
PFRMAT TS  
TARGET T0105
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 4
PARENT 1qhk_A
ATOM      1  N   PHE   600      -7.501  12.157   1.177  1.00  1.00
ATOM      2  CA  PHE   600      -7.334  10.880   0.431  1.00  1.00
ATOM      3  C   PHE   600      -8.126   9.771   1.116  1.00  1.00
ATOM      4  O   PHE   600      -9.308   9.904   1.363  1.00  1.00
ATOM      5  CB  PHE   600      -5.843  10.497   0.442  1.00  1.00
ATOM      6  N   VAL   607      -7.489   8.672   1.422  1.00  1.00
ATOM      7  CA  VAL   607      -8.222   7.567   2.084  1.00  1.00
ATOM      8  C   VAL   607      -7.259   6.585   2.729  1.00  1.00
ATOM      9  O   VAL   607      -6.068   6.793   2.766  1.00  1.00
ATOM     10  CB  VAL   607      -9.032   6.801   1.055  1.00  1.00
ATOM     11  N   CYS   609      -7.783   5.487   3.194  1.00  1.00
ATOM     12  CA  CYS   609      -6.924   4.442   3.811  1.00  1.00
ATOM     13  C   CYS   609      -6.736   3.335   2.783  1.00  1.00
ATOM     14  O   CYS   609      -7.617   3.072   1.989  1.00  1.00
ATOM     15  CB  CYS   609      -7.607   3.878   5.060  1.00  1.00
ATOM     16  N   VAL   612      -5.606   2.688   2.758  1.00  1.00
ATOM     17  CA  VAL   612      -5.435   1.628   1.729  1.00  1.00
ATOM     18  C   VAL   612      -4.722   0.401   2.270  1.00  1.00
ATOM     19  O   VAL   612      -3.534   0.422   2.512  1.00  1.00
ATOM     20  CB  VAL   612      -4.636   2.168   0.554  1.00  1.00
ATOM     21  N   LEU   616      -5.423  -0.692   2.391  1.00  1.00
ATOM     22  CA  LEU   616      -4.762  -1.940   2.847  1.00  1.00
ATOM     23  C   LEU   616      -4.068  -2.528   1.624  1.00  1.00
ATOM     24  O   LEU   616      -4.555  -3.445   0.993  1.00  1.00
ATOM     25  CB  LEU   616      -5.810  -2.923   3.370  1.00  1.00
ATOM     26  N   TYR   617      -2.957  -1.956   1.251  1.00  1.00
ATOM     27  CA  TYR   617      -2.252  -2.419   0.027  1.00  1.00
ATOM     28  C   TYR   617      -1.082  -3.342   0.356  1.00  1.00
ATOM     29  O   TYR   617      -0.453  -3.232   1.391  1.00  1.00
ATOM     30  CB  TYR   617      -1.727  -1.192  -0.709  1.00  1.00
ATOM     31  N   PHE   621      -0.774  -4.245  -0.543  1.00  1.00
ATOM     32  CA  PHE   621       0.365  -5.168  -0.307  1.00  1.00
ATOM     33  C   PHE   621       0.665  -5.973  -1.577  1.00  1.00
ATOM     34  O   PHE   621       1.067  -7.118  -1.512  1.00  1.00
ATOM     35  CB  PHE   621       0.020  -6.123   0.836  1.00  1.00
ATOM     36  N   GLN   623       0.489  -5.385  -2.731  1.00  1.00
ATOM     37  CA  GLN   623       0.784  -6.125  -3.993  1.00  1.00
ATOM     38  C   GLN   623       2.217  -6.654  -3.930  1.00  1.00
ATOM     39  O   GLN   623       2.487  -7.793  -4.258  1.00  1.00
ATOM     40  CB  GLN   623       0.645  -5.181  -5.192  1.00  1.00
ATOM     41  N   GLY   624       3.137  -5.831  -3.507  1.00  1.00
ATOM     42  CA  GLY   624       4.556  -6.274  -3.415  1.00  1.00
ATOM     43  C   GLY   624       5.431  -5.076  -3.041  1.00  1.00
ATOM     44  O   GLY   624       5.028  -3.937  -3.175  1.00  1.00
ATOM     45  N   THR   625       6.624  -5.319  -2.572  1.00  1.00
