Residue-by-residue listing for refined_10 Page 1
----------------------------------------
This listing highlights the residues in the structure which may need investigation.
The ideal values and standard deviations against which the structure has been compared are shown in the following table:
<------------------------------- I D E A L V A L U E S ------------------------------->
Chi-1 dihedral Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality
g(-) trans g(+) Chi-2 phi helix psi rt-hand lf-hand bond dihedral en. C-alpha
------------------------------------------------------------------------------------------
Ideal value 64.1 183.6 -66.7 177.4 -65.4 -65.3 -39.4 96.8 -85.8 2.0 180.0 -2.0 33.9
Standard deviation 15.7 16.8 15.0 18.5 11.2 11.9 11.3 14.8 10.7 .1 5.8 .8 3.5
------------------------------------------------------------------------------------------
In the listing below, properties that deviate from these values are highlighted by asterisks and plus-signs. Each asterisk
represents one standard deviation, and each plus-sign represents half a standard deviation. So, a highlight such as +***, indicates
that the value of the parameter is between 3.5 and 4.0 standard deviations from the ideal value shown above.
Where the deviation is greater than 4.5 standard deviations its numerical value is shown; for example, *5.5*.
The final column gives the maximum deviation in each row, while the maximum column deviations are shown at the end of the listing.
Also at the end are the keys to the codes used for the secondary structure and Ramachandran plot assignments.
Full print-out.
...................................................................................................................................
Residue Kabsch Region
--------- Sander of
No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max
Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev
-----------------------------------------------------------------------------------------------------------------------------------
1 MET 1 - - - -63.6 180.6 - - - - - - 171.0 - 35.9 -
+* +*
2 THR 2 B 49.3 - - - - - - - - - 192.0 - 34.0 -
** **
3 GLU 3 e b - 184.2 - 177.0 - - - - - - 181.7 -.9 33.0 -
+* +*
4 VAL 4 E B - - -66.4 - - - - - - - 175.7 -1.5 34.1 -
5 TYR 5 E B - - -59.7 - - - - - - - 171.0 -3.0 35.1 -
+* * +*
6 ASP 6 E B - - -63.2 - - - - - - - 185.4 - 33.2 -
7 LEU 7 E B - - -66.4 - - - - - - - 174.5 -3.3 34.7 -
+* +*
8 GLU 8 E B - 178.9 - 177.2 - - - - - - 183.1 -2.2 35.3 -
9 ILE 9 E B - - -61.7 - - - - - - - 178.0 -3.6 32.6 -
** **
10 THR 10 E B 46.8 - - - - - - - - - 184.7 -3.5 34.5 -
* +* +*
11 THR 11 E B - - -40.4 - - - - - - - 181.1 -.7 34.5 -
+* +* +*
12 ASN 12 e A - 173.7 - - - - - - - - 185.6 -1.9 36.5 -
13 ALA 13 T a - - - - - - - - - - 178.9 - 32.3 -
14 THR 14 E B 58.9 - - - - - - - - - 177.9 -1.1 34.6 -
* *
15 ASP 15 E A - 176.2 - - - - - - - - 177.9 - 33.2 -
16 PHE 16 E B - 179.0 - - - - - - - - 179.2 - 34.2 -
17 PRO 17 E - - - - - -80.0 - - - - - 184.1 - 38.4 -
* * *
18 MET 18 E B - 179.8 - 184.5 - - - - - - 177.8 -2.6 35.3 -
Residue-by-residue listing for refined_10 Page 2
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...................................................................................................................................
