
PFRMAT TS  
TARGET T0106
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 2
PARENT 1boe_A
ATOM      1  N   ALA     2       1.986 -13.408  -3.875  1.00  1.00
ATOM      2  CA  ALA     2       1.232 -12.180  -3.500  1.00  1.00
ATOM      3  C   ALA     2       1.631 -11.036  -4.437  1.00  1.00
ATOM      4  O   ALA     2       2.504 -11.180  -5.270  1.00  1.00
ATOM      5  CB  ALA     2       1.572 -11.796  -2.051  1.00  1.00
ATOM      6  N   CYS     3       1.001  -9.901  -4.307  1.00  1.00
ATOM      7  CA  CYS     3       1.347  -8.748  -5.191  1.00  1.00
ATOM      8  C   CYS     3       2.851  -8.476  -5.100  1.00  1.00
ATOM      9  O   CYS     3       3.552  -9.058  -4.297  1.00  1.00
ATOM     10  CB  CYS     3       0.612  -7.497  -4.699  1.00  1.00
ATOM     11  N   PRO     5       3.351  -7.594  -5.923  1.00  1.00
ATOM     12  CA  PRO     5       4.808  -7.280  -5.891  1.00  1.00
ATOM     13  C   PRO     5       5.034  -5.978  -5.117  1.00  1.00
ATOM     14  O   PRO     5       4.244  -5.599  -4.275  1.00  1.00
ATOM     15  CB  PRO     5       5.322  -7.119  -7.324  1.00  1.00
ATOM     16  N   VAL     6       6.108  -5.289  -5.398  1.00  1.00
ATOM     17  CA  VAL     6       6.389  -4.011  -4.682  1.00  1.00
ATOM     18  C   VAL     6       6.085  -2.830  -5.609  1.00  1.00
ATOM     19  O   VAL     6       6.590  -2.751  -6.712  1.00  1.00
ATOM     20  CB  VAL     6       7.866  -3.969  -4.279  1.00  1.00
ATOM     21  N   ARG     7       5.268  -1.910  -5.173  1.00  1.00
ATOM     22  CA  ARG     7       4.943  -0.728  -6.048  1.00  1.00
ATOM     23  C   ARG     7       3.573  -0.920  -6.706  1.00  1.00
ATOM     24  O   ARG     7       3.038  -0.014  -7.313  1.00  1.00
ATOM     25  CB  ARG     7       6.009  -0.632  -7.156  1.00  1.00
ATOM     26  N   ILE     8       2.998  -2.089  -6.602  1.00  1.00
ATOM     27  CA  ILE     8       1.667  -2.322  -7.235  1.00  1.00
ATOM     28  C   ILE     8       0.583  -1.607  -6.428  1.00  1.00
ATOM     29  O   ILE     8       0.527  -1.709  -5.219  1.00  1.00
ATOM     30  CB  ILE     8       1.371  -3.823  -7.264  1.00  1.00
ATOM     31  N   LEU    10      -0.287  -0.886  -7.086  1.00  1.00
ATOM     32  CA  LEU    10      -1.369  -0.176  -6.348  1.00  1.00
ATOM     33  C   LEU    10      -2.291  -1.212  -5.703  1.00  1.00
ATOM     34  O   LEU    10      -2.836  -2.071  -6.367  1.00  1.00
ATOM     35  CB  LEU    10      -2.170   0.695  -7.316  1.00  1.00
ATOM     36  N   CYS    11      -2.455  -1.150  -4.411  1.00  1.00
ATOM     37  CA  CYS    11      -3.323  -2.145  -3.720  1.00  1.00
ATOM     38  C   CYS    11      -4.134  -1.462  -2.615  1.00  1.00
ATOM     39  O   CYS    11      -4.410  -0.279  -2.659  1.00  1.00
ATOM     40  CB  CYS    11      -2.425  -3.206  -3.080  1.00  1.00
ATOM     41  N   SER    13      -4.485  -2.215  -1.606  1.00  1.00
ATOM     42  CA  SER    13      -5.246  -1.654  -0.457  1.00  1.00
ATOM     43  C   SER    13      -5.164  -2.650   0.695  1.00  1.00
ATOM     44  O   SER    13      -5.141  -3.847   0.488  1.00  1.00
ATOM     45  CB  SER    13      -6.720  -1.482  -0.868  1.00  1.00
