
#######################################################
#                                                     #
#                        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 (  100),  selected   20 , name T0321TS103_2-D1
# Molecule2: number of CA atoms   96 (  710),  selected   20 , name T0321_D1.pdb
# PARAMETERS: T0321TS103_2-D1.T0321_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:    19         1 - 89          4.97     5.14
  LCS_AVERAGE:     19.53

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10        79 - 88          1.90     9.78
  LCS_AVERAGE:      8.85

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        79 - 86          0.38     9.94
  LCS_AVERAGE:      5.83

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:   96
LCS_GDT     M       1     M       1      5    7   19     3    4    6    7    8    9   12   14   14   14   16   16   19   19   19   19   19   20   20   20 
LCS_GDT     W       2     W       2      5    7   19     4    5    6    7    9    9   11   14   14   14   16   16   19   19   19   19   19   20   20   20 
LCS_GDT     E       3     E       3      5    7   19     4    4    6    7    8    9   11   12   13   14   16   16   19   19   19   19   19   20   20   20 
LCS_GDT     I       4     I       4      5    7   19     4    4    6    7    8    9   11   12   13   14   16   16   19   19   19   19   19   20   20   20 
LCS_GDT     Y       5     Y       5      5    7   19     4    5    6    7    9    9   11   14   14   14   16   16   19   19   19   19   19   20   20   20 
LCS_GDT     D       6     D       6      4    7   19     4    4    4    7    8    9    9   12   13   13   14   15   19   19   19   19   19   20   20   20 
LCS_GDT     A       7     A       7      4    7   19     4    4    4    7    8    9    9   12   13   13   14   15   19   19   19   19   19   20   20   20 
LCS_GDT     S      76     S      76      3    9   19     0    3    3    3    4    7    9    9    9   10   11   13   13   14   16   17   18   20   20   20 
LCS_GDT     L      79     L      79      8   10   19     8    8    8    8   10   11   12   14   14   14   16   16   19   19   19   19   19   20   20   20 
LCS_GDT     A      80     A      80      8   10   19     8    8    8    8   10   11   12   14   14   14   16   16   19   19   19   19   19   20   20   20 
LCS_GDT     A      81     A      81      8   10   19     8    8    8    8   10   11   12   14   14   14   16   16   19   19   19   19   19   20   20   20 
LCS_GDT     I      82     I      82      8   10   19     8    8    8    8   10   11   12   14   14   14   16   16   19   19   19   19   19   20   20   20 
LCS_GDT     N      83     N      83      8   10   19     8    8    8    8   10   11   12   14   14   14   16   16   19   19   19   19   19   20   20   20 
LCS_GDT     A      84     A      84      8   10   19     8    8    8    8   10   11   12   14   14   14   16   16   19   19   19   19   19   20   20   20 
LCS_GDT     Y      85     Y      85      8   10   19     8    8    8    8   10   11   12   14   14   14   16   16   19   19   19   19   19   20   20   20 
LCS_GDT     Y      86     Y      86      8   10   19     8    8    8    8    9   11   12   14   14   14   16   16   19   19   19   19   19   20   20   20 
LCS_GDT     N      87     N      87      3   10   19     3    3    4    6    7    9   10   11   12   12   14   15   19   19   19   19   19   20   20   20 
LCS_GDT     N      88     N      88      3   10   19     3    3    4    7   10   11   12   14   14   14   16   16   19   19   19   19   19   20   20   20 
LCS_GDT     P      89     P      89      3    6   19     3    5    6    8   10   11   12   14   14   14   16   16   19   19   19   19   19   20   20   20 
LCS_GDT     Q      90     Q      90      3    6   14     3    3    5    8   10   11   12   14   14   14   16   16   19   19   19   19   19   20   20   20 
LCS_AVERAGE  LCS_A:  11.41  (   5.83    8.85   19.53 )