Residue Kabsch Region
--------- Sander of
No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max
Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev
-----------------------------------------------------------------------------------------------------------------------------------
19 GLU 19 E B 59.1 - - 182.1 - - - - - - 179.7 - 33.3 -
20 LYS 20 E B - - -73.5 - - - - - - - 181.3 -1.8 34.5 -
21 LYS 21 E B - 186.1 - 185.3 - - - - - - 178.5 - 36.1 -
22 TYR 22 E B - - -67.0 - - - - - - - 177.4 -3.0 32.9 -
* *
23 PRO 23 E - - - - - -60.6 - - - - - 180.5 - 39.1 -
* *
24 ALA 24 e A - - - - - - - - - - 179.9 -2.2 32.8 -
25 GLY 25 T - - - - - - - - - - - 179.1 -.6 - -
+* +*
26 MET 26 t B - 183.3 - - - - - - - - 179.4 -1.8 35.1 -
27 SER 27 h B 52.0 - - - - - - - - - 177.1 - 35.2 -
28 LEU 28 H A - 188.4 - - - -64.7 -33.5 - - - 182.7 -1.0 36.4 -
* *
29 ASN 29 H A - - -68.5 - - -66.0 -31.2 - - - 176.8 - 30.4 -
30 ASP 30 H A - 187.7 - - - -76.0 -35.3 - - - 180.0 - 34.9 -
31 LEU 31 H A - 189.5 - 169.8 - -65.8 -45.1 - - - 176.4 -1.5 35.1 -
32 LYS 32 H A - - -57.6 183.2 - -58.7 -50.0 - - - 180.8 -3.0 35.4 -
* *
33 LYS 33 H A - 193.0 - 175.0 - -59.9 -35.7 - - - 177.3 -2.2 36.3 -
34 LYS 34 H A - 196.6 - - - -65.8 -42.1 - - - 176.8 -2.2 36.3 -
35 LEU 35 H A - - -70.4 183.8 - -67.1 -39.7 - - - 177.2 -2.3 34.0 -
36 GLU 36 H A - - -69.2 - - -62.1 -30.2 - - - 173.8 -3.1 32.1 -
* * *
37 LEU 37 H A - 183.2 - - - -63.6 -29.0 - - - 178.9 -1.4 34.8 -
38 VAL 38 H A - 183.0 - - - -89.4 -41.2 - - - 183.6 -1.1 35.2 -
** * **
39 VAL 39 H A - 181.2 - - - -79.6 -28.0 - - - 177.3 -3.1 33.6 -
* * * *
40 GLY 40 h - - - - - - - - - - - 182.5 -2.8 - -
41 THR 41 S b - - -49.0 - - - - - - - 176.5 - 35.3 -
* *
42 THR 42 t B 55.0 - - - - - - - - - 186.9 - 33.0 -
* *
43 VAL 43 T A - 182.9 - - - - - - - - 179.4 - 34.7 -
44 ASP 44 T A - 178.6 - - - - - - - - 181.1 - 33.6 -
45 SER 45 e A - - -60.6 - - - - - - - 181.0 -1.0 36.0 -
* *
46 MET 46 E B - 189.2 - - - - - - - - 184.4 -.6 35.7 -
+* +*
47 ARG 47 E B - 184.2 - 174.9 - - - - - - 186.2 -3.3 34.8 -
* +* +*
48 ILE 48 E B - - -68.0 182.3 - - - - - - 171.7 - 33.5 -
* *
49 GLN 49 E B - - -69.2 178.9 - - - - - - 179.9 -2.6 34.3 -
50 LEU 50 E B - 190.6 - 171.5 - - - - - - 177.9 -2.1 32.8 -
51 PHE 51 E B - - -61.0 - - - - - - - 176.9 -2.5 35.5 -
52 ASP 52 e b 68.1 - - - - - - - - - 179.7 -1.1 34.5 -
* *
53 GLY 53 S - - - - - - - - - - - 179.0 - - -
54 ASP 54 S b - 177.4 - - - - - - - - 172.9 - 31.3 -
* *
55 ASP 55 S a - 190.7 - - - - - - - - 180.3 - 33.8 -
56 GLN 56 e p - - -54.0 - - - - - - - 181.2 - 32.2 -
57 LEU 57 E B - 179.8 - - - - - - - - 177.7 - 34.7 -
58 LYS 58 E A - - -53.8 - - - - - - - 178.6 -3.0 36.5 -
* *
Residue-by-residue listing for refined_10 Page 3
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...................................................................................................................................