ATOM     46  CA  THR   625       7.515  -4.188  -2.192  1.00  1.00
ATOM     47  C   THR   625       7.035  -3.586  -0.870  1.00  1.00
ATOM     48  O   THR   625       6.018  -3.978  -0.331  1.00  1.00
ATOM     49  CB  THR   625       7.465  -3.118  -3.285  1.00  1.00
ATOM     50  N   SER   626       7.757  -2.635  -0.343  1.00  1.00
ATOM     51  CA  SER   626       7.337  -2.008   0.940  1.00  1.00
ATOM     52  C   SER   626       5.906  -1.485   0.802  1.00  1.00
ATOM     53  O   SER   626       5.665  -0.463   0.190  1.00  1.00
ATOM     54  CB  SER   626       8.277  -0.846   1.270  1.00  1.00
ATOM     55  N   LYS   627       4.955  -2.182   1.359  1.00  1.00
ATOM     56  CA  LYS   627       3.540  -1.729   1.252  1.00  1.00
ATOM     57  C   LYS   627       2.859  -1.835   2.617  1.00  1.00
ATOM     58  O   LYS   627       3.506  -1.845   3.646  1.00  1.00
ATOM     59  CB  LYS   627       2.799  -2.613   0.248  1.00  1.00
ATOM     60  N   LYS   628       1.556  -1.915   2.636  1.00  1.00
ATOM     61  CA  LYS   628       0.833  -2.020   3.932  1.00  1.00
ATOM     62  C   LYS   628      -0.401  -1.120   3.898  1.00  1.00
ATOM     63  O   LYS   628      -0.912  -0.790   2.844  1.00  1.00
ATOM     64  CB  LYS   628       1.766  -1.537   5.058  1.00  1.00
ATOM     65  N   CYS   629      -0.892  -0.728   5.039  1.00  1.00
ATOM     66  CA  CYS   629      -2.091   0.137   5.064  1.00  1.00
ATOM     67  C   CYS   629      -1.693   1.604   4.900  1.00  1.00
ATOM     68  O   CYS   629      -0.730   2.066   5.478  1.00  1.00
ATOM     69  CB  CYS   629      -2.832  -0.045   6.382  1.00  1.00
ATOM     70  N   ILE   630      -2.441   2.342   4.126  1.00  1.00
ATOM     71  CA  ILE   630      -2.124   3.786   3.933  1.00  1.00
ATOM     72  C   ILE   630      -3.273   4.624   4.458  1.00  1.00
ATOM     73  O   ILE   630      -4.250   4.111   4.970  1.00  1.00
ATOM     74  CB  ILE   630      -1.973   4.099   2.455  1.00  1.00
ATOM     75  N   GLN   631      -3.155   5.911   4.340  1.00  1.00
ATOM     76  CA  GLN   631      -4.206   6.807   4.832  1.00  1.00
ATOM     77  C   GLN   631      -3.930   8.189   4.255  1.00  1.00
ATOM     78  O   GLN   631      -3.636   9.129   4.966  1.00  1.00
ATOM     79  CB  GLN   631      -4.064   6.819   6.326  1.00  1.00
ATOM     80  N   SER   632      -3.977   8.309   2.959  1.00  1.00
ATOM     81  CA  SER   632      -3.670   9.611   2.339  1.00  1.00
ATOM     82  C   SER   632      -4.211   9.667   0.918  1.00  1.00
ATOM     83  O   SER   632      -4.626   8.672   0.355  1.00  1.00
ATOM     84  CB  SER   632      -2.151   9.780   2.293  1.00  1.00
ATOM     85  N   GLU   633      -4.164  10.823   0.319  1.00  1.00
ATOM     86  CA  GLU   633      -4.607  10.938  -1.090  1.00  1.00
ATOM     87  C   GLU   633      -3.465  10.427  -1.952  1.00  1.00
ATOM     88  O   GLU   633      -3.636   9.610  -2.835  1.00  1.00
ATOM     89  CB  GLU   633      -4.891  12.395  -1.435  1.00  1.00
ATOM     90  N   ASP   634      -2.288  10.917  -1.678  1.00  1.00
ATOM     91  CA  ASP   634      -1.096  10.493  -2.442  1.00  1.00
ATOM     92  C   ASP   634      -0.804   9.026  -2.142  1.00  1.00