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      8      8      8      8     10     11     12     14     14     14     16     16     19     19     19     19     19     20     20     20 
GDT PERCENT_CA   8.33   8.33   8.33   8.33  10.42  11.46  12.50  14.58  14.58  14.58  16.67  16.67  19.79  19.79  19.79  19.79  19.79  20.83  20.83  20.83
GDT RMS_LOCAL    0.38   0.38   0.38   0.38   1.64   1.81   2.41   2.78   2.78   2.78   3.51   3.51   4.30   4.30   4.30   4.30   4.30   5.02   5.02   5.02
GDT RMS_ALL_CA   9.94   9.94   9.94   9.94   7.35   7.54   6.01   5.45   5.45   5.45   5.09   5.09   5.06   5.06   5.06   5.06   5.06   5.02   5.02   5.02

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1          3.777
LGA    W       2      W       2          3.042
LGA    E       3      E       3          8.534
LGA    I       4      I       4          7.685
LGA    Y       5      Y       5          3.558
LGA    D       6      D       6          9.716
LGA    A       7      A       7         10.350
LGA    S      76      S      76         10.314
LGA    L      79      L      79          3.583
LGA    A      80      A      80          3.652
LGA    A      81      A      81          3.521
LGA    I      82      I      82          2.731
LGA    N      83      N      83          0.674
LGA    A      84      A      84          1.527
LGA    Y      85      Y      85          1.305
LGA    Y      86      Y      86          3.365
LGA    N      87      N      87          6.745
LGA    N      88      N      88          2.643
LGA    P      89      P      89          1.009
LGA    Q      90      Q      90          1.360

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   20   96    4.0     14    2.78    12.760    11.977     0.487

LGA_LOCAL      RMSD =  2.776  Number of atoms =   14  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.446  Number of atoms =   20 
Std_ALL_ATOMS  RMSD =  5.015  (standard rmsd on all 20 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.161328 * X  +   0.294898 * Y  +  -0.941811 * Z  +  -9.465332
  Y_new =   0.726090 * X  +  -0.681801 * Y  +  -0.089108 * Z  +  29.676270
  Z_new =  -0.668405 * X  +  -0.669464 * Y  +  -0.324116 * Z  + 113.656143 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.021678    1.119915  [ DEG:  -115.8336     64.1664 ]
  Theta =   0.732063    2.409530  [ DEG:    41.9441    138.0559 ]
  Phi   =   1.352160   -1.789432  [ DEG:    77.4731   -102.5269 ]
 