Residue Kabsch Region
--------- Sander of
No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max
Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev
-----------------------------------------------------------------------------------------------------------------------------------
59 GLY 59 E - - - - - - - - - - - 181.9 -.9 - -
+* +*
60 GLU 60 E B - 180.7 - 182.2 - - - - - - 181.9 - 35.9 -
61 LEU 61 e ~a 54.6 - - 172.3 - - - - - - 175.0 -.9 25.9 -
** * ** **
62 THR 62 l - 194.7 - - - - - - - - 179.9 - 26.4 -
** **
63 ASP 63 a - - -59.2 - - - - - - - 179.9 - 35.2 -
64 GLY 64 - - - - - - - - - - - 176.7 - - -
65 ALA 65 S A - - - - - - - - - - 179.5 - 34.0 -
66 LYS 66 S B 51.8 - - 175.7 - - - - - - 183.5 - 35.0 -
67 SER 67 h B 53.7 - - - - - - - - - 177.9 - 35.6 -
68 LEU 68 H A - - -60.7 180.5 - -65.9 -31.1 - - - 183.0 -1.7 35.8 -
69 LYS 69 H A - 189.7 - - - -69.2 -41.2 - - - 182.3 -2.6 35.1 -
70 ASP 70 H A - 196.3 - - - -74.9 -29.8 - - - 178.9 - 35.4 -
71 LEU 71 H A - - -69.9 170.6 - -75.3 -13.8 - - - 179.9 -1.8 34.1 -
** **
72 GLY 72 h - - - - - - - - - - - 176.6 -.7 - -
+* +*
73 VAL 73 t B - 180.7 - - - - - - - - 183.7 -2.8 35.4 -
* *
74 ARG 74 t b - - -53.6 - - - - - - - 182.1 -.6 34.5 -
+* +*
75 ASP 75 T B - 187.6 - - - - - - - - 179.8 - 34.8 -
76 GLY 76 T - - - - - - - - - - - 179.0 -2.8 - -
77 TYR 77 e B - - -69.4 - - - - - - - 182.5 -1.2 33.3 -
* *
78 ARG 78 E B 59.9 - - 171.3 - - - - - - 177.8 -2.3 30.9 -
79 ILE 79 E B - - -61.6 - - - - - - - 179.3 -2.6 35.5 -
80 HIS 80 E B - 175.5 - - - - - - - - 179.7 -3.7 33.5 -
** **
81 ALA 81 E B - - - - - - - - - - 177.3 -3.5 35.5 -
+* +*
82 VAL 82 E B 60.4 - - - - - - - - - 177.1 -2.3 33.5 -
83 ASP 83 E B 58.3 - - - - - - - - - 182.5 - 34.9 -
84 VAL 84 e A - - -59.5 - - - - - - - 184.8 -2.9 33.7 -
* *
85 THR 85 S A - - -49.4 - - - - - - - 181.5 - 34.0 -
* *
86 GLY 86 S - - - - - - - - - - - 186.0 - - -
* *
87 GLY 87 - - - - - - - - - - - 176.5 - - -
88 ASN 88 S B - - -73.7 - - - - - - - 180.6 - 31.6 -
89 GLU 89 l - - -59.0 184.1 - - - - - - 177.7 -.6 30.1 -
+* * +*
90 ASP 90 - - 176.0 - - - - - - - - - - 34.0 -
-----------------------------------------------------------------------------------------------------------------------------------
Max deviations: ** * +* * ** ** ** ** ** **
-----------------------------------------------------------------------------------------------------------------------------------
Mean values: 56.0 184.3 -62.0 178.2 -70.3 -69.0 -34.8 - - - 179.7 -2.1 34.2
Standard deviations: 5.6 6.3 7.8 5.1 13.7 8.1 8.5 - - - 3.5 .9 2.0
Numbers of values: 13 32 30 21 2 16 16 0 0 0 89 52 81 0
Residue-by-residue listing for refined_10 Page 4
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KEY TO CODES:
------------
Regions of the Ramachandran plot Secondary structure (extended Kabsch/Sander)
-------------------------------- --------------------------------------------
A - Core alpha B - residue in isolated beta-bridge
a - Allowed alpha E - extended strand, participates in beta-ladder
~a - Generous alpha ** Generous G - 3-helix (3/10 helix)
B - Core beta H - 4-helix (alpha-helix)
b - Allowed beta I - 5-helix (pi-helix)
~b - Generous beta ** Generous S - bend
L - Core left-handed alpha T - hydrogen-bonded turn
l - Allowed left-handed alpha
~l - Generous left-handed alpha ** Generous e - extension of beta-strand
p - Allowed epsilon g - extension of 3/10 helix
~p - Generous epsilon ** Generous h - extension of alpha-helix
XX - Outside major areas **** Disallowed
Residue-by-residue listing for refined_10 Page 5
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M A I N C H A I N B O N D L E N G T H S A N D B O N D A N G L E S
..................................... Small molecule data .........................................
<---------- Bond lengths ----------> <---------------------- Bond angles ---------------------->
C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N
---------------------------------------------------------------------------------------------------
Any - 1.231 - - - - - - - - - -
( .020)
Pro 1.341 - - - 1.466 122.60 116.90 - - 111.80 103.00 122.00
( .016) ( .015) ( 5.00) ( 1.50) ( 2.50) ( 1.10) ( 1.40)
Except Pro 1.329 - - - - - - - - - - 123.00
( .014) ( 1.60)
Gly - - 1.516 - 1.451 120.60 116.40 120.80 - 112.50 - -
( .018) ( .016) ( 1.70) ( 2.10) ( 2.10) ( 2.90)
Except Gly - - 1.525 - - - - 120.80 - - - -
( .021) ( 1.70)
Ala - - - 1.521 - - - - 110.50 - 110.40 -
( .033) ( 1.50) ( 1.50)
Ile,Thr,Val - - - 1.540 - - - - 109.10 - 111.50 -
( .027) ( 2.20) ( 1.70)
Except Gly,Pro - - - - 1.458 121.70 116.20 - - 111.20 - -
( .019) ( 1.80) ( 2.00) ( 2.80)
The rest - - - 1.530 - - - - 110.10 - 110.50 -
( .020) ( 1.90) ( 1.70)
Note. The table above shows the mean values obtained from small molecule data by Engh & Huber (1991). The values shown in brackets
are standard deviations
...................................................................................................................................
