
#######################################################
#                                                     #
#                        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   18 (  137),  selected   18 , name T0318TS469_4-D1
# Molecule2: number of CA atoms  154 ( 1200),  selected   18 , name T0318_D1.pdb
# PARAMETERS: T0318TS469_4-D1.T0318_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:    11       145 - 155         4.38    16.90
  LCS_AVERAGE:      6.89

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       143 - 148         1.53    12.68
  LONGEST_CONTINUOUS_SEGMENT:     6       145 - 150         1.88    14.15
  LCS_AVERAGE:      3.35

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       138 - 141         0.37    18.37
  LONGEST_CONTINUOUS_SEGMENT:     4       143 - 146         0.88    14.39
  LONGEST_CONTINUOUS_SEGMENT:     4       144 - 147         0.43    13.46
  LONGEST_CONTINUOUS_SEGMENT:     4       145 - 148         0.96    12.33
  LONGEST_CONTINUOUS_SEGMENT:     4       147 - 150         0.78    17.13
  LONGEST_CONTINUOUS_SEGMENT:     4       152 - 155         0.43    18.23
  LCS_AVERAGE:      2.53

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:  154
LCS_GDT     T     138     T     138      4    5   10     4    4    4    4    4    5    5    5    5    5    6    7    8   10   10   11   11   12   12   13 
LCS_GDT     S     139     S     139      4    5   10     4    4    4    4    4    5    5    5    6    8    9    9    9   10   10   11   11   12   12   13 
LCS_GDT     G     140     G     140      4    5   10     4    4    4    4    4    5    5    6    7    8    9    9    9   10   10   11   11   12   12   13 
LCS_GDT     I     141     I     141      4    5   10     4    4    4    4    4    5    5    5    7    7    9    9    9   10   10   11   11   12   12   13 
LCS_GDT     R     142     R     142      3    5   10     3    3    3    3    4    5    5    6    7    8    9    9    9   10   10   11   11   12   12   13 
LCS_GDT     E     143     E     143      4    6   10     1    3    4    5    6    6    6    6    7    8    9    9    9   10   10   11   11   12   12   13 
LCS_GDT     L     144     L     144      4    6   10     3    4    4    5    6    6    7    7    7    8    9    9    9   10   10   11   12   12   12   13 
LCS_GDT     N     145     N     145      4    6   11     3    4    4    5    6    6    7    7    7    8   10   10   11   11   11   11   12   12   12   13 
LCS_GDT     V     146     V     146      4    6   11     3    4    4    5    6    6    7    7    7    9   10   10   11   11   11   11   12   12   12   13 
LCS_GDT     N     147     N     147      4    6   11     3    4    4    5    6    6    7    7    9    9   10   10   11   11   11   11   12   12   12   13 
LCS_GDT     I     148     I     148      4    6   11     3    4    4    5    6    6    7    7    9    9   10   10   11   11   11   11   12   12   12   13 
LCS_GDT     D     149     D     149      4    6   11     3    4    4    5    5    5    7    7    9    9   10   10   11   11   11   11   12   12   12   13 
LCS_GDT     V     150     V     150      4    6   11     3    4    4    5    5    5    7    7    9    9   10   10   11   11   11   11   12   12   12   13 
LCS_GDT     V     151     V     151      3    4   11     3    3    3    3    4    5    5    7    9    9   10   10   11   11   11   11   12   12   12   13 
LCS_GDT     C     152     C     152      4    4   11     3    4    4    4    4    5    5    7    9    9    9   10   11   11   11   11   12   12   12   13 
