
PFRMAT TS  
TARGET T0099
AUTHOR 6239-5975-6267
METHOD Results from The Sausage Machine server.
METHOD Calculations were done using the "sausage" program.
METHOD
METHOD T. Huber, A.J. Russell, D. Ayers, A.E. Torda, 
METHOD Bioinformatics, 15(12), 1064-1065 (1999).
METHOD
METHOD This used a two step threading approach.  
METHOD The first score function 
METHOD T. Huber and A.E. Torda, J. Comp. Chem., 20(14), 1455 (1999) 
METHOD is for alignment to each member of a library.  This does not use
METHOD the frozen approximation.  The second score function (Huber and
METHOD Torda, Protein Sci, 7, 142-149) is built by optimising the difference
METHOD between native and non-native structure scores.
METHOD Specific parameters for this calculation are rather voluminous,
METHOD so they are listed under remarks.
REMARK ========================================================================
REMARK Mon Jul  3 12:35:54 2000
REMARK This software is guaranteed 100% free of any Biosym, MSI,
REMARK Oxford Molecular or other corporate influence.
REMARK 
REMARK Input script
REMARK 
REMARK #  Get the parameters from the argument list
REMARK set Sequence      [lindex $argv 0]
REMARK set Title         [lindex $argv 1]
REMARK set StructFormat  [lindex $argv 2]
REMARK 
REMARK version
REMARK set verbosity 2
REMARK 
REMARK source /rsc/appenzeller/u5/arussell/WWW/cgi-bin/Sausage/ExecSausage.tcl 
REMARK 
REMARK Parameters:
REMARK non specific force field
REMARK pnlty_scl = 4000.0 ovrlp_scl = 1500.0
REMARK pnlty_med = 1 pnlty_lrg = 1
REMARK ovrlp_opn = -0.052287 ovrlp_wdn = -0.019144
REMARK strct_opn = -0.0092699 strct_wdn = -0.0039544
REMARK enrgy_av = 181.28
REMARK 
REMARK Rescore, resort in all-atom force field with
REMARK pnlty_scl = 80.0 ovrlp_scl = 620.0
REMARK 
REMARK set PDBLIB        /rsc/appenzeller/data1/pdblib6apr00
REMARK set PARAM_FILE    $param_directory/cx_allat.param
REMARK set SECOND_PARAM  $param_directory/cc_allat_p370+0.param
REMARK  
REMARK ========================================================================
REMARK ========================================================================
REMARK About to look for version idents
REMARK /rsc/appenzeller/u5/arussell/WWW/cgi-bin/Sausage/sausage:
REMARK      $tclfile: $
REMARK      $Revision: 1.8 $
REMARK ========================================================================
MODEL 3
PARENT 1afp
ATOM      1  N   GLU     1       2.995 -10.967   8.469  1.00  1.00
ATOM      2  CA  GLU     1       3.743 -10.967   7.223  1.00  1.00
ATOM      3  C   GLU     1       3.466  -9.666   6.467  1.00  1.00
ATOM      4  O   GLU     1       3.769  -9.557   5.280  1.00  1.00
ATOM      5  CB  GLU     1       3.375 -12.206   6.406  1.00  1.00
ATOM      6  N   PHE     2       2.893  -8.711   7.185  1.00  1.00
ATOM      7  CA  PHE     2       2.572  -7.422   6.597  1.00  1.00
ATOM      8  C   PHE     2       3.850  -6.697   6.170  1.00  1.00
ATOM      9  O   PHE     2       4.871  -6.781   6.850  1.00  1.00
ATOM     10  CB  PHE     2       1.735  -6.636   7.608  1.00  1.00