Residue
------------- <---------- Bond lengths ----------> <---------------------- Bond angles ---------------------->
No. Type Seq Max
Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev
-----------------------------------------------------------------------------------------------------------------------------------
1 MET 1 - 1.229 1.494 1.544 1.469 - 116.90 120.06 107.46 109.28 111.34 123.04
* * *
2 THR 2 1.319 1.237 1.512 1.547 1.426 119.99 116.42 120.75 111.73 105.92 111.11 122.83
+* * +* +*
3 GLU 3 1.297 1.229 1.500 1.536 1.413 121.23 113.93 122.56 113.90 109.65 109.27 123.43
** * ** * * ** **
4 VAL 4 1.295 1.239 1.509 1.567 1.425 123.23 116.21 120.52 109.02 109.64 112.80 123.24
** +* **
5 TYR 5 1.287 1.234 1.506 1.540 1.447 122.37 116.93 120.02 108.37 108.96 111.72 122.93
*** ***
6 ASP 6 1.304 1.246 1.494 1.525 1.443 120.95 115.01 121.33 109.86 106.84 113.68 123.63
+* * +* +* +*
7 LEU 7 1.274 1.242 1.502 1.541 1.422 123.11 114.75 121.42 108.48 111.48 111.74 123.82
+*** * +* +***
8 GLU 8 1.297 1.215 1.505 1.520 1.429 123.26 115.93 121.41 111.25 106.65 109.13 122.59
** +* +* **
9 ILE 9 1.270 1.232 1.507 1.580 1.433 121.33 114.46 121.41 109.76 110.35 114.05 124.13
**** * * * ****
10 THR 10 1.279 1.225 1.499 1.540 1.431 124.23 117.95 119.83 110.36 108.05 111.16 122.22
+*** * * * * +***
11 THR 11 1.293 1.225 1.501 1.553 1.422 119.72 111.97 122.34 109.38 109.92 111.78 125.69
+** * +* * ** +* +**
Residue-by-residue listing for refined_10 Page 6
----------------------------------------
...................................................................................................................................
Residue
------------- <---------- Bond lengths ----------> <---------------------- Bond angles ---------------------->
No. Type Seq Max
Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev
-----------------------------------------------------------------------------------------------------------------------------------
12 ASN 12 1.259 1.234 1.504 1.531 1.455 128.57 116.12 120.86 110.16 113.09 106.67 123.00
*5.0* * +*** ** *5.0*
13 ALA 13 1.287 1.243 1.512 1.508 1.418 119.60 116.05 121.25 113.17 112.42 109.52 122.67
*** ** * +* ***
14 THR 14 1.302 1.229 1.507 1.538 1.439 120.68 117.14 120.02 108.87 109.54 111.83 122.84
+* * +*
15 ASP 15 1.291 1.231 1.522 1.528 1.452 120.74 115.55 121.44 111.55 109.71 110.96 122.99
+** +**
16 PHE 16 1.311 1.245 1.532 1.536 1.444 122.04 117.11 120.60 110.49 109.92 110.47 122.29
* *
17 PRO 17 1.340 1.232 1.526 1.527 1.451 122.66 116.33 120.86 110.79 111.22 103.57 122.79
18 MET 18 1.300 1.218 1.507 1.537 1.447 121.87 117.00 120.27 109.44 109.61 110.27 122.73
** **
19 GLU 19 1.296 1.239 1.518 1.514 1.434 120.92 115.94 120.84 111.32 110.28 110.69 123.17
** * **
20 LYS 20 1.306 1.229 1.513 1.519 1.428 123.47 115.92 120.57 109.98 110.46 110.44 123.51
+* +* +*
21 LYS 21 1.304 1.234 1.517 1.531 1.441 122.54 116.99 120.17 109.16 108.96 109.41 122.84
+* +*
22 TYR 22 1.306 1.237 1.509 1.543 1.441 121.66 117.51 120.10 110.67 110.28 112.34 122.34
+* * +*
23 PRO 23 1.341 1.227 1.516 1.530 1.459 122.57 116.54 120.63 109.49 111.23 104.03 122.83
24 ALA 24 1.315 1.228 1.517 1.508 1.460 121.56 115.22 121.26 110.86 112.01 111.04 123.52
* *
25 GLY 25 1.304 1.228 1.515 - 1.444 121.92 116.58 120.63 - 112.31 - 122.78
+* +*
26 MET 26 1.316 1.234 1.525 1.541 1.450 121.77 116.42 120.43 110.17 108.97 109.89 123.16
