
PFRMAT CMF1
TARGET T0003
AUTHOR 5865-8356-4011 ANDRAS ASZODI, NIMR, a-aszodi@nimr.mrc.ac.uk
MODEL  1
BEGPDB
PDBSET 1 NOREFINE DRAGON (C-alpha trace)
REMARK Average of 20 C-alpha structures produced by DRAGON-4.
REMARK C-alpha RMS deviation of structures from average:
REMARK     BEST RMS=3.9980e-01 A
REMARK     WORST RMS=1.8716e+00 A
REMARK     AVERAGE RMS=1.0019e+00 +/- 3.8821e-01 A
REMARK THE B-FACTOR FIELD CONTAINS THE STANDARD DEVIATION OF
REMARK DISTANCES OF C-ALPHA ATOMS FROM THE CORRESPONDING AVERAGE
REMARK POSITIONS. THIS IS A MEASURE OF PRECISION RATHER THAN ACCURACY.
ATOM      1  CA  MET 0   1     -16.232   1.071  11.898  1.00  6.98
ATOM      2  CA  TRP 0   2     -14.844   0.461  11.132  1.00  6.03
ATOM      3  CA  PHE 0   3     -14.513   0.837   9.228  1.00  5.45
ATOM      4  CA  PHE 0   4     -15.379   2.993   8.025  1.00  4.68
ATOM      5  CA  ASN 0   5     -16.140   5.183   9.614  1.00  3.60
ATOM      6  CA  LYS 0   6     -14.227   6.983  11.011  1.00  2.72
ATOM      7  CA  ASN 0   7     -12.535   8.190   9.446  1.00  1.16
ATOM      8  CA  LEU 0   8     -11.639   5.242   7.851  1.00  1.63
ATOM      9  CA  LYS 0   9      -9.073   3.643   9.242  1.00  0.97
ATOM     10  CA  VAL 0  10      -6.384   3.409   6.499  1.00  0.46
ATOM     11  CA  LEU 0  11      -3.488   2.912   9.246  1.00  0.43
ATOM     12  CA  ALA 0  12      -0.908   5.039   7.476  1.00  0.36
ATOM     13  CA  PRO 0  13       0.325   2.142   5.019  1.00  0.25
ATOM     14  CA  CYS 0  14       3.857   2.162   5.591  1.00  0.17
ATOM     15  CA  ASP 0  15       5.500   5.106   7.130  1.00  0.18
ATOM     16  CA  GLY 0  16       7.624   6.488   4.532  1.00  0.15
ATOM     17  CA  THR 0  17       7.649   9.686   3.243  1.00  0.18
ATOM     18  CA  ILE 0  18       4.258  10.649   1.950  1.00  0.18
ATOM     19  CA  ILE 0  19       5.614  12.073  -1.536  1.00  0.21
ATOM     20  CA  THR 0  20       2.303  13.422  -2.727  1.00  0.29
ATOM     21  CA  LEU 0  21       1.575  10.649  -5.492  1.00  0.24
ATOM     22  CA  ASP 0  22       3.006  12.838  -8.433  1.00  0.28
ATOM     23  CA  GLU 0  23       6.768  11.914  -8.117  1.00  0.24
ATOM     24  CA  VAL 0  24       6.507   8.123  -8.816  1.00  0.22
ATOM     25  CA  GLU 0  25       7.889   7.760 -12.181  1.00  0.28
ATOM     26  CA  ASP 0  26       6.276   5.576 -14.413  1.00  0.33
ATOM     27  CA  GLU 0  27       3.469   6.832 -16.629  1.00  0.38
ATOM     28  CA  VAL 0  28       1.112   3.518 -15.938  1.00  0.37
ATOM     29  CA  PHE 0  29       0.262   4.676 -12.274  1.00  0.31
ATOM     30  CA  LYS 0  30       0.792   8.503 -12.817  1.00  0.34
ATOM     31  CA  GLU 0  31      -2.086  10.343 -14.384  1.00  0.42