ATOM     11  N   ILE     3       3.750  -6.001   5.047  1.00  1.00
ATOM     12  CA  ILE     3       4.885  -5.262   4.522  1.00  1.00
ATOM     13  C   ILE     3       4.808  -3.785   4.916  1.00  1.00
ATOM     14  O   ILE     3       4.057  -3.419   5.819  1.00  1.00
ATOM     15  CB  ILE     3       4.796  -5.376   2.999  1.00  1.00
ATOM     16  N   ALA     4       5.469   0.334   2.989  1.00  1.00
ATOM     17  CA  ALA     4       5.810   1.142   1.830  1.00  1.00
ATOM     18  C   ALA     4       5.205   2.543   1.941  1.00  1.00
ATOM     19  O   ALA     4       5.273   3.170   2.997  1.00  1.00
ATOM     20  CB  ALA     4       5.228   0.461   0.577  1.00  1.00
ATOM     21  N   ILE     5       4.627   2.992   0.837  1.00  1.00
ATOM     22  CA  ILE     5       4.011   4.307   0.797  1.00  1.00
ATOM     23  C   ILE     5       2.804   4.272  -0.144  1.00  1.00
ATOM     24  O   ILE     5       2.698   3.385  -0.990  1.00  1.00
ATOM     25  CB  ILE     5       5.045   5.373   0.430  1.00  1.00
ATOM     26  N   TYR     6       1.925   5.246   0.036  1.00  1.00
ATOM     27  CA  TYR     6       0.731   5.338  -0.786  1.00  1.00
ATOM     28  C   TYR     6       0.558   6.794  -1.222  1.00  1.00
ATOM     29  O   TYR     6       1.013   7.709  -0.537  1.00  1.00
ATOM     30  CB  TYR     6      -0.504   4.812  -0.051  1.00  1.00
ATOM     31  N   ASP     7      -0.100   6.964  -2.359  1.00  1.00
ATOM     32  CA  ASP     7      -0.339   8.293  -2.894  1.00  1.00
ATOM     33  C   ASP     7      -1.834   8.619  -2.908  1.00  1.00
ATOM     34  O   ASP     7      -2.649   7.795  -3.319  1.00  1.00
ATOM     35  CB  ASP     7       0.178   8.267  -4.334  1.00  1.00
ATOM     36  N   TYR     8      -2.149   9.823  -2.452  1.00  1.00
ATOM     37  CA  TYR     8      -3.531  10.268  -2.407  1.00  1.00
ATOM     38  C   TYR     8      -3.994  10.625  -3.820  1.00  1.00
ATOM     39  O   TYR     8      -5.063  10.196  -4.254  1.00  1.00
ATOM     40  CB  TYR     8      -3.694  11.408  -1.400  1.00  1.00
ATOM     41  N   LYS     9      -3.168  11.407  -4.500  1.00  1.00
ATOM     42  CA  LYS     9      -3.480  11.826  -5.856  1.00  1.00
ATOM     43  C   LYS     9      -3.748  10.591  -6.718  1.00  1.00
ATOM     44  O   LYS     9      -4.738  10.541  -7.446  1.00  1.00
ATOM     45  CB  LYS     9      -2.375  12.731  -6.404  1.00  1.00
ATOM     46  N   ALA    10      -2.848   9.625  -6.608  1.00  1.00
ATOM     47  CA  ALA    10      -2.975   8.394  -7.368  1.00  1.00
ATOM     48  C   ALA    10      -3.785   7.380  -6.558  1.00  1.00
ATOM     49  O   ALA    10      -4.112   6.303  -7.054  1.00  1.00
ATOM     50  CB  ALA    10      -1.603   7.781  -7.657  1.00  1.00
ATOM     51  N   GLU    11      -4.084   7.760  -5.325  1.00  1.00
ATOM     52  CA  GLU    11      -4.850   6.897  -4.441  1.00  1.00
ATOM     53  C   GLU    11      -4.411   5.446  -4.646  1.00  1.00
ATOM     54  O   GLU    11      -5.215   4.600  -5.035  1.00  1.00
ATOM     55  CB  GLU    11      -6.346   6.986  -4.745  1.00  1.00
ATOM     56  N   THR    12      -3.137   5.203  -4.376  1.00  1.00