27 SER 27 1.302 1.243 1.498 1.521 1.429 122.56 115.38 121.17 110.12 110.16 109.44 123.45
+* * +* +*
28 LEU 28 1.307 1.202 1.505 1.506 1.438 121.75 115.53 121.03 108.38 108.74 109.54 123.42
+* * * * +*
29 ASN 29 1.319 1.235 1.510 1.540 1.472 121.89 117.02 120.16 112.65 112.91 112.36 122.78
* * *
30 ASP 30 1.324 1.223 1.504 1.515 1.459 120.62 114.53 121.60 108.76 108.62 111.37 123.83
31 LEU 31 1.316 1.226 1.524 1.549 1.446 123.16 115.60 120.88 112.03 108.13 108.34 123.52
* * * *
32 LYS 32 1.327 1.175 1.498 1.533 1.466 122.55 116.56 120.16 107.43 109.36 111.93 123.27
+** * * +**
33 LYS 33 1.319 1.235 1.523 1.472 1.429 123.34 115.78 121.01 110.29 111.37 106.69 123.20
+** +* ** +**
34 LYS 34 1.314 1.227 1.528 1.525 1.448 122.62 114.98 121.52 109.18 108.12 108.99 123.50
* * *
35 LEU 35 1.323 1.202 1.512 1.531 1.436 123.55 116.30 120.46 111.61 110.77 109.59 123.21
* * * *
36 GLU 36 1.302 1.215 1.502 1.503 1.432 124.29 116.32 120.98 112.86 112.48 110.07 122.70
+* * * * * * +*
37 LEU 37 1.303 1.226 1.544 1.531 1.450 121.47 115.57 121.26 110.15 109.17 110.09 123.17
+* +*
38 VAL 38 1.318 1.233 1.541 1.558 1.454 123.13 116.32 121.07 108.72 110.46 110.83 122.59
39 VAL 39 1.320 1.229 1.531 1.569 1.464 122.31 116.67 120.76 110.65 111.41 110.98 122.54
* *
40 GLY 40 1.310 1.230 1.511 - 1.446 120.75 116.56 120.53 - 113.02 - 122.90
* *
41 THR 41 1.305 1.235 1.559 1.559 1.455 122.01 118.06 119.86 111.73 108.98 108.05 122.02
+* +* * ** **
Residue-by-residue listing for refined_10 Page 7
----------------------------------------
...................................................................................................................................
Residue
------------- <---------- Bond lengths ----------> <---------------------- Bond angles ---------------------->
No. Type Seq Max
Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev
-----------------------------------------------------------------------------------------------------------------------------------
42 THR 42 1.319 1.237 1.531 1.535 1.435 121.26 115.80 120.66 110.48 110.81 111.91 123.41
* *
43 VAL 43 1.329 1.242 1.541 1.564 1.472 123.84 116.44 120.84 109.64 112.17 110.10 122.71
* *
44 ASP 44 1.307 1.227 1.521 1.522 1.454 122.27 116.27 120.82 110.23 111.67 110.90 122.89
+* +*
45 SER 45 1.311 1.240 1.536 1.504 1.428 123.18 115.26 121.36 110.39 111.37 107.40 123.38
* * +* +* +*
46 MET 46 1.296 1.233 1.527 1.530 1.444 123.34 116.64 120.63 111.89 107.99 107.40 122.70
** * +* **
47 ARG 47 1.299 1.234 1.544 1.530 1.450 123.01 117.44 120.06 113.01 109.29 107.05 122.47
** +* ** **
48 ILE 48 1.338 1.236 1.531 1.567 1.472 121.34 114.63 121.46 108.88 114.59 111.63 123.90
* *
49 GLN 49 1.322 1.218 1.513 1.517 1.444 123.87 117.95 119.88 109.69 108.38 111.41 122.16
* * *
50 LEU 50 1.296 1.242 1.530 1.564 1.474 119.99 115.75 121.11 112.17 110.55 110.81 123.14
** +* * **
51 PHE 51 1.314 1.241 1.519 1.546 1.453 122.80 117.52 120.11 108.36 108.02 111.38 122.35
* * *
52 ASP 52 1.309 1.239 1.511 1.520 1.442 120.25 115.41 120.50 109.16 110.03 111.36 124.09
* *
53 GLY 53 1.320 1.240 1.524 - 1.455 122.24 116.30 120.17 - 112.81 - 123.51
54 ASP 54 1.331 1.235 1.515 1.539 1.460 122.99 114.90 121.46 110.36 111.96 113.95 123.45
** **
55 ASP 55 1.306 1.234 1.510 1.508 1.459 124.25 112.25 123.13 111.92 106.56 110.43 124.54
+* * * +* * +* +*
56 GLN 56 1.319 1.231 1.529 1.508 1.424 126.30 115.76 120.98 112.67 112.83 109.89 123.18
* +* +** * +**