LCS_GDT     D     153     D     153      4    4   11     3    4    4    4    4    5    5    7    9    9   10   10   11   11   11   11   12   12   12   13 
LCS_GDT     K     154     K     154      4    4   11     3    4    4    4    4    5    5    7    9    9   10   10   11   11   11   11   12   12   12   13 
LCS_GDT     L     155     L     155      4    4   11     3    4    4    4    4    5    5    7    9    9   10   10   11   11   11   11   12   12   12   13 
LCS_AVERAGE  LCS_A:   4.26  (   2.53    3.35    6.89 )

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      4      4      4      5      6      6      7      7      9      9     10     10     11     11     11     11     12     12     12     13 
GDT PERCENT_CA   2.60   2.60   2.60   3.25   3.90   3.90   4.55   4.55   5.84   5.84   6.49   6.49   7.14   7.14   7.14   7.14   7.79   7.79   7.79   8.44
GDT RMS_LOCAL    0.37   0.37   0.37   1.06   1.53   1.53   2.54   2.54   3.35   3.35   4.14   3.82   4.38   4.38   4.38   4.38   5.33   5.33   5.33   6.48
GDT RMS_ALL_CA  18.37  18.37  18.37  12.44  12.68  12.68  11.52  11.52  19.41  19.41  16.51  18.08  16.90  16.90  16.90  16.90  15.34  15.34  15.34  13.36

#      Molecule1      Molecule2       DISTANCE
LGA    T     138      T     138         14.953
LGA    S     139      S     139         18.651
LGA    G     140      G     140         19.454
LGA    I     141      I     141         15.802
LGA    R     142      R     142         12.876
LGA    E     143      E     143          6.650
LGA    L     144      L     144          3.208
LGA    N     145      N     145          1.062
LGA    V     146      V     146          1.983
LGA    N     147      N     147          2.807
LGA    I     148      I     148          2.255
LGA    D     149      D     149          2.680
LGA    V     150      V     150          3.112
LGA    V     151      V     151         10.270
LGA    C     152      C     152         13.061
LGA    D     153      D     153         13.393
LGA    K     154      K     154         15.254
LGA    L     155      L     155         15.710

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   18  154    4.0      7    2.54     4.383     4.376     0.265

LGA_LOCAL      RMSD =  2.541  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 11.522  Number of atoms =   18 
Std_ALL_ATOMS  RMSD = 10.755  (standard rmsd on all 18 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.704271 * X  +   0.602258 * Y  +   0.375882 * Z  +  64.868416
  Y_new =   0.403797 * X  +  -0.775300 * Y  +   0.485652 * Z  +  47.220665
  Z_new =   0.583909 * X  +  -0.190251 * Y  +  -0.789212 * Z  +  21.790930 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.905042    0.236551  [ DEG:  -166.4466     13.5534 ]
  Theta =  -0.623536   -2.518057  [ DEG:   -35.7260   -144.2740 ]
  Phi   =   0.520597   -2.620996  [ DEG:    29.8280   -150.1720 ]
 
# 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: T0318TS469_4-D1                               
REMARK     2: T0318_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0318TS469_4-D1.T0318_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   18  154   4.0    7   2.54   4.376    10.76
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS469_4-D1
PFRMAT TS
TARGET T0318
MODEL  4 
PARENT  n/a
ATOM      1  N   THR   138      28.049  52.314  10.922  1.00  0.00           N  
ATOM      2  CA  THR   138      27.027  53.330  10.790  1.00  0.00           C  
ATOM      3  C   THR   138      25.644  52.772  11.134  1.00  0.00           C  
ATOM      4  O   THR   138      24.711  53.513  11.460  1.00  0.00           O  