ATOM     57  CA  THR    12      -2.582   3.868  -4.526  1.00  1.00
ATOM     58  C   THR    12      -1.571   3.612  -3.406  1.00  1.00
ATOM     59  O   THR    12      -1.139   4.545  -2.730  1.00  1.00
ATOM     60  CB  THR    12      -2.004   3.683  -5.930  1.00  1.00
ATOM     61  N   GLU    13      -1.222   2.344  -3.245  1.00  1.00
ATOM     62  CA  GLU    13      -0.270   1.954  -2.220  1.00  1.00
ATOM     63  C   GLU    13       0.884   1.210  -2.894  1.00  1.00
ATOM     64  O   GLU    13       0.708   0.095  -3.383  1.00  1.00
ATOM     65  CB  GLU    13      -0.930   1.112  -1.126  1.00  1.00
ATOM     66  N   GLU    14       2.041   1.857  -2.899  1.00  1.00
ATOM     67  CA  GLU    14       3.224   1.270  -3.505  1.00  1.00
ATOM     68  C   GLU    14       4.163   0.775  -2.404  1.00  1.00
ATOM     69  O   GLU    14       4.393   1.473  -1.418  1.00  1.00
ATOM     70  CB  GLU    14       3.877   2.260  -4.472  1.00  1.00
ATOM     71  N   ASP    15       4.681  -0.427  -2.609  1.00  1.00
ATOM     72  CA  ASP    15       5.591  -1.025  -1.646  1.00  1.00
ATOM     73  C   ASP    15       6.345  -2.204  -2.262  1.00  1.00
ATOM     74  O   ASP    15       5.885  -2.799  -3.236  1.00  1.00
ATOM     75  CB  ASP    15       4.715  -1.537  -0.500  1.00  1.00
ATOM     76  N   LEU    16       7.491  -2.507  -1.670  1.00  1.00
ATOM     77  CA  LEU    16       8.314  -3.605  -2.149  1.00  1.00
ATOM     78  C   LEU    16       7.838  -4.910  -1.508  1.00  1.00
ATOM     79  O   LEU    16       8.029  -5.125  -0.312  1.00  1.00
ATOM     80  CB  LEU    16       9.796  -3.308  -1.911  1.00  1.00
ATOM     81  N   THR    17       7.227  -5.748  -2.333  1.00  1.00
ATOM     82  CA  THR    17       6.722  -7.027  -1.861  1.00  1.00
ATOM     83  C   THR    17       7.840  -7.774  -1.131  1.00  1.00
ATOM     84  O   THR    17       9.017  -7.472  -1.317  1.00  1.00
ATOM     85  CB  THR    17       6.164  -7.823  -3.043  1.00  1.00
ATOM     86  N   ILE    18       7.431  -8.735  -0.316  1.00  1.00
ATOM     87  CA  ILE    18       8.383  -9.528   0.443  1.00  1.00
ATOM     88  C   ILE    18       9.379 -10.207  -0.499  1.00  1.00
ATOM     89  O   ILE    18      10.463 -10.609  -0.078  1.00  1.00
ATOM     90  CB  ILE    18       7.666 -10.558   1.317  1.00  1.00
ATOM     91  N   LYS    19       8.976 -10.313  -1.757  1.00  1.00
ATOM     92  CA  LYS    19       9.820 -10.937  -2.762  1.00  1.00
ATOM     93  C   LYS    19       9.898 -10.047  -4.005  1.00  1.00
ATOM     94  O   LYS    19      10.333 -10.493  -5.065  1.00  1.00
ATOM     95  CB  LYS    19       9.297 -12.325  -3.136  1.00  1.00
ATOM     96  N   LYS    20       9.470  -8.805  -3.832  1.00  1.00
ATOM     97  CA  LYS    20       9.486  -7.849  -4.926  1.00  1.00
ATOM     98  C   LYS    20       8.423  -8.194  -5.971  1.00  1.00
ATOM     99  O   LYS    20       8.335  -7.542  -7.010  1.00  1.00
ATOM    100  CB  LYS    20      10.868  -7.911  -5.603  1.00  1.00
ATOM    101  N   GLY    21       4.823  -8.406  -5.494  1.00  1.00
ATOM    102  CA  GLY    21       3.758  -7.421  -5.409  1.00  1.00
