
#######################################################
#                                                     #
#                        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 (   72),  selected   18 , name T0329AL170_3-D2
# Molecule2: number of CA atoms   92 (  716),  selected   18 , name T0329_D2.pdb
# PARAMETERS: T0329AL170_3-D2.T0329_D2.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:    18        17 - 34          0.51     0.51
  LCS_AVERAGE:     19.57

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18        17 - 34          0.51     0.51
  LCS_AVERAGE:     19.57

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18        17 - 34          0.51     0.51
  LCS_AVERAGE:     19.57

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:   92
LCS_GDT     T      17     T      17     18   18   18    12   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     S      18     S      18     18   18   18    13   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     A      19     A      19     18   18   18    13   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     D      20     D      20     18   18   18    13   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     L      21     L      21     18   18   18    13   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     T      22     T      22     18   18   18    13   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     S      23     S      23     18   18   18    13   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     A      24     A      24     18   18   18    13   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     L      25     L      25     18   18   18    13   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     N      26     N      26     18   18   18    13   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     Y      27     Y      27     18   18   18    13   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     A      28     A      28     18   18   18    13   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     F      29     F      29     18   18   18    13   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     E      30     E      30     18   18   18    13   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     Q      31     Q      31     18   18   18    13   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     T      32     T      32     18   18   18    13   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     G      33     G      33     18   18   18    12   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     H      34     H      34     18   18   18     3   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_AVERAGE  LCS_A:  19.57  (  19.57   19.57   19.57 )

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     13     18     18     18     18     18     18     18     18     18     18     18     18     18     18     18     18     18     18     18 
GDT PERCENT_CA  14.13  19.57  19.57  19.57  19.57  19.57  19.57  19.57  19.57  19.57  19.57  19.57  19.57  19.57  19.57  19.57  19.57  19.57  19.57  19.57
GDT RMS_LOCAL    0.33   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51
GDT RMS_ALL_CA   0.59   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51

#      Molecule1      Molecule2       DISTANCE
LGA    T      17      T      17          0.771
LGA    S      18      S      18          0.535
LGA    A      19      A      19          0.427
LGA    D      20      D      20          0.204
LGA    L      21      L      21          0.371
LGA    T      22      T      22          0.648
LGA    S      23      S      23          0.625
LGA    A      24      A      24          0.556
LGA    L      25      L      25          0.401
LGA    N      26      N      26          0.381
LGA    Y      27      Y      27          0.245
LGA    A      28      A      28          0.329
LGA    F      29      F      29          0.392
LGA    E      30      E      30          0.418
LGA    Q      31      Q      31          0.134
LGA    T      32      T      32          0.190
LGA    G      33      G      33          0.780
LGA    H      34      H      34          0.895

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   18   92    4.0     18    0.51    19.565    19.565     2.965

LGA_LOCAL      RMSD =  0.507  Number of atoms =   18  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.507  Number of atoms =   18 
Std_ALL_ATOMS  RMSD =  0.507  (standard rmsd on all 18 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.353204 * X  +  -0.932419 * Y  +   0.076434 * Z  +  45.524578
  Y_new =  -0.161524 * X  +   0.141250 * Y  +   0.976708 * Z  +  -8.644876
  Z_new =  -0.921497 * X  +   0.332631 * Y  +  -0.200498 * Z  +  49.420364 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.113245   -1.028347  [ DEG:   121.0800    -58.9200 ]
  Theta =   1.171918    1.969674  [ DEG:    67.1460    112.8540 ]
  Phi   =  -2.712676    0.428917  [ DEG:  -155.4249     24.5751 ]
 
