
#######################################################
#                                                     #
#                        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   27 (  108),  selected   27 , name T0329AL242_4-D2
# Molecule2: number of CA atoms   92 (  716),  selected   27 , name T0329_D2.pdb
# PARAMETERS: T0329AL242_4-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:    14        86 - 99          4.76    15.59
  LCS_AVERAGE:     13.08

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        94 - 98          1.81    20.00
  LONGEST_CONTINUOUS_SEGMENT:     5       103 - 107         1.83    17.39
  LCS_AVERAGE:      4.55

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        95 - 98          0.37    21.59
  LCS_AVERAGE:      3.42

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      3    3    4     3    3    4    4    5    6    8    8    9   10   11   13   14   16   17   18   19   19   20   21 
LCS_GDT     S      18     S      18      3    3    4     3    3    3    4    5    6    8    8    9   10   11   13   14   16   17   18   19   19   20   21 
LCS_GDT     A      19     A      19      3    3    4     3    3    3    4    5    5    7    7    9   10   11   13   14   16   17   18   19   19   20   21 
LCS_GDT     D      20     D      20      3    3    4     3    3    3    3    3    3    4    4    7    8   10   11   13   15   17   17   19   19   20   21 
LCS_GDT     Q      86     Q      86      3    4   14     3    3    3    4    4    4    5    6    7    9   11   13   14   14   14   15   15   16   16   16 
LCS_GDT     T      87     T      87      3    4   14     3    3    3    4    4    4    5    6    7    8    9   13   14   14   14   15   15   16   16   16 
LCS_GDT     E      88     E      88      3    4   14     3    3    3    4    4    4    5    6    7    9   11   13   14   14   14   15   15   16   16   16 
LCS_GDT     V      89     V      89      3    4   14     1    3    3    4    4    4    6    8    9   10   11   13   14   14   14   15   15   16   17   17 
LCS_GDT     N      90     N      90      3    4   14     3    3    3    4    4    4    6    8    9   10   11   13   14   14   14   15   15   16   17   17 
LCS_GDT     R      91     R      91      3    4   14     3    3    3    4    4    4    7    8    9   10   11   13   14   14   14   15   15   16   19   21 
LCS_GDT     V      92     V      92      3    4   14     3    3    3    4    5    6    7    8    9   10   11   13   14   14   14   16   19   19   20   21 
LCS_GDT     L      93     L      93      3    3   14     0    3    4    4    5    6    8    8    9   10   11   13   14   14   17   18   19   19   20   21 
LCS_GDT     E      94     E      94      3    5   14     1    3    3    4    5    6    8    8    9   10   11   13   14   16   17   18   19   19   20   21 
LCS_GDT     V      95     V      95      4    5   14     4    4    4    4    5    6    8    8    9   10   11   13   14   16   17   18   19   19   20   21 
LCS_GDT     F      96     F      96      4    5   14     4    4    4    4    4    5    5    6    8   10   10   13   14   16   17   18   19   19   20   21 
LCS_GDT     K      97     K      97      4    5   14     4    4    4    4    4    5    5    7    9   10   11   13   14   16   17   18   19   19   20   21 
LCS_GDT     P      98     P      98      4    5   14     4    4    4    4    5    6    8    8    9   10   11   13   14   16   17   18   19   19   20   21 
LCS_GDT     Y      99     Y      99      3    4   14     3    3    4    4    5    6    8    8    9   10   11   13   14   16   17   18   19   19   20   21 
LCS_GDT     Y     100     Y     100      3    4   13     3    3    3    3    4    6    8    8    9   10   11   13   14   16   17   18   19   19   20   21 
LCS_GDT     A     101     A     101      3    4   13     3    3    3    4    5    5    7    7    9   10   11   13   14   16   17   18   19   19   20   21 
LCS_GDT     D     102     D     102      3    4   13     3    3    4    4    5    5    7    7    9   10   10   13   14   16   17   18   19   19   20   21 
LCS_GDT     H     103     H     103      3    5   13     3    3    4    4    4    5    7    7    8   10   11   13   14   16   17   18   19   19   20   21 
LCS_GDT     C     104     C     104      3    5   13     3    3    4    4    4    5    5    7    9   10   11   13   14   16   17   18   19   19   20   21 
LCS_GDT     Q     105     Q     105      3    5   13     3    3    4    4    4    5    5    7    9   10   11   13   14   16   17   18   19   19   20   21 
LCS_GDT     I     106     I     106      3    5   13     3    3    4    4    4    5    5    6    9   10   10   12   14   16   17   18   19   19   20   21 
LCS_GDT     K     107     K     107      3    5   13     3    3    4    4    4    5    5    6    7    7    7    8   11   13   13   14   15   15   20   21 
LCS_GDT     T     108     T     108      3    4    9     3    3    3    3    4    5    5    6    7    8    9    9   11   12   17   18   19   19   20   21 
LCS_AVERAGE  LCS_A:   7.02  (   3.42    4.55   13.08 )

