
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 5
PARENT 1c4e_A
ATOM      1  N   ALA     1     -13.148  -5.723  -3.432  1.00  1.00
ATOM      2  CA  ALA     1     -13.263  -4.336  -3.867  1.00  1.00
ATOM      3  C   ALA     1     -11.955  -3.837  -4.459  1.00  1.00
ATOM      4  O   ALA     1     -10.928  -4.513  -4.397  1.00  1.00
ATOM      5  CB  ALA     1     -13.674  -3.441  -2.698  1.00  1.00
ATOM      6  N   ALA     2     -12.007  -2.645  -5.035  1.00  1.00
ATOM      7  CA  ALA     2     -10.836  -2.033  -5.646  1.00  1.00
ATOM      8  C   ALA     2      -9.931  -1.408  -4.591  1.00  1.00
ATOM      9  O   ALA     2     -10.012  -1.732  -3.408  1.00  1.00
ATOM     10  CB  ALA     2     -11.257  -0.950  -6.638  1.00  1.00
ATOM     11  N   CYS     3      -9.085  -0.489  -5.042  1.00  1.00
ATOM     12  CA  CYS     3      -8.170   0.220  -4.161  1.00  1.00
ATOM     13  C   CYS     3      -7.872   1.603  -4.720  1.00  1.00
ATOM     14  O   CYS     3      -7.473   1.745  -5.876  1.00  1.00
ATOM     15  CB  CYS     3      -6.847  -0.536  -3.966  1.00  1.00
ATOM     16  N   PRO     5      -8.081   2.616  -3.898  1.00  1.00
ATOM     17  CA  PRO     5      -7.849   3.990  -4.308  1.00  1.00
ATOM     18  C   PRO     5      -6.359   4.317  -4.323  1.00  1.00
ATOM     19  O   PRO     5      -5.600   3.836  -3.482  1.00  1.00
ATOM     20  CB  PRO     5      -8.585   4.944  -3.372  1.00  1.00
ATOM     21  N   VAL     6      -5.947   5.139  -5.283  1.00  1.00
ATOM     22  CA  VAL     6      -4.548   5.532  -5.405  1.00  1.00
ATOM     23  C   VAL     6      -4.055   6.178  -4.114  1.00  1.00
ATOM     24  O   VAL     6      -4.767   6.969  -3.494  1.00  1.00
ATOM     25  CB  VAL     6      -4.366   6.499  -6.576  1.00  1.00
ATOM     26  N   ARG     7      -2.837   5.832  -3.712  1.00  1.00
ATOM     27  CA  ARG     7      -2.251   6.375  -2.492  1.00  1.00
ATOM     28  C   ARG     7      -2.510   5.446  -1.311  1.00  1.00
ATOM     29  O   ARG     7      -1.887   5.574  -0.258  1.00  1.00
ATOM     30  CB  ARG     7      -2.820   7.764  -2.198  1.00  1.00
ATOM     31  N   ILE     8      -3.431   4.505  -1.497  1.00  1.00
ATOM     32  CA  ILE     8      -3.767   3.548  -0.451  1.00  1.00
ATOM     33  C   ILE     8      -2.877   2.315  -0.554  1.00  1.00
ATOM     34  O   ILE     8      -2.489   1.912  -1.648  1.00  1.00
ATOM     35  CB  ILE     8      -5.239   3.143  -0.549  1.00  1.00
ATOM     36  N   PRO     9      -2.545   1.729   0.590  1.00  1.00
ATOM     37  CA  PRO     9      -1.692   0.554   0.626  1.00  1.00
ATOM     38  C   PRO     9      -2.341  -0.632  -0.080  1.00  1.00
ATOM     39  O   PRO     9      -3.423  -0.516  -0.653  1.00  1.00
ATOM     40  CB  PRO     9      -1.376   0.199   2.074  1.00  1.00
ATOM     41  N   CYS    11      -1.660  -1.774  -0.032  1.00  1.00
ATOM     42  CA  CYS    11      -2.147  -2.993  -0.662  1.00  1.00