# 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: T0329AL170_3-D2                               
REMARK     2: T0329_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0329AL170_3-D2.T0329_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   18   92   4.0   18   0.51  19.565     0.51
REMARK  ---------------------------------------------------------- 
MOLECULE T0329AL170_3-D2
REMARK Aligment from pdb entry: 2AH5_A
ATOM     65  N   THR    17      -4.243   9.736  46.007  1.00  0.00              
ATOM     66  CA  THR    17      -4.622  11.134  46.229  1.00  0.00              
ATOM     67  C   THR    17      -6.126  11.324  45.947  1.00  0.00              
ATOM     68  O   THR    17      -6.599  12.469  45.882  1.00  0.00              
ATOM     69  N   SER    18      -6.855  10.222  45.722  1.00  0.00              
ATOM     70  CA  SER    18      -8.241  10.311  45.180  1.00  0.00              
ATOM     71  C   SER    18      -9.216  11.121  46.036  1.00  0.00              
ATOM     72  O   SER    18     -10.003  11.870  45.477  1.00  0.00              
ATOM     73  N   ALA    19      -9.183  10.973  47.358  1.00  0.00              
ATOM     74  CA  ALA    19     -10.121  11.750  48.204  1.00  0.00              
ATOM     75  C   ALA    19      -9.944  13.269  48.000  1.00  0.00              
ATOM     76  O   ALA    19     -10.919  13.989  47.782  1.00  0.00              
ATOM     77  N   ASP    20      -8.712  13.759  48.067  1.00  0.00              
ATOM     78  CA  ASP    20      -8.460  15.191  47.873  1.00  0.00              
ATOM     79  C   ASP    20      -8.748  15.704  46.463  1.00  0.00              
ATOM     80  O   ASP    20      -9.198  16.841  46.305  1.00  0.00              
ATOM     81  N   LEU    21      -8.464  14.903  45.427  1.00  0.00              
ATOM     82  CA  LEU    21      -8.777  15.302  44.048  1.00  0.00              
ATOM     83  C   LEU    21     -10.295  15.370  43.884  1.00  0.00              
ATOM     84  O   LEU    21     -10.828  16.377  43.410  1.00  0.00              
ATOM     85  N   THR    22     -10.975  14.316  44.334  1.00  0.00              
ATOM     86  CA  THR    22     -12.435  14.274  44.285  1.00  0.00              
ATOM     87  C   THR    22     -13.012  15.494  44.993  1.00  0.00              
ATOM     88  O   THR    22     -13.884  16.161  44.446  1.00  0.00              
ATOM     89  N   SER    23     -12.550  15.765  46.212  1.00  0.00              
ATOM     90  CA  SER    23     -13.040  16.912  46.980  1.00  0.00              
ATOM     91  C   SER    23     -12.773  18.264  46.310  1.00  0.00              
ATOM     92  O   SER    23     -13.602  19.208  46.373  1.00  0.00              
ATOM     93  N   ALA    24     -11.606  18.401  45.704  1.00  0.00              
ATOM     94  CA  ALA    24     -11.323  19.616  44.946  1.00  0.00              
ATOM     95  C   ALA    24     -12.326  19.782  43.785  1.00  0.00              
ATOM     96  O   ALA    24     -12.824  20.896  43.561  1.00  0.00              
ATOM     97  N   LEU    25     -12.627  18.705  43.046  1.00  0.00              
ATOM     98  CA  LEU    25     -13.635  18.815  41.975  1.00  0.00              
ATOM     99  C   LEU    25     -15.019  19.211  42.498  1.00  0.00              
ATOM    100  O   LEU    25     -15.660  20.129  41.971  1.00  0.00              
ATOM    101  N   ASN    26     -15.447  18.543  43.553  1.00  0.00              
ATOM    102  CA  ASN    26     -16.822  18.765  44.064  1.00  0.00              
ATOM    103  C   ASN    26     -16.931  20.148  44.727  1.00  0.00              
ATOM    104  O   ASN    26     -17.995  20.784  44.674  1.00  0.00              
ATOM    105  N   TYR    27     -15.850  20.597  45.368  1.00  0.00              
ATOM    106  CA  TYR    27     -15.804  21.989  45.874  1.00  0.00              
ATOM    107  C   TYR    27     -16.018  22.970  44.734  1.00  0.00              
ATOM    108  O   TYR    27     -16.745  23.972  44.875  1.00  0.00              
ATOM    109  N   ALA    28     -15.364  22.701  43.599  1.00  0.00              
ATOM    110  CA  ALA    28     -15.478  23.581  42.431  1.00  0.00              
ATOM    111  C   ALA    28     -16.899  23.640  41.897  1.00  0.00              
ATOM    112  O   ALA    28     -17.429  24.719  41.691  1.00  0.00              
ATOM    113  N   PHE    29     -17.513  22.482  41.681  1.00  0.00              
ATOM    114  CA  PHE    29     -18.904  22.434  41.227  1.00  0.00              
ATOM    115  C   PHE    29     -19.880  23.079  42.221  1.00  0.00              
ATOM    116  O   PHE    29     -20.817  23.776  41.788  1.00  0.00              
ATOM    117  N   GLU    30     -19.670  22.862  43.521  1.00  0.00              
ATOM    118  CA  GLU    30     -20.457  23.574  44.562  1.00  0.00              
ATOM    119  C   GLU    30     -20.340  25.109  44.380  1.00  0.00              
ATOM    120  O   GLU    30     -21.335  25.828  44.385  1.00  0.00              
ATOM    121  N   GLN    31     -19.120  25.609  44.189  1.00  0.00              
ATOM    122  CA  GLN    31     -18.926  27.058  44.067  1.00  0.00              
ATOM    123  C   GLN    31     -19.523  27.617  42.794  1.00  0.00              
ATOM    124  O   GLN    31     -20.059  28.754  42.784  1.00  0.00              
ATOM    125  N   THR    32     -19.459  26.822  41.724  1.00  0.00              
ATOM    126  CA  THR    32     -20.017  27.228  40.430  1.00  0.00              
ATOM    127  C   THR    32     -21.547  27.037  40.355  1.00  0.00              
ATOM    128  O   THR    32     -22.203  27.513  39.416  1.00  0.00              
ATOM    129  N   GLY    33     -22.090  26.338  41.344  1.00  0.00              
ATOM    130  CA  GLY    33     -23.521  26.104  41.469  1.00  0.00              
ATOM    131  C   GLY    33     -24.057  25.119  40.447  1.00  0.00              
ATOM    132  O   GLY    33     -25.150  25.310  39.919  1.00  0.00              
ATOM    133  N   HIS    34     -23.271  24.085  40.154  1.00  0.00              
ATOM    134  CA  HIS    34     -23.605  23.071  39.140  1.00  0.00              
ATOM    135  C   HIS    34     -23.557  21.682  39.760  1.00  0.00              
ATOM    136  O   HIS    34     -22.775  21.448  40.682  1.00  0.00              
END