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      4      5      6      8      8      9     10     11     13     14     16     17     18     19     19     20     21 
GDT PERCENT_CA   4.35   4.35   4.35   4.35   5.43   6.52   8.70   8.70   9.78  10.87  11.96  14.13  15.22  17.39  18.48  19.57  20.65  20.65  21.74  22.83
GDT RMS_LOCAL    0.37   0.37   0.37   0.37   1.51   1.95   2.51   2.51   3.13   3.64   3.98   4.44   4.66   5.18   5.43   5.75   5.89   5.89   6.23   6.54
GDT RMS_ALL_CA  21.59  21.59  21.59  21.59  11.80  11.78  11.74  11.74  11.96  13.07  13.86  13.83  13.48  13.60  12.91  13.34  13.22  13.22  12.78  12.79

#      Molecule1      Molecule2       DISTANCE
LGA    T      17      T      17          2.036
LGA    S      18      S      18          2.842
LGA    A      19      A      19          7.536
LGA    D      20      D      20         11.364
LGA    Q      86      Q      86         23.719
LGA    T      87      T      87         24.986
LGA    E      88      E      88         18.378
LGA    V      89      V      89         13.268
LGA    N      90      N      90         12.847
LGA    R      91      R      91         11.130
LGA    V      92      V      92          6.391
LGA    L      93      L      93          1.737
LGA    E      94      E      94          3.023
LGA    V      95      V      95          1.219
LGA    F      96      F      96          8.443
LGA    K      97      K      97          9.186
LGA    P      98      P      98          3.135
LGA    Y      99      Y      99          1.858
LGA    Y     100      Y     100          3.382
LGA    A     101      A     101          8.891
LGA    D     102      D     102         13.241
LGA    H     103      H     103         14.987
LGA    C     104      C     104         15.050
LGA    Q     105      Q     105         15.990
LGA    I     106      I     106         11.194
LGA    K     107      K     107         10.927
LGA    T     108      T     108          9.687

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   27   92    4.0      8    2.51     9.239     7.959     0.306

LGA_LOCAL      RMSD =  2.515  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 11.742  Number of atoms =   27 
Std_ALL_ATOMS  RMSD = 10.378  (standard rmsd on all 27 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.930625 * X  +  -0.332237 * Y  +  -0.153476 * Z  +   3.651769
  Y_new =  -0.325798 * X  +  -0.561065 * Y  +  -0.760961 * Z  +  19.299660
  Z_new =   0.166709 * X  +   0.758172 * Y  +  -0.630384 * Z  +  45.122421 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.264423   -0.877169  [ DEG:   129.7419    -50.2581 ]
  Theta =  -0.167491   -2.974102  [ DEG:    -9.5965   -170.4035 ]
  Phi   =  -0.336751    2.804842  [ DEG:   -19.2944    160.7056 ]
 