ATOM     93  O   ASP   634      -0.781   8.199  -3.028  1.00  1.00
ATOM     94  CB  ASP   634       0.102  11.348  -2.040  1.00  1.00
ATOM     95  N   TRP   637      -0.598   8.696  -0.896  1.00  1.00
ATOM     96  CA  TRP   637      -0.325   7.281  -0.538  1.00  1.00
ATOM     97  C   TRP   637      -1.302   6.393  -1.300  1.00  1.00
ATOM     98  O   TRP   637      -0.983   5.299  -1.719  1.00  1.00
ATOM     99  CB  TRP   637      -0.537   7.100   0.962  1.00  1.00
ATOM    100  N   PHE   638      -2.494   6.873  -1.490  1.00  1.00
ATOM    101  CA  PHE   638      -3.506   6.082  -2.225  1.00  1.00
ATOM    102  C   PHE   638      -3.066   5.913  -3.671  1.00  1.00
ATOM    103  O   PHE   638      -2.475   4.920  -4.049  1.00  1.00
ATOM    104  CB  PHE   638      -4.843   6.819  -2.155  1.00  1.00
ATOM    105  N   THR   639      -3.348   6.879  -4.469  1.00  1.00
ATOM    106  CA  THR   639      -2.968   6.829  -5.890  1.00  1.00
ATOM    107  C   THR   639      -1.462   6.583  -6.029  1.00  1.00
ATOM    108  O   THR   639      -1.027   5.794  -6.844  1.00  1.00
ATOM    109  CB  THR   639      -3.339   8.180  -6.460  1.00  1.00
ATOM    110  N   ARG   641      -0.663   7.249  -5.240  1.00  1.00
ATOM    111  CA  ARG   641       0.812   7.050  -5.331  1.00  1.00
ATOM    112  C   ARG   641       1.139   5.565  -5.176  1.00  1.00
ATOM    113  O   ARG   641       1.855   4.993  -5.975  1.00  1.00
ATOM    114  CB  ARG   641       1.513   7.835  -4.221  1.00  1.00
ATOM    115  N   PHE   643       0.626   4.933  -4.156  1.00  1.00
ATOM    116  CA  PHE   643       0.917   3.489  -3.961  1.00  1.00
ATOM    117  C   PHE   643       0.210   2.685  -5.049  1.00  1.00
ATOM    118  O   PHE   643       0.607   1.586  -5.382  1.00  1.00
ATOM    119  CB  PHE   643       0.418   3.053  -2.584  1.00  1.00
ATOM    120  N   ILE   645      -0.839   3.225  -5.608  1.00  1.00
ATOM    121  CA  ILE   645      -1.570   2.489  -6.672  1.00  1.00
ATOM    122  C   ILE   645      -2.183   3.476  -7.669  1.00  1.00
ATOM    123  O   ILE   645      -3.345   3.818  -7.585  1.00  1.00
ATOM    124  CB  ILE   645      -2.673   1.656  -6.030  1.00  1.00
ATOM    125  N   GLU   646      -1.411   3.925  -8.618  1.00  1.00
ATOM    126  CA  GLU   646      -1.945   4.875  -9.630  1.00  1.00
ATOM    127  C   GLU   646      -1.678   4.304 -11.023  1.00  1.00
ATOM    128  O   GLU   646      -0.570   4.346 -11.520  1.00  1.00
ATOM    129  CB  GLU   646      -1.244   6.224  -9.474  1.00  1.00
ATOM    130  N   GLY   647      -2.681   3.756 -11.648  1.00  1.00
ATOM    131  CA  GLY   647      -2.486   3.162 -12.998  1.00  1.00
ATOM    132  C   GLY   647      -2.511   1.638 -12.871  1.00  1.00
ATOM    133  O   GLY   647      -3.237   0.968 -13.575  1.00  1.00
ATOM    134  N   ASP   648      -1.723   1.112 -11.953  1.00  1.00
ATOM    135  CA  ASP   648      -1.651  -0.367 -11.693  1.00  1.00
ATOM    136  C   ASP   648      -2.569  -1.158 -12.630  1.00  1.00
ATOM    137  O   ASP   648      -3.777  -1.112 -12.513  1.00  1.00
ATOM    138  CB  ASP   648      -2.069  -0.625 -10.244  1.00  1.00
ATOM    139  N   ARG   649      -2.006  -1.889 -13.554  1.00  1.00
