
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   20 (  152),  selected   20 , name T0356TS249_5_4-D1
# Molecule2: number of CA atoms  124 (  963),  selected   20 , name T0356_D1.pdb
# PARAMETERS: T0356TS249_5_4-D1.T0356_D1.pdb  -3  -ie  -o1  -sda  -d:4  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20       328 - 347         4.93     4.93
  LCS_AVERAGE:     16.13

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11       337 - 347         1.67     7.26
  LCS_AVERAGE:      6.33

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       338 - 347         0.63     7.66
  LCS_AVERAGE:      5.24

LCS_GDT    MOLECULE-1    MOLECULE-2    LENGTH_OF_THE
LCS_GDT     RESIDUE       RESIDUE         CONTINUOUS
LCS_GDT   NAME NUMBER   NAME NUMBER          SEGMENT     GLOBAL DISTANCE TEST - GDT_DATA_COLUMNS                             NUMBER OF THE RESIDUES:  124
LCS_GDT     E     328     E     328      3    4   20     0    3    3    3    4    4    4    6    7    8    8    9   15   15   17   17   19   19   20   20 
LCS_GDT     P     329     P     329      3    4   20     3    3    3    7    9   11   12   12   14   15   16   16   17   18   18   19   19   19   20   20 
LCS_GDT     A     330     A     330      3    4   20     3    3    3    7    9   11   12   13   14   15   16   16   17   18   18   19   19   19   20   20 
LCS_GDT     V     331     V     331      3    4   20     3    3    3    7    9   11   12   13   14   15   16   16   17   18   18   19   19   19   20   20 
LCS_GDT     L     332     L     332      3    4   20     3    3    3    4    7   10   12   13   14   15   16   16   17   18   18   19   19   19   20   20 
LCS_GDT     G     333     G     333      3    4   20     3    3    3    4    4    4    5    7    8   12   16   16   17   18   18   19   19   19   20   20 
LCS_GDT     V     334     V     334      3    4   20     3    3    3    4    4    4    6    7   10   13   16   16   17   18   18   19   19   19   20   20 
LCS_GDT     A     335     A     335      3    4   20     3    3    3    4    5    9   13   13   13   15   16   16   17   18   18   19   19   19   20   20 
LCS_GDT     L     336     L     336      3    4   20     3    3    3    3    4    9   13   13   13   14   16   16   17   18   18   19   19   19   20   20 
LCS_GDT     N     337     N     337      3   11   20     3    3    3    3    5    9   13   13   13   15   16   16   17   18   18   19   19   19   20   20 
LCS_GDT     E     338     E     338     10   11   20     5   10   10   10   10   11   13   13   14   15   16   16   17   18   18   19   19   19   20   20 
LCS_GDT     V     339     V     339     10   11   20     3   10   10   10   10   11   13   13   14   15   16   16   17   18   18   19   19   19   20   20 
LCS_GDT     F     340     F     340     10   11   20     7   10   10   10   10   11   13   13   14   15   16   16   17   18   18   19   19   19   20   20 
LCS_GDT     V     341     V     341     10   11   20     7   10   10   10   10   11   13   13   14   15   16   16   17   18   18   19   19   19   20   20 
LCS_GDT     P     342     P     342     10   11   20     7   10   10   10   10   11   13   13   14   15   16   16   17   18   18   19   19   19   20   20 
LCS_GDT     I     343     I     343     10   11   20     7   10   10   10   10   11   13   13   14   15   16   16   17   18   18   19   19   19   20   20 
LCS_GDT     L     344     L     344     10   11   20     7   10   10   10   10   11   13   13   14   15   16   16   17   18   18   19   19   19   20   20 