# 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: T0329AL242_4-D2                               
REMARK     2: T0329_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0329AL242_4-D2.T0329_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   27   92   4.0    8   2.51   7.959    10.38
REMARK  ---------------------------------------------------------- 
MOLECULE T0329AL242_4-D2
REMARK Aligment from pdb entry: 1u7p_A
ATOM     65  N   THR    17      -4.777  10.750  46.784  1.00  0.00              
ATOM     66  CA  THR    17      -6.072  10.149  46.483  1.00  0.00              
ATOM     67  C   THR    17      -6.020   9.450  45.139  1.00  0.00              
ATOM     68  O   THR    17      -5.044   9.597  44.401  1.00  0.00              
ATOM     69  N   SER    18      -7.065   8.682  44.836  1.00  0.00              
ATOM     70  CA  SER    18      -7.181   8.012  43.543  1.00  0.00              
ATOM     71  C   SER    18      -8.044   8.940  42.694  1.00  0.00              
ATOM     72  O   SER    18      -9.158   9.288  43.091  1.00  0.00              
ATOM     73  N   ALA    19      -7.534   9.344  41.537  1.00  0.00              
ATOM     74  CA  ALA    19      -8.280  10.245  40.669  1.00  0.00              
ATOM     75  C   ALA    19      -9.563   9.618  40.104  1.00  0.00              
ATOM     76  O   ALA    19     -10.478  10.334  39.702  1.00  0.00              
ATOM     77  N   ASP    20      -9.643   8.287  40.093  1.00  0.00              
ATOM     78  CA  ASP    20     -10.831   7.614  39.568  1.00  0.00              
ATOM     79  C   ASP    20     -11.834   7.258  40.667  1.00  0.00              
ATOM     80  O   ASP    20     -12.844   6.607  40.401  1.00  0.00              
ATOM     81  N   GLN    86     -11.570   7.706  41.891  1.00  0.00              
ATOM     82  CA  GLN    86     -12.441   7.375  43.009  1.00  0.00              
ATOM     83  C   GLN    86     -12.854   8.505  43.951  1.00  0.00              
ATOM     84  O   GLN    86     -14.043   8.714  44.194  1.00  0.00              
ATOM     85  N   THR    87     -11.873   9.222  44.487  1.00  0.00              
ATOM     86  CA  THR    87     -12.138  10.275  45.460  1.00  0.00              
ATOM     87  C   THR    87     -12.587  11.637  44.952  1.00  0.00              
ATOM     88  O   THR    87     -13.015  12.479  45.737  1.00  0.00              
ATOM     89  N   GLU    88     -12.487  11.860  43.650  1.00  0.00              
ATOM     90  CA  GLU    88     -12.875  13.140  43.082  1.00  0.00              
ATOM     91  C   GLU    88     -13.868  12.979  41.946  1.00  0.00              
ATOM     92  O   GLU    88     -14.102  11.874  41.463  1.00  0.00              
ATOM     93  N   VAL    89     -14.449  14.091  41.518  1.00  0.00              
ATOM     94  CA  VAL    89     -15.428  14.071  40.440  1.00  0.00              
ATOM     95  C   VAL    89     -15.041  15.110  39.383  1.00  0.00              
ATOM     96  O   VAL    89     -15.354  16.294  39.515  1.00  0.00              
ATOM     97  N   ASN    90     -14.325  14.669  38.332  1.00  0.00              
ATOM     98  CA  ASN    90     -13.852  15.497  37.214  1.00  0.00              
ATOM     99  C   ASN    90     -15.021  16.001  36.365  1.00  0.00              
ATOM    100  O   ASN    90     -16.106  15.434  36.407  1.00  0.00              
ATOM    101  N   ARG    91     -14.807  17.060  35.571  1.00  0.00              
ATOM    102  CA  ARG    91     -13.558  17.813  35.413  1.00  0.00              
ATOM    103  C   ARG    91     -13.247  18.713  36.605  1.00  0.00              
ATOM    104  O   ARG    91     -14.065  18.872  37.518  1.00  0.00              
ATOM    105  N   VAL    92     -12.061  19.312  36.579  1.00  0.00              
ATOM    106  CA  VAL    92     -11.624  20.206  37.640  1.00  0.00              
ATOM    107  C   VAL    92     -11.533  21.632  37.105  1.00  0.00              
ATOM    108  O   VAL    92     -11.664  21.861  35.907  1.00  0.00              
ATOM    109  N   LEU    93     -11.300  22.585  38.003  1.00  0.00              
ATOM    110  CA  LEU    93     -11.181  23.988  37.618  1.00  0.00              
ATOM    111  C   LEU    93     -10.574  24.795  38.761  1.00  0.00              
ATOM    112  O   LEU    93     -10.732  24.440  39.929  1.00  0.00              
ATOM    113  N   GLU    94      -9.884  25.879  38.421  1.00  0.00              
ATOM    114  CA  GLU    94      -9.297  26.736  39.442  1.00  0.00              
ATOM    115  C   GLU    94     -10.376  27.661  39.980  1.00  0.00              