ATOM    140  CA  ARG   649      -2.851  -2.684 -14.489  1.00  1.00
ATOM    141  C   ARG   649      -3.812  -3.562 -13.685  1.00  1.00
ATOM    142  O   ARG   649      -4.885  -3.902 -14.140  1.00  1.00
ATOM    143  CB  ARG   649      -1.936  -3.595 -15.328  1.00  1.00
ATOM    144  N   GLY   650      -3.435  -3.931 -12.490  1.00  1.00
ATOM    145  CA  GLY   650      -4.325  -4.787 -11.658  1.00  1.00
ATOM    146  C   GLY   650      -3.680  -5.016 -10.291  1.00  1.00
ATOM    147  O   GLY   650      -3.472  -6.137  -9.872  1.00  1.00
ATOM    148  N   ALA   651      -3.357  -3.963  -9.592  1.00  1.00
ATOM    149  CA  ALA   651      -2.721  -4.122  -8.255  1.00  1.00
ATOM    150  C   ALA   651      -3.722  -4.774  -7.288  1.00  1.00
ATOM    151  O   ALA   651      -4.900  -4.866  -7.569  1.00  1.00
ATOM    152  CB  ALA   651      -2.297  -2.744  -7.735  1.00  1.00
ATOM    153  N   SER   652      -3.259  -5.246  -6.158  1.00  1.00
ATOM    154  CA  SER   652      -4.182  -5.909  -5.182  1.00  1.00
ATOM    155  C   SER   652      -4.883  -4.860  -4.328  1.00  1.00
ATOM    156  O   SER   652      -6.081  -4.894  -4.139  1.00  1.00
ATOM    157  CB  SER   652      -3.378  -6.840  -4.267  1.00  1.00
ATOM    158  N   TRP   655      -4.110  -3.947  -3.821  1.00  1.00
ATOM    159  CA  TRP   655      -4.611  -2.841  -2.949  1.00  1.00
ATOM    160  C   TRP   655      -6.066  -3.023  -2.502  1.00  1.00
ATOM    161  O   TRP   655      -6.988  -2.957  -3.292  1.00  1.00
ATOM    162  CB  TRP   655      -4.494  -1.535  -3.712  1.00  1.00
ATOM    163  N   LEU   657      -6.277  -3.194  -1.223  1.00  1.00
ATOM    164  CA  LEU   657      -7.666  -3.322  -0.700  1.00  1.00
ATOM    165  C   LEU   657      -8.068  -1.964  -0.126  1.00  1.00
ATOM    166  O   LEU   657      -7.790  -1.650   1.017  1.00  1.00
ATOM    167  CB  LEU   657      -7.722  -4.385   0.400  1.00  1.00
ATOM    168  N   ILE   659      -8.687  -1.143  -0.926  1.00  1.00
ATOM    169  CA  ILE   659      -9.077   0.214  -0.458  1.00  1.00
ATOM    170  C   ILE   659      -9.807   0.142   0.879  1.00  1.00
ATOM    171  O   ILE   659     -10.502  -0.810   1.175  1.00  1.00
ATOM    172  CB  ILE   659      -9.986   0.868  -1.495  1.00  1.00
ATOM    173  N   CYS   661      -9.647   1.153   1.691  1.00  1.00
ATOM    174  CA  CYS   661     -10.324   1.155   3.012  1.00  1.00
ATOM    175  C   CYS   661     -10.435   2.578   3.559  1.00  1.00
ATOM    176  O   CYS   661      -9.774   3.497   3.107  1.00  1.00
ATOM    177  CB  CYS   661      -9.522   0.310   3.977  1.00  1.00
ATOM    178  N   TYR   664     -11.268   2.754   4.543  1.00  1.00
ATOM    179  CA  TYR   664     -11.446   4.092   5.156  1.00  1.00
ATOM    180  C   TYR   664     -11.361   3.933   6.671  1.00  1.00
ATOM    181  O   TYR   664     -12.005   4.639   7.423  1.00  1.00
ATOM    182  CB  TYR   664     -12.820   4.617   4.771  1.00  1.00
ATOM    183  N   THR   665     -10.580   2.992   7.118  1.00  1.00
ATOM    184  CA  THR   665     -10.448   2.747   8.574  1.00  1.00
ATOM    185  C   THR   665      -9.397   1.659   8.788  1.00  1.00