LCS_GDT     Q     345     Q     345     10   11   20     7   10   10   10   10   11   13   13   14   15   16   16   17   18   18   19   19   19   20   20 
LCS_GDT     K     346     K     346     10   11   20     7   10   10   10   10   11   13   13   14   15   16   16   17   18   18   19   19   19   20   20 
LCS_GDT     Q     347     Q     347     10   11   20     3   10   10   10   10   11   13   13   14   15   16   16   17   18   18   19   19   19   20   20 
LCS_AVERAGE  LCS_A:   9.23  (   5.24    6.33   16.13 )

GLOBAL_DISTANCE_TEST (the largest set of residues that can fit under specified DISTANCE_CUTOFF)
GDT DIST_CUTOFF  0.50   1.00   1.50   2.00   2.50   3.00   3.50   4.00   4.50   5.00   5.50   6.00   6.50   7.00   7.50   8.00   8.50   9.00   9.50  10.00
GDT NUMBER_CA      7     10     10     10     10     11     13     13     14     15     16     16     17     18     18     19     19     19     20     20 
GDT PERCENT_CA   5.65   8.06   8.06   8.06   8.06   8.87  10.48  10.48  11.29  12.10  12.90  12.90  13.71  14.52  14.52  15.32  15.32  15.32  16.13  16.13
GDT RMS_LOCAL    0.21   0.63   0.63   0.63   0.63   1.79   2.28   2.28   2.75   3.09   3.37   3.37   3.91   4.19   4.12   4.45   4.45   4.45   4.93   4.93
GDT RMS_ALL_CA   8.50   7.66   7.66   7.66   7.66   5.71   8.05   8.05   5.22   5.08   5.01   5.01   5.15   5.34   4.97   5.05   5.05   5.05   4.93   4.93

#      Molecule1      Molecule2       DISTANCE
LGA    E     328      E     328         19.267
LGA    P     329      P     329         14.731
LGA    A     330      A     330         16.751
LGA    V     331      V     331         12.890
LGA    L     332      L     332          7.783
LGA    G     333      G     333         10.132
LGA    V     334      V     334          8.294
LGA    A     335      A     335          3.623
LGA    L     336      L     336          3.889
LGA    N     337      N     337          3.605
LGA    E     338      E     338          2.650
LGA    V     339      V     339          1.812
LGA    F     340      F     340          1.463
LGA    V     341      V     341          1.482
LGA    P     342      P     342          0.757
LGA    I     343      I     343          1.376
LGA    L     344      L     344          1.736
LGA    Q     345      Q     345          0.908
LGA    K     346      K     346          1.660
LGA    Q     347      Q     347          2.429

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   20  124    4.0     13    2.28    10.484     9.446     0.547

LGA_LOCAL      RMSD =  2.276  Number of atoms =   13  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  8.179  Number of atoms =   20 
Std_ALL_ATOMS  RMSD =  4.933  (standard rmsd on all 20 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.286913 * X  +   0.756015 * Y  +   0.588322 * Z  + -21.260849
  Y_new =  -0.035785 * X  +  -0.605255 * Y  +   0.795227 * Z  +  82.690613
  Z_new =   0.957288 * X  +  -0.249214 * Y  +  -0.146601 * Z  +   3.146091 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.102535    1.039058  [ DEG:  -120.4664     59.5336 ]
  Theta =  -1.277472   -1.864120  [ DEG:   -73.1938   -106.8062 ]
  Phi   =  -0.124085    3.017508  [ DEG:    -7.1095    172.8905 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0356TS249_5_4-D1                             
REMARK     2: T0356_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356TS249_5_4-D1.T0356_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   20  124   4.0   13   2.28   9.446     4.93