ATOM     32  CA  ARG 0  32      -5.184   8.717 -12.765  1.00  0.42
ATOM     33  CA  MET 0  33      -4.644   5.018 -13.699  1.00  0.40
ATOM     34  CA  LEU 0  34      -4.040   3.160 -10.470  1.00  0.35
ATOM     35  CA  GLY 0  35      -5.552   5.315  -7.846  1.00  0.35
ATOM     36  CA  ASP 0  36      -3.995   8.403  -6.421  1.00  0.32
ATOM     37  CA  GLY 0  37      -3.185   7.033  -2.767  1.00  0.29
ATOM     38  CA  PHE 0  38       0.043   5.756  -3.252  1.00  0.26
ATOM     39  CA  ALA 0  39       3.261   6.628  -3.357  1.00  0.23
ATOM     40  CA  ILE 0  40       4.329   6.397   0.604  1.00  0.16
ATOM     41  CA  ASN 0  41       8.066   6.545  -0.629  1.00  0.14
ATOM     42  CA  PRO 0  42       9.130   2.956   0.294  1.00  0.12
ATOM     43  CA  LYS 0  43      10.059   4.053   3.947  1.00  0.16
ATOM     44  CA  SER 0  44      10.653   1.401   5.953  1.00  0.23
ATOM     45  CA  ASN 0  45       9.990  -1.961   4.889  1.00  0.20
ATOM     46  CA  ASP 0  46       7.547  -3.388   7.222  1.00  0.25
ATOM     47  CA  PHE 0  47       4.301  -3.141   5.862  1.00  0.24
ATOM     48  CA  HIS 0  48       1.688  -3.508   8.116  1.00  0.30
ATOM     49  CA  ALA 0  49      -1.341  -4.841   6.634  1.00  0.31
ATOM     50  CA  PRO 0  50      -3.188  -1.470   5.703  1.00  0.32
ATOM     51  CA  VAL 0  51      -6.321  -1.809   7.533  1.00  0.41
ATOM     52  CA  SER 0  52      -7.208  -5.423   8.047  1.00  0.45
ATOM     53  CA  GLY 0  53      -9.423  -6.180   5.139  1.00  0.47
ATOM     54  CA  LYS 0  54      -9.158  -9.529   4.144  1.00  0.44
ATOM     55  CA  LEU 0  55      -6.045 -10.651   2.382  1.00  0.37
ATOM     56  CA  VAL 0  56      -7.553 -10.431  -1.199  1.00  0.35
ATOM     57  CA  THR 0  57      -5.339 -11.321  -3.459  1.00  0.37
ATOM     58  CA  ALA 0  58      -1.637 -11.624  -2.099  1.00  0.25
ATOM     59  CA  PHE 0  59      -0.518 -11.274  -6.039  1.00  0.22
ATOM     60  CA  PRO 0  60       0.764 -15.030  -6.252  1.00  0.26
ATOM     61  CA  THR 0  61       4.601 -13.688  -5.937  1.00  0.25
ATOM     62  CA  LYS 0  62       3.703 -10.132  -5.426  1.00  0.77
ATOM     63  CA  HIS 0  63       2.745  -8.464  -2.513  1.00  0.28
ATOM     64  CA  ALA 0  64       0.941  -5.384  -2.945  1.00  0.31
ATOM     65  CA  PHE 0  65      -2.369  -5.793  -3.946  1.00  0.22
ATOM     66  CA  GLY 0  66      -5.342  -7.235  -3.146  1.00  0.33
ATOM     67  CA  ILE 0  67      -5.908  -6.806   0.660  1.00  0.34
ATOM     68  CA  GLN 0  68      -9.571  -5.337   0.076  1.00  0.43
ATOM     69  CA  THR 0  69      -9.628  -3.611   3.693  1.00  0.46
ATOM     70  CA  LYS 0  70     -13.345  -4.919   4.330  1.00  0.55