ATOM     46  N   LEU    14      -5.115  -2.178   1.907  1.00  1.00
ATOM     47  CA  LEU    14      -5.030  -3.129   3.052  1.00  1.00
ATOM     48  C   LEU    14      -6.209  -4.101   2.969  1.00  1.00
ATOM     49  O   LEU    14      -6.189  -5.170   3.545  1.00  1.00
ATOM     50  CB  LEU    14      -5.057  -2.371   4.383  1.00  1.00
ATOM     51  N   TRP    16      -7.231  -3.743   2.236  1.00  1.00
ATOM     52  CA  TRP    16      -8.404  -4.649   2.090  1.00  1.00
ATOM     53  C   TRP    16      -8.266  -5.432   0.781  1.00  1.00
ATOM     54  O   TRP    16      -9.186  -6.094   0.342  1.00  1.00
ATOM     55  CB  TRP    16      -9.694  -3.824   2.053  1.00  1.00
ATOM     56  N   MET    18      -7.123  -5.356   0.148  1.00  1.00
ATOM     57  CA  MET    18      -6.927  -6.088  -1.135  1.00  1.00
ATOM     58  C   MET    18      -6.183  -7.401  -0.854  1.00  1.00
ATOM     59  O   MET    18      -6.458  -8.077   0.118  1.00  1.00
ATOM     60  CB  MET    18      -6.108  -5.207  -2.085  1.00  1.00
ATOM     61  N   MET    21      -5.242  -7.775  -1.685  1.00  1.00
ATOM     62  CA  MET    21      -4.497  -9.043  -1.439  1.00  1.00
ATOM     63  C   MET    21      -3.389  -8.775  -0.422  1.00  1.00
ATOM     64  O   MET    21      -3.361  -7.741   0.218  1.00  1.00
ATOM     65  CB  MET    21      -3.873  -9.544  -2.746  1.00  1.00
ATOM     66  N   PRO    22      -2.472  -9.690  -0.264  1.00  1.00
ATOM     67  CA  PRO    22      -1.371  -9.471   0.712  1.00  1.00
ATOM     68  C   PRO    22      -0.037  -9.439  -0.020  1.00  1.00
ATOM     69  O   PRO    22       0.613 -10.449  -0.152  1.00  1.00
ATOM     70  CB  PRO    22      -1.368 -10.606   1.739  1.00  1.00
ATOM     71  N   CYS    48       0.375  -8.284  -0.491  1.00  1.00
ATOM     72  CA  CYS    48       1.679  -8.201  -1.214  1.00  1.00
ATOM     73  C   CYS    48       2.717  -9.036  -0.478  1.00  1.00
ATOM     74  O   CYS    48       2.511  -9.416   0.657  1.00  1.00
ATOM     75  CB  CYS    48       2.142  -6.767  -1.350  1.00  1.00
ATOM     76  N   SER    49       3.812  -9.348  -1.132  1.00  1.00
ATOM     77  CA  SER    49       4.872 -10.197  -0.503  1.00  1.00
ATOM     78  C   SER    49       4.884 -10.013   1.010  1.00  1.00
ATOM     79  O   SER    49       4.813  -8.911   1.506  1.00  1.00
ATOM     80  CB  SER    49       6.244  -9.808  -1.052  1.00  1.00
ATOM     81  N   PRO    50       4.952 -11.099   1.730  1.00  1.00
ATOM     82  CA  PRO    50       4.964 -11.035   3.225  1.00  1.00
ATOM     83  C   PRO    50       5.715  -9.777   3.693  1.00  1.00
ATOM     84  O   PRO    50       5.117  -8.818   4.140  1.00  1.00
ATOM     85  CB  PRO    50       5.647 -12.307   3.766  1.00  1.00
ATOM     86  N   LEU    52       7.014  -9.775   3.593  1.00  1.00
ATOM     87  CA  LEU    52       7.792  -8.579   4.033  1.00  1.00
ATOM     88  C   LEU    52       7.116  -7.315   3.495  1.00  1.00
ATOM     89  O   LEU    52       7.172  -6.261   4.095  1.00  1.00
ATOM     90  CB  LEU    52       9.213  -8.669   3.446  1.00  1.00
ATOM     91  N   LEU    53       6.473  -7.420   2.363  1.00  1.00