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS249_5_4-D1
REMARK PARENT number 4
PFRMAT TS
TARGET T0356
PARENT 1aa6 1cr5_A 1e32_A 1g8k_A
ATOM      1  N   GLU   328      78.420  67.411  74.842  1.00  0.00
ATOM      2  CA  GLU   328      77.017  66.951  74.751  1.00  0.00
ATOM      3  CB  GLU   328      76.444  66.688  76.155  1.00  0.00
ATOM      4  CG  GLU   328      77.046  65.455  76.834  1.00  0.00
ATOM      5  CD  GLU   328      78.467  65.800  77.260  1.00  0.00
ATOM      6  OE1 GLU   328      78.626  66.790  78.022  1.00  0.00
ATOM      7  OE2 GLU   328      79.408  65.084  76.826  1.00  0.00
ATOM      8  C   GLU   328      76.170  67.971  74.065  1.00  0.00
ATOM      9  O   GLU   328      76.628  69.037  73.676  1.00  0.00
ATOM     10  N   PRO   329      74.930  67.620  73.887  1.00  0.00
ATOM     11  CA  PRO   329      74.014  68.521  73.252  1.00  0.00
ATOM     12  CD  PRO   329      74.573  66.232  73.665  1.00  0.00
ATOM     13  CB  PRO   329      72.867  67.657  72.716  1.00  0.00
ATOM     14  CG  PRO   329      73.065  66.282  73.380  1.00  0.00
ATOM     15  C   PRO   329      73.594  69.579  74.214  1.00  0.00
ATOM     16  O   PRO   329      73.680  69.361  75.421  1.00  0.00
ATOM     17  N   ALA   330      73.155  70.743  73.701  1.00  0.00
ATOM     18  CA  ALA   330      72.733  71.803  74.565  1.00  0.00
ATOM     19  CB  ALA   330      72.518  73.140  73.839  1.00  0.00
ATOM     20  C   ALA   330      71.428  71.396  75.158  1.00  0.00
ATOM     21  O   ALA   330      70.676  70.623  74.565  1.00  0.00
ATOM     22  N   VAL   331      71.137  71.895  76.373  1.00  0.00
ATOM     23  CA  VAL   331      69.901  71.540  76.997  1.00  0.00
ATOM     24  CB  VAL   331      70.077  70.701  78.228  1.00  0.00
ATOM     25  CG1 VAL   331      70.868  71.513  79.267  1.00  0.00
ATOM     26  CG2 VAL   331      68.688  70.250  78.714  1.00  0.00
ATOM     27  C   VAL   331      69.209  72.796  77.408  1.00  0.00
ATOM     28  O   VAL   331      69.843  73.782  77.780  1.00  0.00
ATOM     29  N   LEU   332      67.867  72.783  77.318  1.00  0.00
ATOM     30  CA  LEU   332      67.067  73.906  77.699  1.00  0.00
ATOM     31  CB  LEU   332      66.352  74.594  76.525  1.00  0.00
ATOM     32  CG  LEU   332      67.311  75.289  75.543  1.00  0.00
ATOM     33  CD1 LEU   332      68.241  74.277  74.858  1.00  0.00
ATOM     34  CD2 LEU   332      66.539  76.166  74.543  1.00  0.00
ATOM     35  C   LEU   332      66.007  73.392  78.610  1.00  0.00
ATOM     36  O   LEU   332      66.048  72.240  79.041  1.00  0.00
ATOM     37  N   GLY   333      65.028  74.254  78.939  1.00  0.00
ATOM     38  CA  GLY   333      63.965  73.836  79.802  1.00  0.00
ATOM     39  C   GLY   333      63.173  72.846  79.018  1.00  0.00
ATOM     40  O   GLY   333      63.430  72.637  77.834  1.00  0.00
ATOM     41  N   VAL   334      62.184  72.198  79.661  1.00  0.00
ATOM     42  CA  VAL   334      61.447  71.200  78.946  1.00  0.00
ATOM     43  CB  VAL   334      60.638  70.307  79.839  1.00  0.00
ATOM     44  CG1 VAL   334      59.791  69.372  78.962  1.00  0.00
ATOM     45  CG2 VAL   334      61.597  69.572  80.791  1.00  0.00
ATOM     46  C   VAL   334      60.499  71.889  78.027  1.00  0.00
ATOM     47  O   VAL   334      59.567  72.566  78.459  1.00  0.00
ATOM     48  N   ALA   335      60.733  71.727  76.711  1.00  0.00
ATOM     49  CA  ALA   335      59.872  72.314  75.731  1.00  0.00