ATOM     71  CA  SER 0  71     -14.998  -2.666   1.773  1.00  0.77
ATOM     72  CA  GLY 0  72     -14.287  -2.522  -1.630  1.00  0.54
ATOM     73  CA  VAL 0  73     -11.714   0.374  -2.152  1.00  0.47
ATOM     74  CA  GLU 0  74      -9.254  -1.941  -3.938  1.00  0.42
ATOM     75  CA  ILE 0  75      -6.267  -0.942  -1.322  1.00  0.33
ATOM     76  CA  LEU 0  76      -3.916  -2.219  -3.936  1.00  0.29
ATOM     77  CA  LEU 0  77      -0.893  -2.546  -2.226  1.00  0.21
ATOM     78  CA  HIS 0  78       1.171  -3.077  -5.811  1.00  0.17
ATOM     79  CA  ILE 0  79       4.269  -2.213  -4.161  1.00  0.13
ATOM     80  CA  GLY 0  80       6.188   0.228  -5.855  1.00  0.11
ATOM     81  CA  LEU 0  81       5.730  -0.377  -9.516  1.00  0.19
ATOM     82  CA  ASP 0  82       6.808  -3.287 -11.256  1.00  0.23
ATOM     83  CA  THR 0  83       8.530  -5.599  -8.475  1.00  0.19
ATOM     84  CA  VAL 0  84       7.034  -8.919 -10.203  1.00  0.23
ATOM     85  CA  SER 0  85      10.009  -9.336 -12.762  1.00  0.31
ATOM     86  CA  LEU 0  86      12.743 -10.104  -9.948  1.00  0.31
ATOM     87  CA  ASP 0  87      11.295 -13.533  -8.921  1.00  0.29
ATOM     88  CA  GLY 0  88      10.019 -13.208  -5.397  1.00  0.22
ATOM     89  CA  ASN 0  89      13.619 -12.882  -3.645  1.00  0.28
ATOM     90  CA  GLY 0  90      12.806 -10.180  -1.112  1.00  0.23
ATOM     91  CA  PHE 0  91       9.657 -11.043   0.092  1.00  0.37
ATOM     92  CA  GLU 0  92       8.928 -13.195   2.562  1.00  0.26
ATOM     93  CA  SER 0  93       6.266 -12.330   4.573  1.00  0.34
ATOM     94  CA  PHE 0  94       3.688 -14.221   4.996  1.00  0.37
ATOM     95  CA  VAL 0  95       0.422 -13.896   4.722  1.00  0.34
ATOM     96  CA  THR 0  96      -0.887 -16.720   2.448  1.00  0.29
ATOM     97  CA  GLN 0  97      -3.982 -15.182   1.283  1.00  0.31
ATOM     98  CA  ASP 0  98      -6.588 -14.251   3.423  1.00  0.40
ATOM     99  CA  GLN 0  99      -6.005 -14.359   7.068  1.00  0.44
ATOM    100  CA  GLU 0 100      -8.290 -11.348   8.181  1.00  0.48
ATOM    101  CA  VAL 0 101      -5.892  -8.748   8.524  1.00  0.43
ATOM    102  CA  ASN 0 102      -5.252  -7.121  11.708  1.00  0.48
ATOM    103  CA  ALA 0 103      -4.081  -3.622  10.355  1.00  0.43
ATOM    104  CA  GLY 0 104      -0.568  -3.426  11.156  1.00  0.39
ATOM    105  CA  ASP 0 105       1.175  -6.471  11.738  1.00  0.40
ATOM    106  CA  LYS 0 106       2.169  -9.117   9.588  1.00  0.45
ATOM    107  CA  LEU 0 107       2.683  -8.264   6.298  1.00  0.27
ATOM    108  CA  VAL 0 108       5.262  -7.808   4.482  1.00  0.23
ATOM    109  CA  THR 0 109       8.667  -7.770   5.752  1.00  0.24