ATOM     43  C   CYS    11      -1.141  -4.116  -0.464  1.00  1.00
ATOM     44  O   CYS    11      -0.153  -3.952   0.251  1.00  1.00
ATOM     45  CB  CYS    11      -2.386  -2.765  -2.155  1.00  1.00
ATOM     46  N   LEU    14      -1.390  -5.256  -1.093  1.00  1.00
ATOM     47  CA  LEU    14      -0.493  -6.389  -0.967  1.00  1.00
ATOM     48  C   LEU    14      -0.375  -7.157  -2.279  1.00  1.00
ATOM     49  O   LEU    14      -1.372  -7.618  -2.834  1.00  1.00
ATOM     50  CB  LEU    14      -0.968  -7.345   0.136  1.00  1.00
ATOM     51  N   PRO    15       0.857  -7.307  -2.788  1.00  1.00
ATOM     52  CA  PRO    15       1.116  -8.026  -4.038  1.00  1.00
ATOM     53  C   PRO    15       0.787  -9.509  -3.923  1.00  1.00
ATOM     54  O   PRO    15       1.353 -10.219  -3.091  1.00  1.00
ATOM     55  CB  PRO    15       2.618  -7.827  -4.265  1.00  1.00
ATOM     56  N   TRP    16      -0.138  -9.972  -4.758  1.00  1.00
ATOM     57  CA  TRP    16      -0.546 -11.370  -4.744  1.00  1.00
ATOM     58  C   TRP    16      -1.704 -11.584  -3.778  1.00  1.00
ATOM     59  O   TRP    16      -1.950 -12.701  -3.323  1.00  1.00
ATOM     60  CB  TRP    16       0.631 -12.263  -4.347  1.00  1.00
ATOM     61  N   GLU    17      -2.413 -10.504  -3.465  1.00  1.00
ATOM     62  CA  GLU    17      -3.544 -10.572  -2.549  1.00  1.00
ATOM     63  C   GLU    17      -4.715  -9.744  -3.064  1.00  1.00
ATOM     64  O   GLU    17      -5.681 -10.284  -3.603  1.00  1.00
ATOM     65  CB  GLU    17      -3.127 -10.083  -1.161  1.00  1.00
ATOM     66  N   MET    18      -4.625  -8.429  -2.892  1.00  1.00
ATOM     67  CA  MET    18      -5.680  -7.525  -3.338  1.00  1.00
ATOM     68  C   MET    18      -5.267  -6.781  -4.602  1.00  1.00
ATOM     69  O   MET    18      -4.101  -6.803  -4.996  1.00  1.00
ATOM     70  CB  MET    18      -6.022  -6.522  -2.236  1.00  1.00
ATOM     71  N   PRO    22      -6.231  -6.116  -5.230  1.00  1.00
ATOM     72  CA  PRO    22      -5.974  -5.357  -6.447  1.00  1.00
ATOM     73  C   PRO    22      -6.566  -3.956  -6.339  1.00  1.00
ATOM     74  O   PRO    22      -7.482  -3.720  -5.551  1.00  1.00
ATOM     75  CB  PRO    22      -6.560  -6.082  -7.659  1.00  1.00
ATOM     76  N   CYS    48      -6.038  -3.027  -7.130  1.00  1.00
ATOM     77  CA  CYS    48      -6.515  -1.655  -7.114  1.00  1.00
ATOM     78  C   CYS    48      -7.651  -1.460  -8.112  1.00  1.00
ATOM     79  O   CYS    48      -7.902  -2.318  -8.958  1.00  1.00
ATOM     80  CB  CYS    48      -5.366  -0.702  -7.427  1.00  1.00
ATOM     81  N   CYS    57      -8.341  -0.330  -8.000  1.00  1.00
ATOM     82  CA  CYS    57      -9.457  -0.030  -8.885  1.00  1.00
ATOM     83  C   CYS    57      -9.004   0.003 -10.342  1.00  1.00
ATOM     84  O   CYS    57      -9.008  -1.020 -11.028  1.00  1.00
ATOM     85  CB  CYS    57     -10.089   1.309  -8.510  1.00  1.00