ATOM     50  CB  ALA   335      60.307  73.723  75.293  1.00  0.00
ATOM     51  C   ALA   335      59.937  71.445  74.520  1.00  0.00
ATOM     52  O   ALA   335      60.948  70.787  74.272  1.00  0.00
ATOM     53  N   LEU   336      58.839  71.405  73.743  1.00  0.00
ATOM     54  CA  LEU   336      58.855  70.617  72.549  1.00  0.00
ATOM     55  CB  LEU   336      57.684  69.612  72.484  1.00  0.00
ATOM     56  CG  LEU   336      57.748  68.559  71.353  1.00  0.00
ATOM     57  CD1 LEU   336      56.528  67.628  71.414  1.00  0.00
ATOM     58  CD2 LEU   336      57.910  69.179  69.955  1.00  0.00
ATOM     59  C   LEU   336      58.716  71.592  71.427  1.00  0.00
ATOM     60  O   LEU   336      57.681  72.238  71.279  1.00  0.00
ATOM     61  N   ASN   337      59.781  71.734  70.617  1.00  0.00
ATOM     62  CA  ASN   337      59.721  72.639  69.510  1.00  0.00
ATOM     63  CB  ASN   337      60.536  73.922  69.740  1.00  0.00
ATOM     64  CG  ASN   337      59.949  74.645  70.944  1.00  0.00
ATOM     65  OD1 ASN   337      58.737  74.651  71.159  1.00  0.00
ATOM     66  ND2 ASN   337      60.836  75.270  71.764  1.00  0.00
ATOM     67  C   ASN   337      60.360  71.918  68.375  1.00  0.00
ATOM     68  O   ASN   337      61.320  71.176  68.577  1.00  0.00
ATOM     69  N   GLU   338      59.848  72.086  67.140  1.00  0.00
ATOM     70  CA  GLU   338      60.526  71.357  66.115  1.00  0.00
ATOM     71  CB  GLU   338      59.719  70.190  65.528  1.00  0.00
ATOM     72  CG  GLU   338      59.472  69.064  66.537  1.00  0.00
ATOM     73  CD  GLU   338      58.969  67.852  65.766  1.00  0.00
ATOM     74  OE1 GLU   338      59.803  67.214  65.069  1.00  0.00
ATOM     75  OE2 GLU   338      57.750  67.551  65.855  1.00  0.00
ATOM     76  C   GLU   338      60.914  72.257  64.993  1.00  0.00
ATOM     77  O   GLU   338      60.074  72.863  64.332  1.00  0.00
ATOM     78  N   VAL   339      62.239  72.388  64.820  1.00  0.00
ATOM     79  CA  VAL   339      62.930  73.020  63.737  1.00  0.00
ATOM     80  CB  VAL   339      64.402  73.168  63.986  1.00  0.00
ATOM     81  CG1 VAL   339      65.021  71.768  64.120  1.00  0.00
ATOM     82  CG2 VAL   339      65.009  74.011  62.852  1.00  0.00
ATOM     83  C   VAL   339      62.755  72.131  62.573  1.00  0.00
ATOM     84  O   VAL   339      62.893  72.558  61.433  1.00  0.00
ATOM     85  N   PHE   340      62.539  70.836  62.880  1.00  0.00
ATOM     86  CA  PHE   340      62.426  69.775  61.929  1.00  0.00
ATOM     87  CB  PHE   340      62.144  68.418  62.599  1.00  0.00
ATOM     88  CG  PHE   340      63.285  68.117  63.511  1.00  0.00
ATOM     89  CD1 PHE   340      63.305  68.617  64.792  1.00  0.00
ATOM     90  CD2 PHE   340      64.336  67.335  63.091  1.00  0.00
ATOM     91  CE1 PHE   340      64.354  68.344  65.640  1.00  0.00
ATOM     92  CE2 PHE   340      65.388  67.058  63.934  1.00  0.00
ATOM     93  CZ  PHE   340      65.399  67.563  65.212  1.00  0.00
ATOM     94  C   PHE   340      61.272  70.063  61.023  1.00  0.00
ATOM     95  O   PHE   340      61.374  69.868  59.813  1.00  0.00
ATOM     96  N   VAL   341      60.130  70.507  61.574  1.00  0.00
ATOM     97  CA  VAL   341      58.988  70.759  60.743  1.00  0.00
ATOM     98  CB  VAL   341      57.763  71.135  61.526  1.00  0.00
ATOM     99  CG1 VAL   341      56.607  71.390  60.544  1.00  0.00
ATOM    100  CG2 VAL   341      57.475  70.024  62.548  1.00  0.00