ATOM    110  CA  VAL 0 110      10.141  -7.465   2.071  1.00  0.19
ATOM    111  CA  ASP 0 111      13.774  -7.660   3.076  1.00  0.25
ATOM    112  CA  LEU 0 112      14.028  -3.560   2.137  1.00  0.23
ATOM    113  CA  LYS 0 113      17.636  -3.605   1.760  1.00  0.30
ATOM    114  CA  SER 0 114      17.694  -6.089  -1.532  1.00  0.30
ATOM    115  CA  VAL 0 115      15.015  -4.132  -3.509  1.00  0.24
ATOM    116  CA  ALA 0 116      16.209  -0.532  -3.063  1.00  0.27
ATOM    117  CA  LYS 0 117      16.944   0.697  -6.538  1.00  0.28
ATOM    118  CA  LYS 0 118      15.306  -1.732  -8.828  1.00  0.30
ATOM    119  CA  VAL 0 119      11.966  -1.812 -10.421  1.00  0.26
ATOM    120  CA  PRO 0 120      11.180   1.781 -11.373  1.00  0.26
ATOM    121  CA  SER 0 121      11.112   3.736  -8.269  1.00  0.20
ATOM    122  CA  ILE 0 122       9.547   1.204  -5.716  1.00  0.14
ATOM    123  CA  LYS 0 123       7.106   3.624  -4.109  1.00  0.12
ATOM    124  CA  SER 0 124       4.479   1.626  -2.807  1.00  0.12
ATOM    125  CA  PRO 0 125       1.410   2.423  -5.100  1.00  0.19
ATOM    126  CA  ILE 0 126      -0.760   3.582  -2.029  1.00  0.22
ATOM    127  CA  ILE 0 127      -3.928   2.061  -2.447  1.00  0.38
ATOM    128  CA  PHE 0 128      -5.101   2.266  -5.753  1.00  0.46
ATOM    129  CA  THR 0 129      -7.504   0.545  -7.760  1.00  0.38
ATOM    130  CA  ASN 0 130     -10.831   1.511  -6.519  1.00  0.52
ATOM    131  CA  ASN 0 131     -11.625   5.034  -5.341  1.00  0.50
ATOM    132  CA  GLY 0 132     -12.846   6.391  -8.810  1.00  0.53
ATOM    133  CA  GLY 0 133     -13.045   9.892  -8.572  1.00  0.58
ATOM    134  CA  LYS 0 134     -13.342  11.830  -5.922  1.00  1.53
ATOM    135  CA  THR 0 135     -13.914  11.407  -2.690  1.00  0.82
ATOM    136  CA  LEU 0 136     -11.537  13.383  -1.465  1.00  1.92
ATOM    137  CA  GLU 0 137      -8.970  11.463   0.220  1.00  0.53
ATOM    138  CA  ILE 0 138      -7.117  14.454   0.535  1.00  1.11
ATOM    139  CA  VAL 0 139      -3.733  13.709   1.445  1.00  0.36
ATOM    140  CA  LYS 0 140      -4.366  13.475   5.378  1.00  0.46
ATOM    141  CA  MET 0 141      -1.134  14.214   6.617  1.00  0.42
ATOM    142  CA  GLY 0 142       1.791  13.660   4.506  1.00  0.30
ATOM    143  CA  GLU 0 143       4.000  11.403   6.103  1.00  0.29
ATOM    144  CA  VAL 0 144       3.849   8.948   8.370  1.00  0.30
ATOM    145  CA  LYS 0 145       4.813   6.433  10.611  1.00  0.32
ATOM    146  CA  GLN 0 146       4.038   3.127   9.161  1.00  0.31
ATOM    147  CA  GLY 0 147       0.787   1.760  10.280  1.00  0.37
ATOM    148  CA  ASP 0 148       0.001   3.531  13.544  1.00  0.47
ATOM    149  CA  VAL 0 149      -0.106   7.297  12.168  1.00  0.48