# 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: T0321TS103_2-D1                               
REMARK     2: T0321_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0321TS103_2-D1.T0321_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   20   96   4.0   14   2.78  11.977     5.02
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS103_2-D1
PFRMAT TS
TARGET T0321
MODEL 2
PARENT 2b4g_A
ATOM      1  N   MET     1      -7.519  37.194  55.973  1.00  1.00
ATOM      2  CA  MET     1      -6.154  36.957  55.515  1.00  1.00
ATOM      3  C   MET     1      -5.459  38.283  55.280  1.00  1.00
ATOM      4  O   MET     1      -5.707  39.249  55.989  1.00  1.00
ATOM      5  CB  MET     1      -6.208  36.187  54.182  1.00  1.00
ATOM      6  N   TRP     2      -4.609  38.349  54.270  1.00  1.00
ATOM      7  CA  TRP     2      -3.750  39.530  54.078  1.00  1.00
ATOM      8  C   TRP     2      -4.565  40.799  53.813  1.00  1.00
ATOM      9  O   TRP     2      -4.156  41.879  54.203  1.00  1.00
ATOM     10  CB  TRP     2      -2.725  39.299  52.967  1.00  1.00
ATOM     11  N   GLU     3      -5.741  40.661  53.202  1.00  1.00
ATOM     12  CA  GLU     3      -6.620  41.817  52.957  1.00  1.00
ATOM     13  C   GLU     3      -6.966  42.618  54.209  1.00  1.00
ATOM     14  O   GLU     3      -7.154  43.826  54.122  1.00  1.00
ATOM     15  CB  GLU     3      -7.967  41.372  52.386  1.00  1.00
ATOM     16  N   ILE     4      -7.051  41.948  55.361  1.00  1.00
ATOM     17  CA  ILE     4      -7.653  42.590  56.532  1.00  1.00
ATOM     18  C   ILE     4      -6.664  43.042  57.604  1.00  1.00
ATOM     19  O   ILE     4      -7.070  43.584  58.632  1.00  1.00
ATOM     20  CB  ILE     4      -8.759  41.694  57.138  1.00  1.00
ATOM     21  N   TYR     5      -5.360  42.893  57.359  1.00  1.00
ATOM     22  CA  TYR     5      -4.399  43.216  58.436  1.00  1.00
ATOM     23  C   TYR     5      -4.470  44.679  58.929  1.00  1.00
ATOM     24  O   TYR     5      -4.671  44.907  60.126  1.00  1.00
ATOM     25  CB  TYR     5      -2.976  42.789  58.089  1.00  1.00
ATOM     26  N   ASP     6      -4.316  45.670  58.032  1.00  1.00
ATOM     27  CA  ASP     6      -4.496  47.050  58.499  1.00  1.00
ATOM     28  C   ASP     6      -5.844  47.375  59.159  1.00  1.00
ATOM     29  O   ASP     6      -5.902  48.166  60.120  1.00  1.00
ATOM     30  CB  ASP     6      -4.293  47.885  57.208  1.00  1.00
ATOM     31  N   ALA     7      -6.924  46.800  58.638  1.00  1.00
ATOM     32  CA  ALA     7      -8.237  46.957  59.254  1.00  1.00
ATOM     33  C   ALA     7      -8.252  46.355  60.674  1.00  1.00
ATOM     34  O   ALA     7      -8.750  46.983  61.596  1.00  1.00
ATOM     35  CB  ALA     7      -9.347  46.325  58.362  1.00  1.00
ATOM     36  N   SER    76      -7.693  45.146  60.836  1.00  1.00
ATOM     37  CA  SER    76      -7.634  44.481  62.151  1.00  1.00
ATOM     38  C   SER    76      -6.798  45.292  63.120  1.00  1.00
ATOM     39  O   SER    76      -7.231  45.545  64.229  1.00  1.00
ATOM     40  CB  SER    76      -7.076  43.074  62.046  1.00  1.00
ATOM     41  N   LEU    79      -5.605  45.701  62.679  1.00  1.00
ATOM     42  CA  LEU    79      -4.704  46.435  63.540  1.00  1.00
ATOM     43  C   LEU    79      -5.298  47.751  64.008  1.00  1.00
ATOM     44  O   LEU    79      -5.115  48.113  65.147  1.00  1.00
ATOM     45  CB  LEU    79      -3.358  46.696  62.871  1.00  1.00
ATOM     46  N   ALA    80      -6.008  48.434  63.110  1.00  1.00
ATOM     47  CA  ALA    80      -6.652  49.703  63.400  1.00  1.00