ATOM      5  CB  THR   138      27.040  53.895   9.353  1.00  0.00           C  
ATOM      6  OG1 THR   138      28.278  54.539   9.093  1.00  0.00           O  
ATOM      7  CG2 THR   138      25.895  54.909   9.195  1.00  0.00           C  
ATOM      8  N   SER   139      25.461  51.461  11.039  1.00  0.00           N  
ATOM      9  CA  SER   139      24.230  50.803  11.398  1.00  0.00           C  
ATOM     10  C   SER   139      24.594  49.357  11.638  1.00  0.00           C  
ATOM     11  O   SER   139      25.308  48.736  10.848  1.00  0.00           O  
ATOM     12  CB  SER   139      23.206  50.945  10.261  1.00  0.00           C  
ATOM     13  OG  SER   139      22.015  50.245  10.588  1.00  0.00           O  
ATOM     14  N   GLY   140      24.115  48.784  12.733  1.00  0.00           N  
ATOM     15  CA  GLY   140      24.443  47.412  13.076  1.00  0.00           C  
ATOM     16  C   GLY   140      25.666  47.465  13.957  1.00  0.00           C  
ATOM     17  O   GLY   140      25.821  48.380  14.770  1.00  0.00           O  
ATOM     18  N   ILE   141      26.577  46.501  13.833  1.00  0.00           N  
ATOM     19  CA  ILE   141      27.767  46.540  14.667  1.00  0.00           C  
ATOM     20  C   ILE   141      28.982  46.584  13.741  1.00  0.00           C  
ATOM     21  O   ILE   141      29.878  47.422  13.885  1.00  0.00           O  
ATOM     22  CB  ILE   141      28.406  45.491  15.605  1.00  0.00           C  
ATOM     23  CG1 ILE   141      27.463  45.010  16.719  1.00  0.00           C  
ATOM     24  CG2 ILE   141      29.660  46.003  16.332  1.00  0.00           C  
ATOM     25  CD1 ILE   141      27.042  46.118  17.684  1.00  0.00           C  
ATOM     26  N   ARG   142      29.023  45.672  12.774  1.00  0.00           N  
ATOM     27  CA  ARG   142      30.132  45.629  11.828  1.00  0.00           C  
ATOM     28  C   ARG   142      30.530  47.037  11.378  1.00  0.00           C  
ATOM     29  O   ARG   142      31.711  47.362  11.241  1.00  0.00           O  
ATOM     30  CB  ARG   142      30.002  44.960  10.457  1.00  0.00           C  
ATOM     31  CG  ARG   142      31.299  44.974   9.647  1.00  0.00           C  
ATOM     32  CD  ARG   142      31.212  44.185   8.338  1.00  0.00           C  
ATOM     33  NE  ARG   142      32.494  44.388   7.606  1.00  0.00           N  
ATOM     34  CZ  ARG   142      32.752  43.675   6.471  1.00  0.00           C  
ATOM     35  NH1 ARG   142      31.682  42.861   6.239  1.00  0.00           N  
ATOM     36  NH2 ARG   142      33.979  44.055   6.012  1.00  0.00           N  
ATOM     37  N   GLU   143      29.536  47.891  11.143  1.00  0.00           N  
ATOM     38  CA  GLU   143      29.785  49.269  10.712  1.00  0.00           C  
ATOM     39  C   GLU   143      31.103  49.796  11.261  1.00  0.00           C  
ATOM     40  O   GLU   143      31.891  50.444  10.566  1.00  0.00           O  
ATOM     41  CB  GLU   143      28.802  50.361  11.143  1.00  0.00           C  
ATOM     42  CG  GLU   143      29.032  51.700  10.441  1.00  0.00           C  
ATOM     43  CD  GLU   143      28.824  51.491   8.947  1.00  0.00           C  
ATOM     44  OE1 GLU   143      27.768  50.914   8.573  1.00  0.00           O  
ATOM     45  OE2 GLU   143      29.718  51.905   8.162  1.00  0.00           O  
ATOM     46  N   LEU   144      31.352  49.516  12.538  1.00  0.00           N  
ATOM     47  CA  LEU   144      32.574  49.959  13.203  1.00  0.00           C  
ATOM     48  C   LEU   144      33.721  49.007  12.909  1.00  0.00           C  
ATOM     49  O   LEU   144      34.747  48.990  13.594  1.00  0.00           O  