ATOM    150  CA  VAL 0 150      -3.934   7.416  11.969  1.00  0.62
ATOM    151  CA  ALA 0 151      -5.383  10.016   9.886  1.00  0.60
ATOM    152  CA  ILE 0 152      -3.529   9.822   6.599  1.00  0.43
ATOM    153  CA  LEU 0 153      -5.893   9.033   3.898  1.00  0.44
ATOM    154  CA  LYS 0 154      -9.158  10.823   4.347  1.00  0.57
TER     155      LYS 0 154
ENDPDB
BEGASN
DEFINE NUMBER_OF_PARENTS 2
DEFINE KEY 1 PDB 1GPR (Glucose permease IIA domain, B. subtilis)
DEFINE KEY 2 PDB 1GLAF (Glucose-specific factor III,E. coli)
DEFINE KEY 3 BUILT BKBONE (C-alpha to full backbone)
DEFINE KEY 4 BUILT SIDECH ("sidech" and CHARMM)
ASSIGN   1 M   - -   - - 3 4
ASSIGN   2 W   - -   - - 3 4
ASSIGN   3 F   - -   - - 3 4
ASSIGN   4 F   - -   - - 3 4
ASSIGN   5 N   - -   - - 3 4
ASSIGN   6 K   - -   - - 3 4
ASSIGN   7 N  12 E  19 T 3 4
ASSIGN   8 L  13 E  20 I 3 4
ASSIGN   9 K  14 V  21 E 3 4
ASSIGN  10 V  15 F  22 I 3 4
ASSIGN  11 L  16 V  23 I 3 4
ASSIGN  12 A  17 S  24 A 3 4
ASSIGN  13 P  18 P  25 P 3 4
ASSIGN  14 C  19 I  26 L 3 4
ASSIGN  15 D  20 T  27 S 3 4
ASSIGN  16 G  21 G  28 G 3 4
ASSIGN  17 T  22 E  29 E 3 4
ASSIGN  18 I  23 I  30 I 3 4
ASSIGN  19 I  24 H  31 V 3 4
ASSIGN  20 T  25 P  32 N 3 4
ASSIGN  21 L  26 I  33 I 3 4
ASSIGN  22 D  27 T  34 E 3 4
ASSIGN  23 E  28 D  35 D 3 4
ASSIGN  24 V  29 V  36 V 3 4
ASSIGN  25 E  30 P  37 P 3 4
ASSIGN  26 D  31 D  38 D 3 4
ASSIGN  27 E  32 Q  39 V 3 4
ASSIGN  28 V  33 V  40 V 3 4
ASSIGN  29 F  34 F  41 F 3 4
ASSIGN  30 K  35 S  42 A 3 4
ASSIGN  31 E  36 G  43 E 3 4
ASSIGN  32 R  37 K  44 K 3 4
ASSIGN  33 M  38 M  45 I 3 4
ASSIGN  34 L  39 M  46 V 3 4
ASSIGN  35 G  40 G  47 G 3 4
ASSIGN  36 D  41 D  48 D 3 4
ASSIGN  37 G  42 G  49 G 3 4
ASSIGN  38 F  43 F  50 I 3 4
ASSIGN  39 A  44 A  51 A 3 4
ASSIGN  40 I  45 I  52 I 3 4
ASSIGN  41 N  46 L  53 K 3 4
ASSIGN  42 P  47 P  54 P 3 4
ASSIGN  43 K  48 S  55 T 3 4
ASSIGN  44 S  49 E  56 G 3 4
ASSIGN  45 N  50 G  57 N 3 4
ASSIGN  46 D  51 I  58 K 3 4
ASSIGN  47 F  52 V  59 M 3 4
ASSIGN  48 H  53 V  60 V 3 4
ASSIGN  49 A  54 S  61 A 3 4
ASSIGN  50 P  55 P  62 P 3 4
ASSIGN  51 V  56 V  63 V 3 4
ASSIGN  52 S  57 R  64 D 3 4
ASSIGN  53 G  58 G  65 G 3 4
ASSIGN  54 K  59 K  66 T 3 4
ASSIGN  55 L  60 I  67 I 3 4
ASSIGN  56 V  61 L  68 G 3 4
ASSIGN  57 T  62 N  69 K 3 4
ASSIGN  58 A  63 V  70 I 3 4
ASSIGN  59 F  64 F  71 F 3 4
ASSIGN  60 P  65 P  72 E 3 4
ASSIGN  61 T  66 T  73 T 3 4
ASSIGN  62 K  67 K  74 N 3 4
ASSIGN  63 H  68 H  75 H 3 4
ASSIGN  64 A  69 A  76 A 3 4
ASSIGN  65 F  70 I  77 F 3 4
ASSIGN  66 G  71 G  78 S 3 4
ASSIGN  67 I  72 L  79 I 3 4
ASSIGN  68 Q  73 Q  80 E 3 4