ATOM    186  O   THR   665      -9.685   0.482   8.706  1.00  1.00
ATOM    187  CB  THR   665     -11.797   2.285   9.132  1.00  1.00
ATOM    188  N   LEU   666      -8.182   2.056   9.045  1.00  1.00
ATOM    189  CA  LEU   666      -7.078   1.071   9.260  1.00  1.00
ATOM    190  C   LEU   666      -7.603  -0.166   9.999  1.00  1.00
ATOM    191  O   LEU   666      -7.098  -1.257   9.832  1.00  1.00
ATOM    192  CB  LEU   666      -5.980   1.733  10.095  1.00  1.00
ATOM    193  N   VAL   668      -8.608  -0.002  10.815  1.00  1.00
ATOM    194  CA  VAL   668      -9.165  -1.163  11.572  1.00  1.00
ATOM    195  C   VAL   668      -9.691  -2.226  10.600  1.00  1.00
ATOM    196  O   VAL   668      -9.497  -3.411  10.796  1.00  1.00
ATOM    197  CB  VAL   668     -10.310  -0.683  12.466  1.00  1.00
ATOM    198  N   LEU   669     -10.352  -1.822   9.550  1.00  1.00
ATOM    199  CA  LEU   669     -10.873  -2.811   8.588  1.00  1.00
ATOM    200  C   LEU   669      -9.732  -3.246   7.686  1.00  1.00
ATOM    201  O   LEU   669      -9.435  -4.416   7.546  1.00  1.00
ATOM    202  CB  LEU   669     -11.986  -2.179   7.757  1.00  1.00
ATOM    203  N   MET   670      -9.081  -2.299   7.091  1.00  1.00
ATOM    204  CA  MET   670      -7.940  -2.626   6.210  1.00  1.00
ATOM    205  C   MET   670      -6.978  -3.540   6.967  1.00  1.00
ATOM    206  O   MET   670      -6.530  -4.549   6.458  1.00  1.00
ATOM    207  CB  MET   670      -7.224  -1.332   5.817  1.00  1.00
ATOM    208  N   GLU   671      -6.665  -3.192   8.187  1.00  1.00
ATOM    209  CA  GLU   671      -5.736  -4.041   8.990  1.00  1.00
ATOM    210  C   GLU   671      -6.395  -5.391   9.268  1.00  1.00
ATOM    211  O   GLU   671      -5.767  -6.425   9.163  1.00  1.00
ATOM    212  CB  GLU   671      -5.379  -3.340  10.304  1.00  1.00
ATOM    213  N   ASN   672      -7.658  -5.402   9.602  1.00  1.00
ATOM    214  CA  ASN   672      -8.331  -6.698   9.856  1.00  1.00
ATOM    215  C   ASN   672      -8.276  -7.529   8.574  1.00  1.00
ATOM    216  O   ASN   672      -8.354  -8.742   8.598  1.00  1.00
ATOM    217  CB  ASN   672      -9.788  -6.456  10.246  1.00  1.00
ATOM    218  N   PHE   674      -8.132  -6.875   7.452  1.00  1.00
ATOM    219  CA  PHE   674      -8.057  -7.599   6.158  1.00  1.00
ATOM    220  C   PHE   674      -6.668  -8.202   6.010  1.00  1.00
ATOM    221  O   PHE   674      -6.509  -9.384   5.779  1.00  1.00
ATOM    222  CB  PHE   674      -8.299  -6.613   5.016  1.00  1.00
ATOM    223  N   LEU   675      -5.661  -7.384   6.131  1.00  1.00
ATOM    224  CA  LEU   675      -4.278  -7.876   5.988  1.00  1.00
ATOM    225  C   LEU   675      -4.129  -9.214   6.713  1.00  1.00
ATOM    226  O   LEU   675      -3.322 -10.045   6.344  1.00  1.00
ATOM    227  CB  LEU   675      -3.304  -6.864   6.593  1.00  1.00
ATOM    228  N   PRO   676      -4.895  -9.425   7.746  1.00  1.00
ATOM    229  CA  PRO   676      -4.790 -10.704   8.500  1.00  1.00
ATOM    230  C   PRO   676      -3.786 -10.533   9.640  1.00  1.00
ATOM    231  O   PRO   676      -3.145 -11.473  10.064  1.00  1.00
ATOM    232  CB  PRO   676      -4.276 -11.800   7.548  1.00  1.00
TER
END