ATOM     48  C   ALA    80      -7.755  49.513  64.427  1.00  1.00
ATOM     49  O   ALA    80      -7.873  50.292  65.384  1.00  1.00
ATOM     50  CB  ALA    80      -7.229  50.304  62.103  1.00  1.00
ATOM     51  N   ALA    81      -8.563  48.467  64.231  1.00  1.00
ATOM     52  CA  ALA    81      -9.652  48.166  65.169  1.00  1.00
ATOM     53  C   ALA    81      -9.121  47.771  66.551  1.00  1.00
ATOM     54  O   ALA    81      -9.572  48.285  67.589  1.00  1.00
ATOM     55  CB  ALA    81     -10.586  47.094  64.583  1.00  1.00
ATOM     56  N   ILE    82      -8.136  46.886  66.578  1.00  1.00
ATOM     57  CA  ILE    82      -7.490  46.537  67.855  1.00  1.00
ATOM     58  C   ILE    82      -7.059  47.791  68.620  1.00  1.00
ATOM     59  O   ILE    82      -7.394  47.976  69.805  1.00  1.00
ATOM     60  CB  ILE    82      -6.260  45.626  67.628  1.00  1.00
ATOM     61  N   ASN    83      -6.309  48.646  67.942  1.00  1.00
ATOM     62  CA  ASN    83      -5.766  49.827  68.597  1.00  1.00
ATOM     63  C   ASN    83      -6.851  50.842  68.974  1.00  1.00
ATOM     64  O   ASN    83      -6.802  51.461  70.040  1.00  1.00
ATOM     65  CB  ASN    83      -4.696  50.466  67.720  1.00  1.00
ATOM     66  N   ALA    84      -7.846  51.000  68.112  1.00  1.00
ATOM     67  CA  ALA    84      -8.985  51.885  68.433  1.00  1.00
ATOM     68  C   ALA    84      -9.676  51.496  69.758  1.00  1.00
ATOM     69  O   ALA    84      -9.935  52.333  70.648  1.00  1.00
ATOM     70  CB  ALA    84      -9.968  51.877  67.296  1.00  1.00
ATOM     71  N   TYR    85      -9.956  50.213  69.908  1.00  1.00
ATOM     72  CA  TYR    85     -10.635  49.736  71.099  1.00  1.00
ATOM     73  C   TYR    85      -9.699  49.649  72.285  1.00  1.00
ATOM     74  O   TYR    85     -10.129  49.865  73.406  1.00  1.00
ATOM     75  CB  TYR    85     -11.354  48.406  70.820  1.00  1.00
ATOM     76  N   TYR    86      -8.420  49.372  72.037  1.00  1.00
ATOM     77  CA  TYR    86      -7.413  49.375  73.097  1.00  1.00
ATOM     78  C   TYR    86      -7.387  50.749  73.776  1.00  1.00
ATOM     79  O   TYR    86      -7.370  50.860  75.007  1.00  1.00
ATOM     80  CB  TYR    86      -6.032  49.007  72.537  1.00  1.00
ATOM     81  N   ASN    87      -9.818  53.066  73.585  1.00  1.00
ATOM     82  CA  ASN    87     -11.140  53.528  74.034  1.00  1.00
ATOM     83  C   ASN    87     -11.713  52.700  75.180  1.00  1.00
ATOM     84  O   ASN    87     -12.596  53.164  75.880  1.00  1.00
ATOM     85  CB  ASN    87     -12.143  53.556  72.880  1.00  1.00
ATOM     86  N   ASN    88     -11.210  51.482  75.359  1.00  1.00
ATOM     87  CA  ASN    88     -11.687  50.609  76.420  1.00  1.00
ATOM     88  C   ASN    88     -10.533  50.170  77.312  1.00  1.00
ATOM     89  O   ASN    88     -10.158  48.990  77.303  1.00  1.00
ATOM     90  CB  ASN    88     -12.373  49.387  75.805  1.00  1.00
ATOM     91  N   PRO    89      -9.964  51.113  78.096  1.00  1.00
ATOM     92  CA  PRO    89      -8.803  50.781  78.951  1.00  1.00
ATOM     93  C   PRO    89      -9.110  49.828  80.112  1.00  1.00
ATOM     94  O   PRO    89      -8.179  49.242  80.654  1.00  1.00
ATOM     95  CB  PRO    89      -8.326  52.149  79.460  1.00  1.00
ATOM     96  N   GLN    90     -10.382  49.673  80.487  1.00  1.00
ATOM     97  CA  GLN    90     -10.695  48.726  81.558  1.00  1.00
ATOM     98  C   GLN    90     -11.088  47.347  80.983  1.00  1.00
ATOM     99  O   GLN    90     -11.476  46.436  81.730  1.00  1.00
ATOM    100  CB  GLN    90     -11.736  49.300  82.546  1.00  1.00
TER
END