ASSIGN  69 T  74 S  81 S 3 4
ASSIGN  70 K  75 D  82 D 3 4
ASSIGN  71 S  76 G  83 S 3 4
ASSIGN  72 G  77 G  84 G 3 4
ASSIGN  73 V  78 R  85 V 3 4
ASSIGN  74 E  79 E  86 E 3 4
ASSIGN  75 I  80 I  87 L 3 4
ASSIGN  76 L  81 L  88 F 3 4
ASSIGN  77 L  82 I  89 V 3 4
ASSIGN  78 H  83 H  90 H 3 4
ASSIGN  79 I  84 F  91 F 3 4
ASSIGN  80 G  85 G  92 G 3 4
ASSIGN  81 L  86 I  93 I 3 4
ASSIGN  82 D  87 D  94 D 3 4
ASSIGN  83 T  88 T  95 T 3 4
ASSIGN  84 V  89 V  96 V 3 4
ASSIGN  85 S  90 S  97 E 3 4
ASSIGN  86 L  91 L  98 L 3 4
ASSIGN  87 D  92 K  99 K 3 4
ASSIGN  88 G  93 G 100 G 3 4
ASSIGN  89 N  94 E 101 E 3 4
ASSIGN  90 G  95 G 102 G 3 4
ASSIGN  91 F  96 F 103 F 3 4
ASSIGN  92 E  97 T 104 K 3 4
ASSIGN  93 S  98 S 105 R 3 4
ASSIGN  94 F  99 F 106 I 3 4
ASSIGN  95 V 100 V 107 A 3 4
ASSIGN  96 T 101 S 108 E 3 4
ASSIGN  97 Q 102 E 109 E 3 4
ASSIGN  98 D 103 G 110 G 3 4
ASSIGN  99 Q 104 D 111 Q 3 4
ASSIGN 100 E 105 R 112 R 3 4
ASSIGN 101 V 106 V 113 V 3 4
ASSIGN 102 N 107 E 114 K 3 4
ASSIGN 103 A 108 P 115 V 3 4
ASSIGN 104 G 109 G 116 G 3 4
ASSIGN 105 D 110 Q 117 D 3 4
ASSIGN 106 K 111 K 118 T 3 4
ASSIGN 107 L 112 L 119 V 3 4
ASSIGN 108 V 113 L 120 I 3 4
ASSIGN 109 T 114 E 121 E 3 4
ASSIGN 110 V 115 V 122 F 3 4
ASSIGN 111 D 116 D 123 D 3 4
ASSIGN 112 L 117 L 124 L 3 4
ASSIGN 113 K 118 D 125 P 3 4
ASSIGN 114 S 119 A 126 L 3 4
ASSIGN 115 V 120 V 127 L 3 4
ASSIGN 116 A 121 K 128 E 3 4
ASSIGN 117 K 122 P 129 E 3 4
ASSIGN 118 K 123 N 130 K 3 4
ASSIGN 119 V 124 V 131 A 3 4
ASSIGN 120 P 125 P 132 K 3 4
ASSIGN 121 S 126 S 133 S 3 4
ASSIGN 122 I 127 L 134 T 3 4
ASSIGN 123 K 128 M 135 L 3 4
ASSIGN 124 S 129 T 136 T 3 4
ASSIGN 125 P 130 P 137 P 3 4
ASSIGN 126 I 131 I 138 V 3 4
ASSIGN 127 I 132 V 139 V 3 4
ASSIGN 128 F 133 F 140 I 3 4
ASSIGN 129 T 134 T 141 S 3 4
ASSIGN 130 N 135 N 142 N 3 4
ASSIGN 131 N 136 L 143 M 3 4
ASSIGN 132 G 137 A 144 D 3 4
ASSIGN 133 G 138 E 145 E 3 4
ASSIGN 134 K 139 G 146 I 3 4
ASSIGN 135 T 140 E 147 K 3 4
ASSIGN 136 L 141 T 148 E 3 4
ASSIGN 137 E 142 V 149 L 3 4
ASSIGN 138 I 143 S 150 I 3 4
ASSIGN 139 V 144 I 151 K 3 4
ASSIGN 140 K 145 K 152 L 3 4
ASSIGN 141 M 146 A   - - 3 4
ASSIGN 142 G 148 G 154 G 3 4
ASSIGN 143 E 149 S 155 S 3 4
ASSIGN 144 V 150 V 156 V 3 4
ASSIGN 145 K 151 N 157 T 3 4
ASSIGN 146 Q 152 R 158 V 3 4
ASSIGN 147 G   - - 159 G 3 4
ASSIGN 148 D 153 E 160 E 3 4
ASSIGN 149 V 154 Q 161 T 3 4
ASSIGN 150 V 155 E 162 P 3 4
ASSIGN 151 A 156 D   - - 3 4
ASSIGN 152 I 157 I 163 V 3 4
ASSIGN 153 L 158 V 164 I 3 4
ASSIGN 154 K 159 K 165 R 3 4
ENDASN
METHOD
REMARK ---- Multiple alignment ----
SEQALN Program MSAP: multiple sequence/structure alignment