ATOM    101  C   VAL   341      59.280  71.860  59.770  1.00  0.00
ATOM    102  O   VAL   341      58.900  71.758  58.600  1.00  0.00
ATOM    103  N   PRO   342      59.909  72.924  60.216  1.00  0.00
ATOM    104  CA  PRO   342      60.233  73.998  59.325  1.00  0.00
ATOM    105  CD  PRO   342      59.770  73.396  61.583  1.00  0.00
ATOM    106  CB  PRO   342      60.770  75.126  60.200  1.00  0.00
ATOM    107  CG  PRO   342      60.039  74.910  61.537  1.00  0.00
ATOM    108  C   PRO   342      61.142  73.583  58.217  1.00  0.00
ATOM    109  O   PRO   342      60.942  74.045  57.092  1.00  0.00
ATOM    110  N   ILE   343      62.129  72.709  58.506  1.00  0.00
ATOM    111  CA  ILE   343      63.057  72.296  57.490  1.00  0.00
ATOM    112  CB  ILE   343      64.227  71.486  57.977  1.00  0.00
ATOM    113  CG2 ILE   343      63.732  70.117  58.461  1.00  0.00
ATOM    114  CG1 ILE   343      65.269  71.366  56.852  1.00  0.00
ATOM    115  CD1 ILE   343      65.903  72.696  56.450  1.00  0.00
ATOM    116  C   ILE   343      62.339  71.510  56.448  1.00  0.00
ATOM    117  O   ILE   343      62.614  71.656  55.258  1.00  0.00
ATOM    118  N   LEU   344      61.410  70.626  56.874  1.00  0.00
ATOM    119  CA  LEU   344      60.699  69.832  55.911  1.00  0.00
ATOM    120  CB  LEU   344      59.755  68.780  56.522  1.00  0.00
ATOM    121  CG  LEU   344      60.475  67.505  56.998  1.00  0.00
ATOM    122  CD1 LEU   344      60.996  66.697  55.799  1.00  0.00
ATOM    123  CD2 LEU   344      61.584  67.817  58.011  1.00  0.00
ATOM    124  C   LEU   344      59.886  70.709  55.006  1.00  0.00
ATOM    125  O   LEU   344      59.827  70.472  53.797  1.00  0.00
ATOM    126  N   GLN   345      59.237  71.749  55.565  1.00  0.00
ATOM    127  CA  GLN   345      58.400  72.577  54.738  1.00  0.00
ATOM    128  CB  GLN   345      57.643  73.656  55.529  1.00  0.00
ATOM    129  CG  GLN   345      56.614  73.087  56.506  1.00  0.00
ATOM    130  CD  GLN   345      55.542  72.360  55.708  1.00  0.00
ATOM    131  OE1 GLN   345      55.825  71.394  55.002  1.00  0.00
ATOM    132  NE2 GLN   345      54.272  72.832  55.824  1.00  0.00
ATOM    133  C   GLN   345      59.236  73.274  53.702  1.00  0.00
ATOM    134  O   GLN   345      58.817  73.389  52.551  1.00  0.00
ATOM    135  N   LYS   346      60.442  73.750  54.080  1.00  0.00
ATOM    136  CA  LYS   346      61.314  74.475  53.185  1.00  0.00
ATOM    137  CB  LYS   346      62.577  75.005  53.881  1.00  0.00
ATOM    138  CG  LYS   346      63.351  76.020  53.036  1.00  0.00
ATOM    139  CD  LYS   346      64.411  76.794  53.822  1.00  0.00
ATOM    140  CE  LYS   346      65.122  77.874  53.003  1.00  0.00
ATOM    141  NZ  LYS   346      65.829  77.261  51.857  1.00  0.00
ATOM    142  C   LYS   346      61.748  73.575  52.065  1.00  0.00
ATOM    143  O   LYS   346      61.942  74.023  50.934  1.00  0.00
ATOM    144  N   GLN   347      61.924  72.269  52.343  1.00  0.00
ATOM    145  CA  GLN   347      62.366  71.375  51.306  1.00  0.00
ATOM    146  CB  GLN   347      62.460  69.914  51.778  1.00  0.00
ATOM    147  CG  GLN   347      62.932  68.959  50.682  1.00  0.00
ATOM    148  CD  GLN   347      62.881  67.538  51.222  1.00  0.00
ATOM    149  OE1 GLN   347      63.749  67.104  51.978  1.00  0.00
ATOM    150  NE2 GLN   347      61.824  66.787  50.817  1.00  0.00
ATOM    151  C   GLN   347      61.330  71.447  50.227  1.00  0.00
ATOM    152  O   GLN   347      61.669  71.348  49.052  1.00  0.00
TER
END