ATOM    103  C   GLY    21       4.247  -6.062  -5.914  1.00  1.00
ATOM    104  O   GLY    21       5.356  -5.951  -6.435  1.00  1.00
ATOM    105  N   GLU    22       3.395  -5.062  -5.743  1.00  1.00
ATOM    106  CA  GLU    22       3.726  -3.715  -6.176  1.00  1.00
ATOM    107  C   GLU    22       2.570  -2.774  -5.830  1.00  1.00
ATOM    108  O   GLU    22       1.813  -3.033  -4.896  1.00  1.00
ATOM    109  CB  GLU    22       4.043  -3.722  -7.673  1.00  1.00
ATOM    110  N   LYS    23       2.471  -1.701  -6.601  1.00  1.00
ATOM    111  CA  LYS    23       1.420  -0.720  -6.388  1.00  1.00
ATOM    112  C   LYS    23       0.096  -1.445  -6.135  1.00  1.00
ATOM    113  O   LYS    23      -0.186  -2.465  -6.761  1.00  1.00
ATOM    114  CB  LYS    23       1.367   0.270  -7.553  1.00  1.00
ATOM    115  N   LEU    24      -0.680  -0.888  -5.217  1.00  1.00
ATOM    116  CA  LEU    24      -1.967  -1.468  -4.875  1.00  1.00
ATOM    117  C   LEU    24      -2.925  -0.332  -4.511  1.00  1.00
ATOM    118  O   LEU    24      -2.780   0.295  -3.463  1.00  1.00
ATOM    119  CB  LEU    24      -1.843  -2.493  -3.745  1.00  1.00
ATOM    120  N   GLU    25      -3.882  -0.101  -5.398  1.00  1.00
ATOM    121  CA  GLU    25      -4.863   0.949  -5.183  1.00  1.00
ATOM    122  C   GLU    25      -5.162   1.064  -3.687  1.00  1.00
ATOM    123  O   GLU    25      -5.248   0.055  -2.988  1.00  1.00
ATOM    124  CB  GLU    25      -6.106   0.705  -6.042  1.00  1.00
ATOM    125  N   ILE    26      -5.314   2.302  -3.240  1.00  1.00
ATOM    126  CA  ILE    26      -5.601   2.562  -1.839  1.00  1.00
ATOM    127  C   ILE    26      -7.076   2.243  -1.585  1.00  1.00
ATOM    128  O   ILE    26      -7.903   3.149  -1.489  1.00  1.00
ATOM    129  CB  ILE    26      -5.252   3.999  -1.447  1.00  1.00
ATOM    130  N   ILE    27      -7.361   0.953  -1.483  1.00  1.00
ATOM    131  CA  ILE    27      -8.722   0.504  -1.242  1.00  1.00
ATOM    132  C   ILE    27      -9.235   1.012   0.107  1.00  1.00
ATOM    133  O   ILE    27      -8.724   0.622   1.156  1.00  1.00
ATOM    134  CB  ILE    27      -8.662  -1.024  -1.209  1.00  1.00
ATOM    135  N   GLU    28     -10.240   1.873   0.036  1.00  1.00
ATOM    136  CA  GLU    28     -10.828   2.437   1.238  1.00  1.00
ATOM    137  C   GLU    28      -9.879   3.486   1.821  1.00  1.00
ATOM    138  O   GLU    28      -8.661   3.352   1.718  1.00  1.00
ATOM    139  CB  GLU    28     -11.167   1.321   2.229  1.00  1.00
ATOM    140  N   LYS    29     -10.473   4.507   2.422  1.00  1.00
ATOM    141  CA  LYS    29      -9.696   5.578   3.022  1.00  1.00
ATOM    142  C   LYS    29      -8.500   5.899   2.123  1.00  1.00
ATOM    143  O   LYS    29      -7.367   5.538   2.438  1.00  1.00
ATOM    144  CB  LYS    29      -9.307   5.219   4.457  1.00  1.00
ATOM    145  N   GLU    30      -8.793   6.575   1.021  1.00  1.00
ATOM    146  CA  GLU    30      -7.756   6.949   0.075  1.00  1.00
ATOM    147  C   GLU    30      -6.513   7.407   0.841  1.00  1.00
ATOM    148  O   GLU    30      -6.600   7.763   2.015  1.00  1.00