SEQALN (Orengo, C. A. et al., Prot. Engng. 6:485-500 (1993))
SEQALN SCORING_MATRIX PAM120
SEQALN The alignment was constructed from the target, the
SEQALN two parent structure sequences and the following
SEQALN homologous sequences (SwissProt codes):
SEQALN YZFA_BACSU,PTGA_HAEIN,PTGA_SALTY,PTAA_KLEPN
REMARK
REMARK ---- Fold generation ----
COREBD DRAGON Program DRAGON-4: Distance Regularisation Algorithm
COREBD DRAGON for Geometry OptimisatioN, Version 4.16.1
COREBD DRAGON Generates C-alpha traces using restraints
COREBD DRAGON derived from multiple alignments
COREBD DRAGON (Aszodi,A. et al., J.Mol.Biol. 251:308 (1995))
COREBD DRAGON (Aszodi,A. and Taylor,W.R., Folding&Design 1:325 (1996))
REMARK
REMARK ---- C-alpha to full main-chain conversion ----
COREBD BKBONE 20 C-alpha traces generated by DRAGON-4 were averaged,
COREBD BKBONE and peptide groups
COREBD BKBONE were inserted between the C-alpha positions
COREBD BKBONE using local software ('sidech', unpublished).
REMARK The averaged C-alpha structures are given as PDBSET 1
REMARK and represent the "raw output" of DRAGON-4.
REMARK
REMARK ---- Sidechain generation ----
SIDEBD SIDECH Partial side chains were built by averaging the
SIDEBD SIDECH topologically equivalent side chains in the parent
SIDEBD SIDECH structures (using the same
SIDEBD SIDECH multiple alignment as DRAGON-4)
SIDEBD SIDECH by the program 'sidech' (unpublished).
SIDEBD SIDECH The rest of the missing side-chain atoms
SIDEBD SIDECH and polar hydrogens
SIDEBD SIDECH were automatically generated by CHARMM, Version 23.1
SIDEBD SIDECH as supplied by Molecular Simulations, Inc.
SIDEBD SIDECH as part of the QUANTA package
REMARK
REMARK ---- Refinement ----
REFINE QUANTA Program QUANTA, Version 4.1
REFINE EMIN Initial geometry regularisation
REFINE EMIN using adopted-basis Newton-Raphson
REFINE EMIN minimisation in vacuo
REFINE MDANNEAL Molecular dynamics/simulated annealing I:
REFINE MDANNEAL starting C-alpha positions restrained
REFINE MDANNEAL by harmonic force
REFINE MDANNEAL heat 0K->1000K 5 ps, equilibrate 2ps,
REFINE MDANNEAL cool 1000K->0K 10 ps, in vacuo
REFINE EMIN 1000 steps of unrestrained adopted-basis
REFINE EMIN Newton-Raphson minimisation
REFINE MDANNEAL Molecular dynamics/simulated annealing II:
REFINE MDANNEAL no restraints, 8 A thick water layer
REFINE MDANNEAL heat 0K->300K 5 ps,
REFINE MDANNEAL equilibrate 2ps,
REFINE MDANNEAL cool 300K->0K 10 ps
REFINE EMIN 1000 steps of adopted-basis
REFINE EMIN Newton-Raphson minimisation
REFINE EMIN with solvent layer held fixed
REMARK The result of this final minimisation
REMARK is given as PDBSET 2,
REMARK without the water coordinates.
ENDMET