57 LEU 57 1.312 1.238 1.525 1.538 1.454 122.81 115.73 120.98 110.24 111.24 109.62 123.27
* *
58 LYS 58 1.317 1.233 1.503 1.531 1.450 121.41 114.80 121.72 107.95 108.08 110.14 123.47
* * * *
59 GLY 59 1.291 1.245 1.489 - 1.415 121.29 115.43 120.78 - 111.21 - 123.79
+** * ** +**
60 GLU 60 1.291 1.237 1.518 1.515 1.421 123.00 116.45 120.60 110.57 108.75 108.23 122.94
+** +* * +**
61 LEU 61 1.305 1.208 1.512 1.573 1.444 120.66 115.58 119.79 114.99 114.11 115.18 124.55
+* * ** +** * +** +**
62 THR 62 1.296 1.227 1.542 1.602 1.497 127.37 116.08 120.71 112.95 113.28 117.01 123.19
** ** ** *** +* *** ***
63 ASP 63 1.333 1.224 1.531 1.542 1.482 123.26 115.45 121.51 107.91 111.67 110.92 123.04
* * *
64 GLY 64 1.329 1.219 1.513 - 1.461 122.54 117.30 119.85 - 114.52 - 122.84
* *
65 ALA 65 1.324 1.232 1.526 1.520 1.468 121.91 114.66 121.90 110.75 109.58 110.27 123.43
66 LYS 66 1.298 1.253 1.524 1.523 1.428 124.68 116.94 119.88 111.00 108.29 109.34 123.17
** * +* +* * **
67 SER 67 1.310 1.240 1.500 1.509 1.413 122.16 114.44 121.55 109.58 112.02 108.95 123.99
* * * ** **
68 LEU 68 1.299 1.232 1.511 1.525 1.449 123.27 114.72 121.45 108.99 109.54 109.71 123.77
** **
69 LYS 69 1.313 1.227 1.518 1.560 1.443 122.92 115.50 121.29 111.73 108.56 108.81 123.17
* * *
70 ASP 70 1.316 1.232 1.528 1.518 1.454 121.80 114.99 121.78 109.83 109.32 109.35 123.23
Residue-by-residue listing for refined_10 Page 8
----------------------------------------
...................................................................................................................................
Residue
------------- <---------- Bond lengths ----------> <---------------------- Bond angles ---------------------->
No. Type Seq Max
Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev
-----------------------------------------------------------------------------------------------------------------------------------
71 LEU 71 1.321 1.234 1.520 1.527 1.469 123.10 117.16 120.04 109.41 113.08 110.55 122.80
72 GLY 72 1.310 1.231 1.512 - 1.445 120.27 115.96 121.01 - 112.07 - 123.03
* *
73 VAL 73 1.307 1.214 1.506 1.549 1.439 121.66 117.51 119.97 109.14 106.49 111.41 122.48
+* * +* +*
74 ARG 74 1.304 1.237 1.516 1.534 1.448 120.67 116.46 120.46 110.30 109.95 110.35 123.07
+* +*
75 ASP 75 1.317 1.230 1.493 1.522 1.455 121.82 114.79 121.30 109.45 110.02 110.61 123.91
* *
76 GLY 76 1.272 1.230 1.532 - 1.464 122.08 117.47 120.22 - 114.60 - 122.31
**** ****
77 TYR 77 1.313 1.246 1.509 1.541 1.460 121.55 117.03 120.25 111.40 110.00 111.00 122.72
* *
78 ARG 78 1.318 1.241 1.502 1.545 1.431 119.37 114.15 122.01 110.70 112.37 114.17 123.85
* * * * ** **
79 ILE 79 1.291 1.230 1.502 1.556 1.421 123.30 116.31 120.60 109.09 107.41 111.35 123.03
+** * +* * +**
80 HIS 80 1.284 1.230 1.508 1.540 1.423 121.74 115.28 120.86 111.45 110.19 110.87 123.85
*** +* ***
81 ALA 81 1.297 1.234 1.496 1.512 1.423 123.09 116.14 120.72 110.07 109.23 109.38 123.11
** * +* **
82 VAL 82 1.290 1.227 1.515 1.571 1.417 121.61 116.03 120.77 111.82 109.69 110.96 123.13
+** * ** * +**
83 ASP 83 1.296 1.224 1.510 1.529 1.407 122.86 116.60 121.08 111.25 108.51 109.44 122.30
** +** +**
84 VAL 84 1.301 1.236 1.525 1.551 1.442 120.86 116.29 120.78 109.84 111.67 111.58 122.92
** **
85 THR 85 1.317 1.231 1.532 1.541 1.441 121.38 117.08 120.57 110.43 112.26 110.25 122.32
86 GLY 86 1.304 1.240 1.500 - 1.434 119.55 115.82 120.78 - 112.10 - 123.33
+* * +*
87 GLY 87 1.317 1.211 1.509 - 1.446 120.24 118.32 119.78 - 109.51 - 121.89