ATOM     50  CB  LEU   144      32.677  50.022  14.729  1.00  0.00           C  
ATOM     51  CG  LEU   144      31.675  50.985  15.369  1.00  0.00           C  
ATOM     52  CD1 LEU   144      31.657  50.978  16.896  1.00  0.00           C  
ATOM     53  CD2 LEU   144      31.886  52.459  15.024  1.00  0.00           C  
ATOM     54  N   ASN   145      33.554  48.196  11.870  1.00  0.00           N  
ATOM     55  CA  ASN   145      34.577  47.241  11.468  1.00  0.00           C  
ATOM     56  C   ASN   145      35.254  46.616  12.689  1.00  0.00           C  
ATOM     57  O   ASN   145      36.232  47.142  13.226  1.00  0.00           O  
ATOM     58  CB  ASN   145      35.688  47.841  10.601  1.00  0.00           C  
ATOM     59  CG  ASN   145      35.074  48.261   9.274  1.00  0.00           C  
ATOM     60  OD1 ASN   145      34.095  47.675   8.814  1.00  0.00           O  
ATOM     61  ND2 ASN   145      35.616  49.301   8.584  1.00  0.00           N  
ATOM     62  N   VAL   146      34.737  45.475  13.145  1.00  0.00           N  
ATOM     63  CA  VAL   146      35.295  44.788  14.313  1.00  0.00           C  
ATOM     64  C   VAL   146      35.360  43.273  14.127  1.00  0.00           C  
ATOM     65  O   VAL   146      34.426  42.638  13.629  1.00  0.00           O  
ATOM     66  CB  VAL   146      34.980  44.432  15.781  1.00  0.00           C  
ATOM     67  CG1 VAL   146      36.074  43.602  16.456  1.00  0.00           C  
ATOM     68  CG2 VAL   146      34.794  45.656  16.679  1.00  0.00           C  
ATOM     69  N   ASN   147      36.476  42.674  14.531  1.00  0.00           N  
ATOM     70  CA  ASN   147      36.661  41.229  14.412  1.00  0.00           C  
ATOM     71  C   ASN   147      35.974  40.553  15.591  1.00  0.00           C  
ATOM     72  O   ASN   147      36.566  39.764  16.333  1.00  0.00           O  
ATOM     73  CB  ASN   147      38.123  40.769  14.402  1.00  0.00           C  
ATOM     74  CG  ASN   147      38.153  39.306  13.983  1.00  0.00           C  
ATOM     75  OD1 ASN   147      37.255  38.826  13.293  1.00  0.00           O  
ATOM     76  ND2 ASN   147      39.187  38.517  14.379  1.00  0.00           N  
ATOM     77  N   ILE   148      34.695  40.868  15.769  1.00  0.00           N  
ATOM     78  CA  ILE   148      33.904  40.332  16.870  1.00  0.00           C  
ATOM     79  C   ILE   148      32.660  39.614  16.382  1.00  0.00           C  
ATOM     80  O   ILE   148      31.887  40.154  15.585  1.00  0.00           O  
ATOM     81  CB  ILE   148      33.113  41.042  17.992  1.00  0.00           C  
ATOM     82  CG1 ILE   148      33.989  41.922  18.899  1.00  0.00           C  
ATOM     83  CG2 ILE   148      32.396  40.071  18.944  1.00  0.00           C  
ATOM     84  CD1 ILE   148      33.186  42.799  19.858  1.00  0.00           C  
ATOM     85  N   ASP   149      32.437  38.448  16.812  1.00  0.00           N  
ATOM     86  CA  ASP   149      31.208  37.684  16.629  1.00  0.00           C  
ATOM     87  C   ASP   149      30.303  37.771  17.853  1.00  0.00           C  
ATOM     88  O   ASP   149      29.076  37.690  17.758  1.00  0.00           O  
ATOM     89  CB  ASP   149      31.363  36.179  16.397  1.00  0.00           C  
ATOM     90  CG  ASP   149      32.114  35.979  15.089  1.00  0.00           C  
ATOM     91  OD1 ASP   149      31.651  36.525  14.051  1.00  0.00           O  
ATOM     92  OD2 ASP   149      33.160  35.278  15.108  1.00  0.00           O  
ATOM     93  N   VAL   150      30.901  37.940  19.030  1.00  0.00           N  