ATOM    149  CB  GLU    30      -8.285   7.988  -0.916  1.00  1.00
ATOM    150  N   GLY    31      -5.386   7.382   0.145  1.00  1.00
ATOM    151  CA  GLY    31      -4.127   7.790   0.745  1.00  1.00
ATOM    152  C   GLY    31      -4.286   9.218   1.271  1.00  1.00
ATOM    153  O   GLY    31      -4.978  10.033   0.663  1.00  1.00
ATOM    154  N   ASP    32      -3.616   9.483   2.424  1.00  1.00
ATOM    155  CA  ASP    32      -3.676  10.798   3.039  1.00  1.00
ATOM    156  C   ASP    32      -2.817  11.803   2.268  1.00  1.00
ATOM    157  O   ASP    32      -3.250  12.925   2.009  1.00  1.00
ATOM    158  CB  ASP    32      -3.204  10.587   4.468  1.00  1.00
ATOM    159  N   TRP    33      -1.615  11.365   1.924  1.00  1.00
ATOM    160  CA  TRP    33      -0.692  12.212   1.188  1.00  1.00
ATOM    161  C   TRP    33       0.478  11.383   0.653  1.00  1.00
ATOM    162  O   TRP    33       1.008  10.525   1.358  1.00  1.00
ATOM    163  CB  TRP    33      -0.149  13.335   2.074  1.00  1.00
ATOM    164  N   TRP    34       0.845  11.668  -0.587  1.00  1.00
ATOM    165  CA  TRP    34       1.942  10.960  -1.224  1.00  1.00
ATOM    166  C   TRP    34       3.037  10.687  -0.191  1.00  1.00
ATOM    167  O   TRP    34       3.432  11.586   0.551  1.00  1.00
ATOM    168  CB  TRP    34       2.554  11.792  -2.353  1.00  1.00
ATOM    169  N   LYS    35       3.495   9.444  -0.174  1.00  1.00
ATOM    170  CA  LYS    35       4.536   9.043   0.756  1.00  1.00
ATOM    171  C   LYS    35       3.937   8.370   1.993  1.00  1.00
ATOM    172  O   LYS    35       4.629   7.647   2.708  1.00  1.00
ATOM    173  CB  LYS    35       5.292  10.306   1.210  1.00  1.00
ATOM    174  N   ALA    36       2.656   8.631   2.206  1.00  1.00
ATOM    175  CA  ALA    36       1.955   8.060   3.344  1.00  1.00
ATOM    176  C   ALA    36       2.320   6.580   3.471  1.00  1.00
ATOM    177  O   ALA    36       2.047   5.790   2.569  1.00  1.00
ATOM    178  CB  ALA    36       0.450   8.277   3.178  1.00  1.00
ATOM    179  N   LYS    37       2.932   6.249   4.599  1.00  1.00
ATOM    180  CA  LYS    37       3.337   4.878   4.856  1.00  1.00
ATOM    181  C   LYS    37       2.096   3.984   4.906  1.00  1.00
ATOM    182  O   LYS    37       1.030   4.420   5.338  1.00  1.00
ATOM    183  CB  LYS    37       4.200   4.801   6.117  1.00  1.00
ATOM    184  N   ALA    38       2.276   2.751   4.458  1.00  1.00
ATOM    185  CA  ALA    38       1.184   1.792   4.446  1.00  1.00
ATOM    186  C   ALA    38       1.781   0.384   4.432  1.00  1.00
ATOM    187  O   ALA    38       2.896   0.183   3.954  1.00  1.00
ATOM    188  CB  ALA    38       0.240   2.024   3.264  1.00  1.00
ATOM    189  N   ILE    39       1.011  -0.556   4.962  1.00  1.00
ATOM    190  CA  ILE    39       1.450  -1.940   5.016  1.00  1.00
ATOM    191  C   ILE    39       0.525  -2.824   4.177  1.00  1.00
ATOM    192  O   ILE    39      -0.657  -2.520   4.023  1.00  1.00
ATOM    193  CB  ILE    39       1.521  -2.437   6.461  1.00  1.00
ATOM    194  N   GLY    40       1.097  -3.900   3.657  1.00  1.00