ATOM     92  CA  LEU    53       5.780  -6.243   1.766  1.00  1.00
ATOM     93  C   LEU    53       4.394  -6.068   2.395  1.00  1.00
ATOM     94  O   LEU    53       3.822  -6.994   2.936  1.00  1.00
ATOM     95  CB  LEU    53       5.618  -6.481   0.267  1.00  1.00
ATOM     96  N   PHE    54       3.846  -4.885   2.314  1.00  1.00
ATOM     97  CA  PHE    54       2.491  -4.638   2.887  1.00  1.00
ATOM     98  C   PHE    54       1.857  -3.438   2.174  1.00  1.00
ATOM     99  O   PHE    54       2.551  -2.590   1.651  1.00  1.00
ATOM    100  CB  PHE    54       2.610  -4.348   4.386  1.00  1.00
ATOM    101  N   CYS    57       0.550  -3.363   2.146  1.00  1.00
ATOM    102  CA  CYS    57      -0.124  -2.216   1.460  1.00  1.00
ATOM    103  C   CYS    57       0.071  -0.938   2.284  1.00  1.00
ATOM    104  O   CYS    57      -0.473  -0.794   3.361  1.00  1.00
ATOM    105  CB  CYS    57      -1.626  -2.506   1.320  1.00  1.00
ATOM    106  N   ILE    63       0.844  -0.009   1.786  1.00  1.00
ATOM    107  CA  ILE    63       1.074   1.260   2.541  1.00  1.00
ATOM    108  C   ILE    63       0.849   2.457   1.607  1.00  1.00
ATOM    109  O   ILE    63       0.953   2.328   0.403  1.00  1.00
ATOM    110  CB  ILE    63       2.519   1.290   3.068  1.00  1.00
ATOM    111  N   CYS    64       0.549   3.592   2.194  1.00  1.00
ATOM    112  CA  CYS    64       0.305   4.837   1.438  1.00  1.00
ATOM    113  C   CYS    64       1.618   5.430   0.919  1.00  1.00
ATOM    114  O   CYS    64       2.692   5.088   1.376  1.00  1.00
ATOM    115  CB  CYS    64      -0.346   5.764   2.470  1.00  1.00
ATOM    116  N   ASP    67       1.538   6.317  -0.036  1.00  1.00
ATOM    117  CA  ASP    67       2.773   6.936  -0.592  1.00  1.00
ATOM    118  C   ASP    67       3.239   8.065   0.330  1.00  1.00
ATOM    119  O   ASP    67       2.542   9.040   0.536  1.00  1.00
ATOM    120  CB  ASP    67       2.477   7.500  -1.984  1.00  1.00
ATOM    121  N   PHE    68       4.408   7.935   0.895  1.00  1.00
ATOM    122  CA  PHE    68       4.917   8.993   1.816  1.00  1.00
ATOM    123  C   PHE    68       5.533  10.151   1.019  1.00  1.00
ATOM    124  O   PHE    68       5.500  11.288   1.445  1.00  1.00
ATOM    125  CB  PHE    68       5.982   8.390   2.736  1.00  1.00
ATOM    126  N   GLN    69       6.104   9.879  -0.125  1.00  1.00
ATOM    127  CA  GLN    69       6.725  10.977  -0.923  1.00  1.00
ATOM    128  C   GLN    69       5.688  11.594  -1.866  1.00  1.00
ATOM    129  O   GLN    69       5.990  12.484  -2.636  1.00  1.00
ATOM    130  CB  GLN    69       7.885  10.414  -1.747  1.00  1.00
ATOM    131  N   GLU    71       4.469  11.133  -1.818  1.00  1.00
ATOM    132  CA  GLU    71       3.424  11.701  -2.719  1.00  1.00
ATOM    133  C   GLU    71       2.782  12.919  -2.055  1.00  1.00
ATOM    134  O   GLU    71       3.010  14.046  -2.445  1.00  1.00
ATOM    135  CB  GLU    71       2.354  10.642  -2.992  1.00  1.00
ATOM    136  N   PRO    72       1.978  12.699  -1.054  1.00  1.00
ATOM    137  CA  PRO    72       1.319  13.842  -0.363  1.00  1.00
ATOM    138  C   PRO    72       0.705  13.351   0.952  1.00  1.00
