
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     1     -16.232   1.071  11.898  1.00  6.98
ATOM      2  CA  TRP     2     -14.844   0.461  11.132  1.00  6.03
ATOM      3  CA  PHE     3     -14.513   0.837   9.228  1.00  5.45
ATOM      4  CA  PHE     4     -15.379   2.993   8.025  1.00  4.68
ATOM      5  CA  ASN     5     -16.140   5.183   9.614  1.00  3.60
ATOM      6  CA  LYS     6     -14.227   6.983  11.011  1.00  2.72
ATOM      7  CA  ASN     7     -12.535   8.190   9.446  1.00  1.16
ATOM      8  CA  LEU     8     -11.639   5.242   7.851  1.00  1.63
ATOM      9  CA  LYS     9      -9.073   3.643   9.242  1.00  0.97
ATOM     10  CA  VAL    10      -6.384   3.409   6.499  1.00  0.46
ATOM     11  CA  LEU    11      -3.488   2.912   9.246  1.00  0.43
ATOM     12  CA  ALA    12      -0.908   5.039   7.476  1.00  0.36
ATOM     13  CA  PRO    13       0.325   2.142   5.019  1.00  0.25
ATOM     14  CA  CYS    14       3.857   2.162   5.591  1.00  0.17
ATOM     15  CA  ASP    15       5.500   5.106   7.130  1.00  0.18
ATOM     16  CA  GLY    16       7.624   6.488   4.532  1.00  0.15
ATOM     17  CA  THR    17       7.649   9.686   3.243  1.00  0.18
ATOM     18  CA  ILE    18       4.258  10.649   1.950  1.00  0.18
ATOM     19  CA  ILE    19       5.614  12.073  -1.536  1.00  0.21
ATOM     20  CA  THR    20       2.303  13.422  -2.727  1.00  0.29
ATOM     21  CA  LEU    21       1.575  10.649  -5.492  1.00  0.24
ATOM     22  CA  ASP    22       3.006  12.838  -8.433  1.00  0.28
ATOM     23  CA  GLU    23       6.768  11.914  -8.117  1.00  0.24
ATOM     24  CA  VAL    24       6.507   8.123  -8.816  1.00  0.22
ATOM     25  CA  GLU    25       7.889   7.760 -12.181  1.00  0.28
ATOM     26  CA  ASP    26       6.276   5.576 -14.413  1.00  0.33
ATOM     27  CA  GLU    27       3.469   6.832 -16.629  1.00  0.38
ATOM     28  CA  VAL    28       1.112   3.518 -15.938  1.00  0.37
ATOM     29  CA  PHE    29       0.262   4.676 -12.274  1.00  0.31
ATOM     30  CA  LYS    30       0.792   8.503 -12.817  1.00  0.34
ATOM     31  CA  GLU    31      -2.086  10.343 -14.384  1.00  0.42
ATOM     32  CA  ARG    32      -5.184   8.717 -12.765  1.00  0.42
ATOM     33  CA  MET    33      -4.644   5.018 -13.699  1.00  0.40
ATOM     34  CA  LEU    34      -4.040   3.160 -10.470  1.00  0.35
ATOM     35  CA  GLY    35      -5.552   5.315  -7.846  1.00  0.35
ATOM     36  CA  ASP    36      -3.995   8.403  -6.421  1.00  0.32
ATOM     37  CA  GLY    37      -3.185   7.033  -2.767  1.00  0.29
ATOM     38  CA  PHE    38       0.043   5.756  -3.252  1.00  0.26
ATOM     39  CA  ALA    39       3.261   6.628  -3.357  1.00  0.23
ATOM     40  CA  ILE    40       4.329   6.397   0.604  1.00  0.16
ATOM     41  CA  ASN    41       8.066   6.545  -0.629  1.00  0.14
ATOM     42  CA  PRO    42       9.130   2.956   0.294  1.00  0.12
ATOM     43  CA  LYS    43      10.059   4.053   3.947  1.00  0.16
ATOM     44  CA  SER    44      10.653   1.401   5.953  1.00  0.23
ATOM     45  CA  ASN    45       9.990  -1.961   4.889  1.00  0.20
ATOM     46  CA  ASP    46       7.547  -3.388   7.222  1.00  0.25
ATOM     47  CA  PHE    47       4.301  -3.141   5.862  1.00  0.24
ATOM     48  CA  HIS    48       1.688  -3.508   8.116  1.00  0.30
ATOM     49  CA  ALA    49      -1.341  -4.841   6.634  1.00  0.31
ATOM     50  CA  PRO    50      -3.188  -1.470   5.703  1.00  0.32
ATOM     51  CA  VAL    51      -6.321  -1.809   7.533  1.00  0.41