* *
88 ASN 88 1.304 1.237 1.498 1.533 1.452 119.55 114.43 120.99 111.59 111.92 112.43 124.55
+* * * * +*
89 GLU 89 1.328 1.241 1.529 1.522 1.459 124.99 115.11 121.71 112.59 113.83 112.31 123.12
+* * * +*
90 ASP 90 1.299 - 1.504 1.540 1.450 122.72 - - 110.82 109.26 110.83 -
** * **
-----------------------------------------------------------------------------------------------------------------------------------
Max deviations: *5.0* +** +* +** +** +*** ** * +** +* *** +* *5.0*
-----------------------------------------------------------------------------------------------------------------------------------
Residue-by-residue listing for refined_10 Page 9
----------------------------------------
A N A L Y S I S O F M A I N C H A I N B O N D L E N G T H S A N D B O N D A N G L E S
+------------------+
| BOND LENGTHS |
+------------------+
-------------------------------------------------------------------------------------------------------------
(Small molecule data) Number of Min Max Mean Standard
Bond X-PLOR labelling Mean St. dev values value value value deviation
-------------------------------------------------------------------------------------------------------------
C-N C-NH1 (except Pro) 1.329 .014 87 1.259 1.338 1.307 .015
*5.0* +*
C-N (Pro) 1.341 .016 2 1.340 1.341 1.340 .000
C-O C-O 1.231 .020 89 1.175 1.253 1.231 .011
+** *
CA-C CH1E-C (except Gly) 1.525 .021 81 1.493 1.559 1.516 .014
* +*
CH2G*-C (Gly) 1.516 .018 9 1.489 1.532 1.512 .012
*
CA-CB CH1E-CH3E (Ala) 1.521 .033 4 1.508 1.520 1.512 .005
CH1E-CH1E (Ile,Thr,Val) 1.540 .027 18 1.535 1.602 1.558 .016
**
CH1E-CH2E (the rest) 1.530 .020 59 1.472 1.573 1.529 .016
+** **
N-CA NH1-CH1E (except Gly,Pro)1.458 .019 79 1.407 1.497 1.444 .017
+** **
NH1-CH2G* (Gly) 1.451 .016 9 1.415 1.464 1.445 .014
**
N-CH1E (Pro) 1.466 .015 2 1.451 1.459 1.455 .004
-------------------------------------------------------------------------------------------------------------
Residue-by-residue listing for refined_10 Page 10
----------------------------------------
+-----------------+
| BOND ANGLES |
+-----------------+
-------------------------------------------------------------------------------------------------------------
(Small molecule data) Number of Min Max Mean Standard
Angle X-PLOR labelling Mean St. dev values value value value deviation
-------------------------------------------------------------------------------------------------------------
CA-C-N CH1E-C-NH1 (except Gly,Pro)116.2 2.0 78 111.97 118.06 115.89 1.14
**
CH2G*-C-NH1 (Gly) 116.4 2.1 9 115.43 118.32 116.64 .86
CH1E-C-N (Pro) 116.9 1.5 2 116.33 116.54 116.43 .10
O-C-N O-C-NH1 (except Pro) 123.0 1.6 87 121.89 125.69 123.16 .62
+*
O-C-N (Pro) 122.0 1.4 2 122.79 122.83 122.81 .02
C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 78 119.37 128.57 122.36 1.61
* +***
C-NH1-CH2G* (Gly) 120.6 1.7 9 119.55 122.54 121.21 .99
*
C-N-CH1E (Pro) 122.6 5.0 2 122.57 122.66 122.62 .04
CA-C-O CH1E-C-O (except Gly) 120.8 1.7 80 119.79 123.13 120.89 .66
*
CH2G*-C-O (Gly) 120.8 2.1 9 119.78 121.01 120.42 .41
CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 4 110.07 113.17 111.22 1.17
+*
CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 18 108.72 112.95 110.14 1.20
+*
CH2E-CH1E-C (the rest) 110.1 1.9 59 107.43 114.99 110.47 1.56
* +**
N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 79 105.92 114.59 110.12 1.87