ATOM    139  O   PRO    72       1.373  13.267   1.963  1.00  1.00
ATOM    140  CB  PRO    72       0.224  14.417  -1.264  1.00  1.00
ATOM    141  N   ILE    73      -0.559  13.020   0.949  1.00  1.00
ATOM    142  CA  ILE    73      -1.202  12.531   2.200  1.00  1.00
ATOM    143  C   ILE    73      -2.278  11.495   1.852  1.00  1.00
ATOM    144  O   ILE    73      -3.435  11.676   2.175  1.00  1.00
ATOM    145  CB  ILE    73      -1.846  13.709   2.937  1.00  1.00
ATOM    146  N   CYS    76      -1.863  10.436   1.203  1.00  1.00
ATOM    147  CA  CYS    76      -2.773   9.350   0.797  1.00  1.00
ATOM    148  C   CYS    76      -3.088   8.445   1.992  1.00  1.00
ATOM    149  O   CYS    76      -2.804   7.264   1.978  1.00  1.00
ATOM    150  CB  CYS    76      -1.974   8.589  -0.264  1.00  1.00
ATOM    151  N   VAL    79      -3.668   8.990   3.027  1.00  1.00
ATOM    152  CA  VAL    79      -3.993   8.158   4.222  1.00  1.00
ATOM    153  C   VAL    79      -5.229   7.301   3.935  1.00  1.00
ATOM    154  O   VAL    79      -5.473   6.307   4.590  1.00  1.00
ATOM    155  CB  VAL    79      -4.274   9.073   5.418  1.00  1.00
ATOM    156  N   CYS    80      -6.010   7.677   2.960  1.00  1.00
ATOM    157  CA  CYS    80      -7.230   6.884   2.632  1.00  1.00
ATOM    158  C   CYS    80      -7.109   6.335   1.208  1.00  1.00
ATOM    159  O   CYS    80      -8.073   6.279   0.470  1.00  1.00
ATOM    160  CB  CYS    80      -8.462   7.785   2.726  1.00  1.00
ATOM    161  N   ALA    83      -5.931   5.940   0.815  1.00  1.00
ATOM    162  CA  ALA    83      -5.745   5.407  -0.567  1.00  1.00
ATOM    163  C   ALA    83      -5.367   3.921  -0.519  1.00  1.00
ATOM    164  O   ALA    83      -5.739   3.152  -1.383  1.00  1.00
ATOM    165  CB  ALA    83      -4.631   6.192  -1.262  1.00  1.00
ATOM    166  N   CYS    87      -4.627   3.509   0.476  1.00  1.00
ATOM    167  CA  CYS    87      -4.223   2.074   0.563  1.00  1.00
ATOM    168  C   CYS    87      -5.308   1.265   1.276  1.00  1.00
ATOM    169  O   CYS    87      -5.019   0.316   1.976  1.00  1.00
ATOM    170  CB  CYS    87      -2.917   1.963   1.351  1.00  1.00
ATOM    171  N   ILE    90      -6.552   1.624   1.111  1.00  1.00
ATOM    172  CA  ILE    90      -7.636   0.861   1.792  1.00  1.00
ATOM    173  C   ILE    90      -8.496   0.146   0.751  1.00  1.00
ATOM    174  O   ILE    90      -8.536  -1.068   0.691  1.00  1.00
ATOM    175  CB  ILE    90      -8.512   1.823   2.597  1.00  1.00
ATOM    176  N   LEU    91      -9.191   0.888  -0.063  1.00  1.00
ATOM    177  CA  LEU    91     -10.057   0.251  -1.095  1.00  1.00
ATOM    178  C   LEU    91      -9.186  -0.368  -2.188  1.00  1.00
ATOM    179  O   LEU    91      -9.538  -1.367  -2.784  1.00  1.00
ATOM    180  CB  LEU    91     -10.979   1.306  -1.708  1.00  1.00
ATOM    181  N   ILE    92      -8.048   0.212  -2.455  1.00  1.00
ATOM    182  CA  ILE    92      -7.158  -0.352  -3.508  1.00  1.00
ATOM    183  C   ILE    92      -6.494   0.788  -4.282  1.00  1.00
ATOM    184  O   ILE    92      -6.448   0.783  -5.496  1.00  1.00