ATOM     86  N   ALA    58      -8.616   1.185 -10.809  1.00  1.00
ATOM     87  CA  ALA    58      -8.163   1.354 -12.186  1.00  1.00
ATOM     88  C   ALA    58      -7.998   2.833 -12.522  1.00  1.00
ATOM     89  O   ALA    58      -8.755   3.677 -12.040  1.00  1.00
ATOM     90  CB  ALA    58      -9.155   0.705 -13.153  1.00  1.00
ATOM     91  N   MET    59      -7.002   3.167 -13.355  1.00  1.00
ATOM     92  CA  MET    59      -6.089   2.186 -13.940  1.00  1.00
ATOM     93  C   MET    59      -4.932   1.844 -13.009  1.00  1.00
ATOM     94  O   MET    59      -3.910   1.311 -13.442  1.00  1.00
ATOM     95  CB  MET    59      -5.581   2.911 -15.181  1.00  1.00
ATOM     96  N   CYS    64      -5.096   2.161 -11.730  1.00  1.00
ATOM     97  CA  CYS    64      -4.062   1.896 -10.736  1.00  1.00
ATOM     98  C   CYS    64      -3.708   0.414 -10.693  1.00  1.00
ATOM     99  O   CYS    64      -4.386  -0.417 -11.296  1.00  1.00
ATOM    100  CB  CYS    64      -4.523   2.365  -9.356  1.00  1.00
ATOM    101  N   ILE    66      -2.636   0.093  -9.973  1.00  1.00
ATOM    102  CA  ILE    66      -2.183  -1.287  -9.845  1.00  1.00
ATOM    103  C   ILE    66      -1.792  -1.599  -8.403  1.00  1.00
ATOM    104  O   ILE    66      -0.813  -1.062  -7.885  1.00  1.00
ATOM    105  CB  ILE    66      -0.994  -1.540 -10.774  1.00  1.00
ATOM    106  N   CYS    76      -2.564  -2.470  -7.761  1.00  1.00
ATOM    107  CA  CYS    76      -2.299  -2.854  -6.377  1.00  1.00
ATOM    108  C   CYS    76      -0.965  -3.585  -6.260  1.00  1.00
ATOM    109  O   CYS    76      -0.916  -4.815  -6.273  1.00  1.00
ATOM    110  CB  CYS    76      -3.429  -3.740  -5.848  1.00  1.00
ATOM    111  N   VAL    79       0.116  -2.819  -6.144  1.00  1.00
ATOM    112  CA  VAL    79       1.449  -3.397  -6.023  1.00  1.00
ATOM    113  C   VAL    79       2.368  -2.483  -5.220  1.00  1.00
ATOM    114  O   VAL    79       1.908  -1.577  -4.526  1.00  1.00
ATOM    115  CB  VAL    79       2.047  -3.649  -7.409  1.00  1.00
ATOM    116  N   CYS    80       3.671  -2.723  -5.324  1.00  1.00
ATOM    117  CA  CYS    80       4.658  -1.920  -4.611  1.00  1.00
ATOM    118  C   CYS    80       4.753  -0.520  -5.205  1.00  1.00
ATOM    119  O   CYS    80       4.925  -0.355  -6.412  1.00  1.00
ATOM    120  CB  CYS    80       6.028  -2.598  -4.657  1.00  1.00
ATOM    121  N   CYS    87       4.647   0.483  -4.342  1.00  1.00
ATOM    122  CA  CYS    87       4.730   1.869  -4.770  1.00  1.00
ATOM    123  C   CYS    87       6.176   2.343  -4.742  1.00  1.00
ATOM    124  O   CYS    87       6.548   3.291  -5.433  1.00  1.00
ATOM    125  CB  CYS    87       3.887   2.786  -3.865  1.00  1.00
ATOM    126  N   GLU    88       6.984   1.667  -3.933  1.00  1.00
ATOM    127  CA  GLU    88       8.393   2.002  -3.801  1.00  1.00