ATOM    116  O   GLU    94     -11.128  28.263  39.217  1.00  0.00              
ATOM    117  N   VAL    95     -10.452  27.761  41.300  1.00  0.00              
ATOM    118  CA  VAL    95     -11.439  28.610  41.947  1.00  0.00              
ATOM    119  C   VAL    95     -10.911  30.041  42.009  1.00  0.00              
ATOM    120  O   VAL    95      -9.754  30.300  41.675  1.00  0.00              
ATOM    121  N   PHE    96     -11.762  30.969  42.435  1.00  0.00              
ATOM    122  CA  PHE    96     -11.372  32.371  42.531  1.00  0.00              
ATOM    123  C   PHE    96     -10.269  32.578  43.565  1.00  0.00              
ATOM    124  O   PHE    96      -9.488  33.524  43.464  1.00  0.00              
ATOM    125  N   LYS    97     -10.209  31.693  44.556  1.00  0.00              
ATOM    126  CA  LYS    97      -9.199  31.793  45.607  1.00  0.00              
ATOM    127  C   LYS    97      -7.900  31.080  45.237  1.00  0.00              
ATOM    128  O   LYS    97      -7.046  30.847  46.091  1.00  0.00              
ATOM    129  N   PRO    98      -7.759  30.730  43.962  1.00  0.00              
ATOM    130  CA  PRO    98      -6.550  30.065  43.497  1.00  0.00              
ATOM    131  C   PRO    98      -6.490  28.553  43.652  1.00  0.00              
ATOM    132  O   PRO    98      -5.594  27.910  43.110  1.00  0.00              
ATOM    133  N   TYR    99      -7.435  27.978  44.387  1.00  0.00              
ATOM    134  CA  TYR    99      -7.443  26.538  44.597  1.00  0.00              
ATOM    135  C   TYR    99      -7.953  25.763  43.381  1.00  0.00              
ATOM    136  O   TYR    99      -8.571  26.327  42.478  1.00  0.00              
ATOM    137  N   TYR   100      -7.670  24.467  43.356  1.00  0.00              
ATOM    138  CA  TYR   100      -8.152  23.603  42.289  1.00  0.00              
ATOM    139  C   TYR   100      -9.356  22.899  42.899  1.00  0.00              
ATOM    140  O   TYR   100      -9.302  22.433  44.039  1.00  0.00              
ATOM    141  N   ALA   101     -10.447  22.835  42.150  1.00  0.00              
ATOM    142  CA  ALA   101     -11.653  22.208  42.668  1.00  0.00              
ATOM    143  C   ALA   101     -12.267  21.236  41.674  1.00  0.00              
ATOM    144  O   ALA   101     -12.028  21.334  40.473  1.00  0.00              
ATOM    145  N   ASP   102     -13.061  20.302  42.188  1.00  0.00              
ATOM    146  CA  ASP   102     -13.739  19.334  41.341  1.00  0.00              
ATOM    147  C   ASP   102     -15.230  19.667  41.399  1.00  0.00              
ATOM    148  O   ASP   102     -15.635  20.578  42.124  1.00  0.00              
ATOM    149  N   HIS   103     -16.038  18.937  40.639  1.00  0.00              
ATOM    150  CA  HIS   103     -17.479  19.177  40.582  1.00  0.00              
ATOM    151  C   HIS   103     -18.208  19.224  41.927  1.00  0.00              
ATOM    152  O   HIS   103     -19.273  19.832  42.033  1.00  0.00              
ATOM    153  N   CYS   104     -17.648  18.584  42.947  1.00  0.00              
ATOM    154  CA  CYS   104     -18.290  18.568  44.258  1.00  0.00              
ATOM    155  C   CYS   104     -17.695  19.574  45.236  1.00  0.00              
ATOM    156  O   CYS   104     -17.863  19.448  46.451  1.00  0.00              
ATOM    157  N   GLN   105     -17.004  20.572  44.694  1.00  0.00              
ATOM    158  CA  GLN   105     -16.413  21.607  45.521  1.00  0.00              
ATOM    159  C   GLN   105     -15.263  21.179  46.414  1.00  0.00              
ATOM    160  O   GLN   105     -14.922  21.882  47.368  1.00  0.00              
ATOM    161  N   ILE   106     -14.656  20.034  46.117  1.00  0.00              
ATOM    162  CA  ILE   106     -13.535  19.555  46.919  1.00  0.00              
ATOM    163  C   ILE   106     -12.256  20.322  46.612  1.00  0.00              
ATOM    164  O   ILE   106     -11.971  20.652  45.464  1.00  0.00              
ATOM    165  N   LYS   107     -11.486  20.596  47.652  1.00  0.00              
ATOM    166  CA  LYS   107     -10.222  21.287  47.483  1.00  0.00              
ATOM    167  C   LYS   107      -9.234  20.199  47.067  1.00  0.00              
ATOM    168  O   LYS   107      -8.981  19.276  47.833  1.00  0.00              
ATOM    169  N   THR   108      -8.694  20.299  45.857  1.00  0.00              
ATOM    170  CA  THR   108      -7.747  19.299  45.367  1.00  0.00              
ATOM    171  C   THR   108      -6.322  19.798  45.581  1.00  0.00              
ATOM    172  O   THR   108      -5.964  20.864  45.097  1.00  0.00              
END