ATOM    195  CA  GLY    40       0.338  -4.829   2.838  1.00  1.00
ATOM    196  C   GLY    40       0.052  -6.124   3.601  1.00  1.00
ATOM    197  O   GLY    40       0.911  -7.001   3.688  1.00  1.00
ATOM    198  N   SER    41      -1.158  -6.204   4.134  1.00  1.00
ATOM    199  CA  SER    41      -1.569  -7.377   4.887  1.00  1.00
ATOM    200  C   SER    41      -1.548  -8.600   3.968  1.00  1.00
ATOM    201  O   SER    41      -2.222  -8.619   2.939  1.00  1.00
ATOM    202  CB  SER    41      -2.991  -7.215   5.427  1.00  1.00
ATOM    203  N   GLY    42      -0.769  -9.592   4.373  1.00  1.00
ATOM    204  CA  GLY    42      -0.652 -10.816   3.598  1.00  1.00
ATOM    205  C   GLY    42      -1.698 -11.831   4.063  1.00  1.00
ATOM    206  O   GLY    42      -1.516 -13.036   3.896  1.00  1.00
ATOM    207  N   GLU    43      -2.771 -11.306   4.636  1.00  1.00
ATOM    208  CA  GLU    43      -3.847 -12.152   5.126  1.00  1.00
ATOM    209  C   GLU    43      -5.112 -11.971   4.285  1.00  1.00
ATOM    210  O   GLU    43      -5.959 -12.862   4.231  1.00  1.00
ATOM    211  CB  GLU    43      -4.129 -11.689   6.556  1.00  1.00
ATOM    212  N   ILE    44      -5.202 -10.811   3.650  1.00  1.00
ATOM    213  CA  ILE    44      -6.350 -10.502   2.815  1.00  1.00
ATOM    214  C   ILE    44      -5.865  -9.959   1.469  1.00  1.00
ATOM    215  O   ILE    44      -6.275 -10.444   0.416  1.00  1.00
ATOM    216  CB  ILE    44      -7.309  -9.562   3.548  1.00  1.00
ATOM    217  N   GLY    45      -4.998  -8.960   1.549  1.00  1.00
ATOM    218  CA  GLY    45      -4.453  -8.345   0.350  1.00  1.00
ATOM    219  C   GLY    45      -4.922  -6.895   0.215  1.00  1.00
ATOM    220  O   GLY    45      -4.973  -6.356  -0.889  1.00  1.00
ATOM    221  N   TYR    46      -5.253  -6.306   1.355  1.00  1.00
ATOM    222  CA  TYR    46      -5.716  -4.929   1.378  1.00  1.00
ATOM    223  C   TYR    46      -4.528  -3.992   1.150  1.00  1.00
ATOM    224  O   TYR    46      -3.577  -4.347   0.455  1.00  1.00
ATOM    225  CB  TYR    46      -6.484  -4.643   2.670  1.00  1.00
ATOM    226  N   ILE    47      -4.621  -2.813   1.749  1.00  1.00
ATOM    227  CA  ILE    47      -3.566  -1.823   1.619  1.00  1.00
ATOM    228  C   ILE    47      -3.688  -0.836   2.782  1.00  1.00
ATOM    229  O   ILE    47      -4.071   0.316   2.585  1.00  1.00
ATOM    230  CB  ILE    47      -3.616  -1.116   0.263  1.00  1.00
ATOM    231  N   ALA    49      -3.355  -1.324   3.968  1.00  1.00
ATOM    232  CA  ALA    49      -3.423  -0.499   5.162  1.00  1.00
ATOM    233  C   ALA    49      -2.798   0.876   4.916  1.00  1.00
ATOM    234  O   ALA    49      -1.585   1.041   5.036  1.00  1.00
ATOM    235  CB  ALA    49      -2.607  -1.233   6.229  1.00  1.00
ATOM    236  N   ILE    52      -3.655   1.827   4.575  1.00  1.00
ATOM    237  CA  ILE    52      -3.203   3.182   4.310  1.00  1.00
ATOM    238  C   ILE    52      -4.076   4.146   5.115  1.00  1.00
ATOM    239  O   ILE    52      -3.623   5.221   5.507  1.00  1.00
ATOM    240  CB  ILE    52      -3.225   3.504   2.815  1.00  1.00
TER
END