+* *
NH1-CH2G*-C (Gly) 112.5 2.9 9 109.51 114.60 112.46 1.48
*
N-CH1E-C (Pro) 111.8 2.5 2 111.22 111.23 111.23 .01
N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 4 109.38 111.04 110.05 .66
NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 18 108.05 117.01 111.60 1.75
** ***
N-CH1E-CH2E (Pro) 103.0 1.1 2 103.57 104.03 103.80 .23
NH1-CH1E-CH2E (the rest) 110.5 1.7 57 106.67 115.18 110.37 1.74
** +**
-------------------------------------------------------------------------------------------------------------
The small molecule data used in the above analysis is from Engh & Huber (1991). The atom labelling follows that used in the
X-PLOR dictionary, with some additional atoms (marked with an asterisk) as defined by Engh & Huber.
Residue-by-residue listing for refined_10 Page 11
----------------------------------------
R A M A C H A N D R A N P L O T S T A T I S T I C S
Residues in most favoured regions [A,B,L] 65 84.4%
Residues in additional allowed regions [a,b,l,p] 11 14.3%
Residues in generously allowed regions [~a,~b,~l,~p] 1 1.3%
Residues in disallowed regions [XX] 0 .0%
---- ------
Number of non-glycine and non-proline residues 77 100.0%
Number of end-residues (excl. Gly and Pro) 2
Number of glycine residues 9
Number of proline residues 2
----
Total number of residues 90
Based on the analysis of 118 structures of resolution of at least 2.0 Angstroms and R-factor no greater than 20%, a good
quality model would be expected to have over 90% in the most favoured regions [E,H,L].
S T E R E O C H E M I S T R Y O F M A I N - C H A I N
Comparison values No. of
No. of Parameter Typical Band band widths
Stereochemical parameter data pts value value width from mean
------------------------ -------- ----- ----- ----- ---------
a. %-tage residues in A, B, L 77 84.4 83.8 10.0 .1 Inside
b. Omega angle st dev 89 3.5 6.0 3.0 -.8 Inside
c. Bad contacts / 100 residues 0 .0 4.2 10.0 -.4 Inside
d. Zeta angle st dev 81 2.0 3.1 1.6 -.7 Inside
e. H-bond energy st dev 52 .9 .8 .2 .7 Inside
f. Overall G-factor 90 -.1 -.4 .3 1.1 BETTER
S T E R E O C H E M I S T R Y O F S I D E - C H A I N
Comparison values No. of
No. of Parameter Typical Band band widths
Stereochemical parameter data pts value value width from mean
------------------------ -------- ----- ----- ----- ---------
a. Chi-1 gauche minus st dev 13 5.6 18.1 6.5 -1.9 BETTER
b. Chi-1 trans st dev 32 6.3 19.0 5.3 -2.4 BETTER
c. Chi-1 gauche plus st dev 30 7.8 17.5 4.9 -2.0 BETTER
d. Chi-1 pooled st dev 75 8.1 18.2 4.8 -2.1 BETTER
e. Chi-2 trans st dev 21 5.1 20.4 5.0 -3.1 BETTER
M O R R I S E T A L . C L A S S I F I C A T I O N
Mean St.dev Classification
Parameter m s 1 2 3 4 Value Class
--------- ---- --- ------------------------------------ ----- -----
Phi-psi distribution - - >75.0% >65.0% >55.0% <55.0% 84.4 1
Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 9.2 1
H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .94 3
Residue-by-residue listing for refined_10 Page 12
----------------------------------------
G - F A C T O R S
Average
Parameter Score Score
--------- ----- -----
Dihedral angles:-
Phi-psi distribution -.37
Chi1-chi2 distribution -.15
Chi1 only -.14
Chi3 & chi4 .18
Omega .01
------ -.13
=====
Main-chain covalent forces:-
Main-chain bond lengths -.21
Main-chain bond angles .34
------ .11
=====
OVERALL AVERAGE -.05
=====
Ideally, scores should be above -0.5. Values below -1.0 may need investigation.