ATOM     94  CA  VAL   150      30.121  38.054  20.257  1.00  0.00           C  
ATOM     95  C   VAL   150      29.188  39.257  20.171  1.00  0.00           C  
ATOM     96  O   VAL   150      28.007  39.191  20.522  1.00  0.00           O  
ATOM     97  CB  VAL   150      30.237  38.415  21.753  1.00  0.00           C  
ATOM     98  CG1 VAL   150      28.886  38.502  22.466  1.00  0.00           C  
ATOM     99  CG2 VAL   150      31.053  37.405  22.563  1.00  0.00           C  
ATOM    100  N   VAL   151      29.714  40.383  19.700  1.00  0.00           N  
ATOM    101  CA  VAL   151      28.918  41.595  19.566  1.00  0.00           C  
ATOM    102  C   VAL   151      27.695  41.363  18.677  1.00  0.00           C  
ATOM    103  O   VAL   151      26.552  41.343  19.140  1.00  0.00           O  
ATOM    104  CB  VAL   151      28.930  43.002  18.928  1.00  0.00           C  
ATOM    105  CG1 VAL   151      27.603  43.750  19.074  1.00  0.00           C  
ATOM    106  CG2 VAL   151      29.983  43.935  19.528  1.00  0.00           C  
ATOM    107  N   CYS   152      27.928  41.183  17.380  1.00  0.00           N  
ATOM    108  CA  CYS   152      26.829  40.960  16.443  1.00  0.00           C  
ATOM    109  C   CYS   152      25.768  40.025  17.002  1.00  0.00           C  
ATOM    110  O   CYS   152      24.568  40.309  16.956  1.00  0.00           O  
ATOM    111  CB  CYS   152      26.932  40.251  15.090  1.00  0.00           C  
ATOM    112  SG  CYS   152      27.907  40.838  14.242  1.00  0.00           S  
ATOM    113  N   ASP   153      26.194  38.892  17.542  1.00  0.00           N  
ATOM    114  CA  ASP   153      25.240  37.946  18.104  1.00  0.00           C  
ATOM    115  C   ASP   153      24.349  38.641  19.128  1.00  0.00           C  
ATOM    116  O   ASP   153      23.320  38.113  19.559  1.00  0.00           O  
ATOM    117  CB  ASP   153      25.815  36.744  18.860  1.00  0.00           C  
ATOM    118  CG  ASP   153      26.414  35.789  17.837  1.00  0.00           C  
ATOM    119  OD1 ASP   153      26.167  35.994  16.620  1.00  0.00           O  
ATOM    120  OD2 ASP   153      27.127  34.840  18.262  1.00  0.00           O  
ATOM    121  N   LYS   154      24.738  39.847  19.534  1.00  0.00           N  
ATOM    122  CA  LYS   154      23.962  40.603  20.510  1.00  0.00           C  
ATOM    123  C   LYS   154      23.233  41.781  19.877  1.00  0.00           C  
ATOM    124  O   LYS   154      22.013  41.931  19.989  1.00  0.00           O  
ATOM    125  CB  LYS   154      24.646  41.326  21.676  1.00  0.00           C  
ATOM    126  CG  LYS   154      25.463  40.395  22.576  1.00  0.00           C  
ATOM    127  CD  LYS   154      24.606  39.432  23.399  1.00  0.00           C  
ATOM    128  CE  LYS   154      25.419  38.535  24.335  1.00  0.00           C  
ATOM    129  NZ  LYS   154      24.521  37.595  25.042  1.00  0.00           N  
ATOM    130  N   LEU   155      23.992  42.647  19.189  1.00  0.00           N  
ATOM    131  CA  LEU   155      23.401  43.805  18.540  1.00  0.00           C  
ATOM    132  C   LEU   155      22.003  43.557  17.981  1.00  0.00           C  
ATOM    133  O   LEU   155      21.118  44.414  18.059  1.00  0.00           O  
ATOM    134  CB  LEU   155      24.044  44.412  17.289  1.00  0.00           C  
ATOM    135  CG  LEU   155      24.304  43.392  16.179  1.00  0.00           C  
ATOM    136  CD1 LEU   155      23.105  43.094  15.282  1.00  0.00           C  
ATOM    137  CD2 LEU   155      25.401  43.780  15.189  1.00  0.00           C  
TER
END