ATOM     52  CA  SER    52      -7.208  -5.423   8.047  1.00  0.45
ATOM     53  CA  GLY    53      -9.423  -6.180   5.139  1.00  0.47
ATOM     54  CA  LYS    54      -9.158  -9.529   4.144  1.00  0.44
ATOM     55  CA  LEU    55      -6.045 -10.651   2.382  1.00  0.37
ATOM     56  CA  VAL    56      -7.553 -10.431  -1.199  1.00  0.35
ATOM     57  CA  THR    57      -5.339 -11.321  -3.459  1.00  0.37
ATOM     58  CA  ALA    58      -1.637 -11.624  -2.099  1.00  0.25
ATOM     59  CA  PHE    59      -0.518 -11.274  -6.039  1.00  0.22
ATOM     60  CA  PRO    60       0.764 -15.030  -6.252  1.00  0.26
ATOM     61  CA  THR    61       4.601 -13.688  -5.937  1.00  0.25
ATOM     62  CA  LYS    62       3.703 -10.132  -5.426  1.00  0.77
ATOM     63  CA  HIS    63       2.745  -8.464  -2.513  1.00  0.28
ATOM     64  CA  ALA    64       0.941  -5.384  -2.945  1.00  0.31
ATOM     65  CA  PHE    65      -2.369  -5.793  -3.946  1.00  0.22
ATOM     66  CA  GLY    66      -5.342  -7.235  -3.146  1.00  0.33
ATOM     67  CA  ILE    67      -5.908  -6.806   0.660  1.00  0.34
ATOM     68  CA  GLN    68      -9.571  -5.337   0.076  1.00  0.43
ATOM     69  CA  THR    69      -9.628  -3.611   3.693  1.00  0.46
ATOM     70  CA  LYS    70     -13.345  -4.919   4.330  1.00  0.55
ATOM     71  CA  SER    71     -14.998  -2.666   1.773  1.00  0.77
ATOM     72  CA  GLY    72     -14.287  -2.522  -1.630  1.00  0.54
ATOM     73  CA  VAL    73     -11.714   0.374  -2.152  1.00  0.47
ATOM     74  CA  GLU    74      -9.254  -1.941  -3.938  1.00  0.42
ATOM     75  CA  ILE    75      -6.267  -0.942  -1.322  1.00  0.33
ATOM     76  CA  LEU    76      -3.916  -2.219  -3.936  1.00  0.29
ATOM     77  CA  LEU    77      -0.893  -2.546  -2.226  1.00  0.21
ATOM     78  CA  HIS    78       1.171  -3.077  -5.811  1.00  0.17
ATOM     79  CA  ILE    79       4.269  -2.213  -4.161  1.00  0.13
ATOM     80  CA  GLY    80       6.188   0.228  -5.855  1.00  0.11
ATOM     81  CA  LEU    81       5.730  -0.377  -9.516  1.00  0.19
ATOM     82  CA  ASP    82       6.808  -3.287 -11.256  1.00  0.23
ATOM     83  CA  THR    83       8.530  -5.599  -8.475  1.00  0.19
ATOM     84  CA  VAL    84       7.034  -8.919 -10.203  1.00  0.23
ATOM     85  CA  SER    85      10.009  -9.336 -12.762  1.00  0.31
ATOM     86  CA  LEU    86      12.743 -10.104  -9.948  1.00  0.31
ATOM     87  CA  ASP    87      11.295 -13.533  -8.921  1.00  0.29
ATOM     88  CA  GLY    88      10.019 -13.208  -5.397  1.00  0.22
ATOM     89  CA  ASN    89      13.619 -12.882  -3.645  1.00  0.28
ATOM     90  CA  GLY    90      12.806 -10.180  -1.112  1.00  0.23
ATOM     91  CA  PHE    91       9.657 -11.043   0.092  1.00  0.37
ATOM     92  CA  GLU    92       8.928 -13.195   2.562  1.00  0.26
ATOM     93  CA  SER    93       6.266 -12.330   4.573  1.00  0.34
ATOM     94  CA  PHE    94       3.688 -14.221   4.996  1.00  0.37
ATOM     95  CA  VAL    95       0.422 -13.896   4.722  1.00  0.34
ATOM     96  CA  THR    96      -0.887 -16.720   2.448  1.00  0.29
ATOM     97  CA  GLN    97      -3.982 -15.182   1.283  1.00  0.31
ATOM     98  CA  ASP    98      -6.588 -14.251   3.423  1.00  0.40
ATOM     99  CA  GLN    99      -6.005 -14.359   7.068  1.00  0.44
ATOM    100  CA  GLU   100      -8.290 -11.348   8.181  1.00  0.48
ATOM    101  CA  VAL   101      -5.892  -8.748   8.524  1.00  0.43
ATOM    102  CA  ASN   102      -5.252  -7.121  11.708  1.00  0.48
ATOM    103  CA  ALA   103      -4.081  -3.622  10.355  1.00  0.43
