) secondary structure elements in 1ffy_A, of which 16 satisfy the size requirements. There are 38 (22 H + 16 S) secondary structure elements in 1pfv_A, of which 9 satisfy the size requirements. 2.69837 [ 1.65547] ((46 . 30) (49 . 32) (50 . 33) (52 . 34) (53 . 35) (54 . 36)) 4.610 {1/8:15} B:0 3.20033 [ 1.80187] ((46 . 30) (49 . 32) (52 . 33) (53 . 35) (54 . 36)) 7.311 {0/3:10} B:0 4.00154 [ 2.25863] ((46 . 32) (49 . 34) (50 . 35) (53 . 37)) 12.690 {0/1:6} B:0 4.00164 [ 2.25917] ((46 . 32) (49 . 33) (50 . 35) (53 . 37)) 12.885 {0/0:6} B:0 4.00223 [ 2.26241] ((50 . 30) (53 . 32) (54 . 33) (60 . 38)) 13.903 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.3706 [and 1/min{score2}: 0.6041] -------------------------------------------------------------------------------------------------------------------------