ATOM    185  CB  ILE    92      -8.014  -1.178  -4.486  1.00  1.00
ATOM    186  N   TYR    94      -5.977   1.764  -3.589  1.00  1.00
ATOM    187  CA  TYR    94      -5.313   2.901  -4.287  1.00  1.00
ATOM    188  C   TYR    94      -3.964   3.193  -3.627  1.00  1.00
ATOM    189  O   TYR    94      -3.257   4.103  -4.015  1.00  1.00
ATOM    190  CB  TYR    94      -6.204   4.141  -4.204  1.00  1.00
ATOM    191  N   CYS   104      -3.596   2.428  -2.635  1.00  1.00
ATOM    192  CA  CYS   104      -2.291   2.665  -1.959  1.00  1.00
ATOM    193  C   CYS   104      -1.191   1.917  -2.714  1.00  1.00
ATOM    194  O   CYS   104      -1.377   1.495  -3.836  1.00  1.00
ATOM    195  CB  CYS   104      -2.370   2.113  -0.524  1.00  1.00
ATOM    196  N   VAL   109      -0.049   1.745  -2.108  1.00  1.00
ATOM    197  CA  VAL   109       1.058   1.017  -2.793  1.00  1.00
ATOM    198  C   VAL   109       1.763   0.114  -1.777  1.00  1.00
ATOM    199  O   VAL   109       1.923   0.472  -0.628  1.00  1.00
ATOM    200  CB  VAL   109       2.059   2.028  -3.360  1.00  1.00
ATOM    201  N   CYS   115       2.184  -1.055  -2.182  1.00  1.00
ATOM    202  CA  CYS   115       2.868  -1.959  -1.229  1.00  1.00
ATOM    203  C   CYS   115       4.363  -1.668  -1.191  1.00  1.00
ATOM    204  O   CYS   115       5.084  -1.918  -2.136  1.00  1.00
ATOM    205  CB  CYS   115       2.631  -3.404  -1.651  1.00  1.00
ATOM    206  N   ILE   116       4.835  -1.154  -0.091  1.00  1.00
ATOM    207  CA  ILE   116       6.285  -0.861   0.030  1.00  1.00
ATOM    208  C   ILE   116       6.890  -1.827   1.045  1.00  1.00
ATOM    209  O   ILE   116       6.221  -2.275   1.955  1.00  1.00
ATOM    210  CB  ILE   116       6.479   0.578   0.514  1.00  1.00
ATOM    211  N   SER   117       8.144  -2.159   0.902  1.00  1.00
ATOM    212  CA  SER   117       8.777  -3.099   1.870  1.00  1.00
ATOM    213  C   SER   117       8.352  -2.718   3.292  1.00  1.00
ATOM    214  O   SER   117       8.045  -1.577   3.571  1.00  1.00
ATOM    215  CB  SER   117      10.299  -3.011   1.741  1.00  1.00
ATOM    216  N   ALA   120       8.330  -3.662   4.193  1.00  1.00
ATOM    217  CA  ALA   120       7.922  -3.349   5.595  1.00  1.00
ATOM    218  C   ALA   120       9.141  -2.880   6.387  1.00  1.00
ATOM    219  O   ALA   120       9.313  -3.215   7.542  1.00  1.00
ATOM    220  CB  ALA   120       7.337  -4.598   6.262  1.00  1.00
ATOM    221  N   ILE   121       9.980  -2.091   5.781  1.00  1.00
ATOM    222  CA  ILE   121      11.178  -1.580   6.501  1.00  1.00
ATOM    223  C   ILE   121      10.794  -0.253   7.139  1.00  1.00
ATOM    224  O   ILE   121      10.616  -0.153   8.337  1.00  1.00
ATOM    225  CB  ILE   121      12.328  -1.367   5.514  1.00  1.00
ATOM    226  N   VAL   122      10.627   0.761   6.339  1.00  1.00
ATOM    227  CA  VAL   122      10.208   2.070   6.892  1.00  1.00
ATOM    228  C   VAL   122       8.798   1.909   7.462  1.00  1.00
ATOM    229  O   VAL   122       8.309   2.749   8.191  1.00  1.00
ATOM    230  CB  VAL   122      10.198   3.117   5.781  1.00  1.00
TER
END