ATOM    104  CA  GLY   104      -0.568  -3.426  11.156  1.00  0.39
ATOM    105  CA  ASP   105       1.175  -6.471  11.738  1.00  0.40
ATOM    106  CA  LYS   106       2.169  -9.117   9.588  1.00  0.45
ATOM    107  CA  LEU   107       2.683  -8.264   6.298  1.00  0.27
ATOM    108  CA  VAL   108       5.262  -7.808   4.482  1.00  0.23
ATOM    109  CA  THR   109       8.667  -7.770   5.752  1.00  0.24
ATOM    110  CA  VAL   110      10.141  -7.465   2.071  1.00  0.19
ATOM    111  CA  ASP   111      13.774  -7.660   3.076  1.00  0.25
ATOM    112  CA  LEU   112      14.028  -3.560   2.137  1.00  0.23
ATOM    113  CA  LYS   113      17.636  -3.605   1.760  1.00  0.30
ATOM    114  CA  SER   114      17.694  -6.089  -1.532  1.00  0.30
ATOM    115  CA  VAL   115      15.015  -4.132  -3.509  1.00  0.24
ATOM    116  CA  ALA   116      16.209  -0.532  -3.063  1.00  0.27
ATOM    117  CA  LYS   117      16.944   0.697  -6.538  1.00  0.28
ATOM    118  CA  LYS   118      15.306  -1.732  -8.828  1.00  0.30
ATOM    119  CA  VAL   119      11.966  -1.812 -10.421  1.00  0.26
ATOM    120  CA  PRO   120      11.180   1.781 -11.373  1.00  0.26
ATOM    121  CA  SER   121      11.112   3.736  -8.269  1.00  0.20
ATOM    122  CA  ILE   122       9.547   1.204  -5.716  1.00  0.14
ATOM    123  CA  LYS   123       7.106   3.624  -4.109  1.00  0.12
ATOM    124  CA  SER   124       4.479   1.626  -2.807  1.00  0.12
ATOM    125  CA  PRO   125       1.410   2.423  -5.100  1.00  0.19
ATOM    126  CA  ILE   126      -0.760   3.582  -2.029  1.00  0.22
ATOM    127  CA  ILE   127      -3.928   2.061  -2.447  1.00  0.38
ATOM    128  CA  PHE   128      -5.101   2.266  -5.753  1.00  0.46
ATOM    129  CA  THR   129      -7.504   0.545  -7.760  1.00  0.38
ATOM    130  CA  ASN   130     -10.831   1.511  -6.519  1.00  0.52
ATOM    131  CA  ASN   131     -11.625   5.034  -5.341  1.00  0.50
ATOM    132  CA  GLY   132     -12.846   6.391  -8.810  1.00  0.53
ATOM    133  CA  GLY   133     -13.045   9.892  -8.572  1.00  0.58
ATOM    134  CA  LYS   134     -13.342  11.830  -5.922  1.00  1.53
ATOM    135  CA  THR   135     -13.914  11.407  -2.690  1.00  0.82
ATOM    136  CA  LEU   136     -11.537  13.383  -1.465  1.00  1.92
ATOM    137  CA  GLU   137      -8.970  11.463   0.220  1.00  0.53
ATOM    138  CA  ILE   138      -7.117  14.454   0.535  1.00  1.11
ATOM    139  CA  VAL   139      -3.733  13.709   1.445  1.00  0.36
ATOM    140  CA  LYS   140      -4.366  13.475   5.378  1.00  0.46
ATOM    141  CA  MET   141      -1.134  14.214   6.617  1.00  0.42
ATOM    142  CA  GLY   142       1.791  13.660   4.506  1.00  0.30
ATOM    143  CA  GLU   143       4.000  11.403   6.103  1.00  0.29
ATOM    144  CA  VAL   144       3.849   8.948   8.370  1.00  0.30
ATOM    145  CA  LYS   145       4.813   6.433  10.611  1.00  0.32
ATOM    146  CA  GLN   146       4.038   3.127   9.161  1.00  0.31
ATOM    147  CA  GLY   147       0.787   1.760  10.280  1.00  0.37
ATOM    148  CA  ASP   148       0.001   3.531  13.544  1.00  0.47
ATOM    149  CA  VAL   149      -0.106   7.297  12.168  1.00  0.48
ATOM    150  CA  VAL   150      -3.934   7.416  11.969  1.00  0.62
ATOM    151  CA  ALA   151      -5.383  10.016   9.886  1.00  0.60
ATOM    152  CA  ILE   152      -3.529   9.822   6.599  1.00  0.43
ATOM    153  CA  LEU   153      -5.893   9.033   3.898  1.00  0.44
ATOM    154  CA  LYS   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