ATOM    128  C   GLU    88       9.242   0.742  -3.697  1.00  1.00
ATOM    129  O   GLU    88       9.272  -0.080  -4.612  1.00  1.00
ATOM    130  CB  GLU    88       8.611   2.868  -2.566  1.00  1.00
ATOM    131  N   PRO    89       9.929   0.598  -2.569  1.00  1.00
ATOM    132  CA  PRO    89      10.779  -0.557  -2.331  1.00  1.00
ATOM    133  C   PRO    89      10.370  -1.278  -1.050  1.00  1.00
ATOM    134  O   PRO    89      10.757  -2.423  -0.820  1.00  1.00
ATOM    135  CB  PRO    89      12.243  -0.127  -2.233  1.00  1.00
ATOM    136  N   ILE    90       9.589  -0.598  -0.217  1.00  1.00
ATOM    137  CA  ILE    90       9.132  -1.171   1.043  1.00  1.00
ATOM    138  C   ILE    90       7.638  -0.937   1.249  1.00  1.00
ATOM    139  O   ILE    90       6.946  -1.766   1.839  1.00  1.00
ATOM    140  CB  ILE    90       9.917  -0.571   2.209  1.00  1.00
ATOM    141  N   LEU    91       7.147   0.199   0.763  1.00  1.00
ATOM    142  CA  LEU    91       5.735   0.541   0.900  1.00  1.00
ATOM    143  C   LEU    91       4.933   0.059  -0.303  1.00  1.00
ATOM    144  O   LEU    91       5.243   0.394  -1.447  1.00  1.00
ATOM    145  CB  LEU    91       5.568   2.052   1.064  1.00  1.00
ATOM    146  N   CYS   104       3.900  -0.732  -0.037  1.00  1.00
ATOM    147  CA  CYS   104       3.051  -1.264  -1.091  1.00  1.00
ATOM    148  C   CYS   104       1.683  -0.586  -1.079  1.00  1.00
ATOM    149  O   CYS   104       0.980  -0.607  -0.070  1.00  1.00
ATOM    150  CB  CYS   104       2.887  -2.772  -0.915  1.00  1.00
ATOM    151  N   TYR   110       1.312   0.013  -2.206  1.00  1.00
ATOM    152  CA  TYR   110       0.031   0.693  -2.323  1.00  1.00
ATOM    153  C   TYR   110      -0.532   0.553  -3.732  1.00  1.00
ATOM    154  O   TYR   110      -0.317  -0.456  -4.408  1.00  1.00
ATOM    155  CB  TYR   110       0.181   2.174  -1.972  1.00  1.00
ATOM    156  N   CYS   115      -1.257   1.574  -4.162  1.00  1.00
ATOM    157  CA  CYS   115      -1.866   1.589  -5.479  1.00  1.00
ATOM    158  C   CYS   115      -1.093   2.499  -6.427  1.00  1.00
ATOM    159  O   CYS   115      -0.809   3.651  -6.101  1.00  1.00
ATOM    160  CB  CYS   115      -3.310   2.064  -5.364  1.00  1.00
ATOM    161  N   ILE   116      -0.759   1.977  -7.601  1.00  1.00
ATOM    162  CA  ILE   116      -0.022   2.745  -8.593  1.00  1.00
ATOM    163  C   ILE   116      -0.773   2.785  -9.920  1.00  1.00
ATOM    164  O   ILE   116      -1.988   2.972  -9.949  1.00  1.00
ATOM    165  CB  ILE   116       1.383   2.159  -8.826  1.00  1.00
ATOM    166  N   SER   117      -0.042   2.607 -11.014  1.00  1.00
ATOM    167  CA  SER   117      -0.656   2.625 -12.328  1.00  1.00
ATOM    168  C   SER   117       0.354   2.460 -13.445  1.00  1.00
ATOM    169  O   SER   117       0.537   1.318 -13.915  1.00  1.00
ATOM    170  CB  SER   117      -1.345   3.990 -12.510  1.00  1.00
TER
END

