
#######################################################
#                                                     #
#                        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 T0330AL242_4-D2
# Molecule2: number of CA atoms   72 (  556),  selected   27 , name T0330_D2.pdb
# PARAMETERS: T0330AL242_4-D2.T0330_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        69 - 82          4.82    16.35
  LONGEST_CONTINUOUS_SEGMENT:    14        77 - 90          4.96    16.28
  LCS_AVERAGE:     17.34

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        77 - 81          1.88    19.99
  LONGEST_CONTINUOUS_SEGMENT:     5        86 - 90          1.87    16.12
  LCS_AVERAGE:      5.97

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        17 - 20          0.81    19.52
  LONGEST_CONTINUOUS_SEGMENT:     4        69 - 72          0.91    15.87
  LONGEST_CONTINUOUS_SEGMENT:     4        78 - 81          0.20    18.24
  LONGEST_CONTINUOUS_SEGMENT:     4        86 - 89          0.66    17.30
  LCS_AVERAGE:      4.99

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:   72
LCS_GDT     V      17     V      17      4    4    4     3    4    5    6    6    6    7    7    9   10   12   14   15   17   18   19   19   20   20   22 
LCS_GDT     E      18     E      18      4    4    4     3    4    5    6    6    6    7    7    8   10   12   14   15   17   18   19   19   20   20   22 
LCS_GDT     S      19     S      19      4    4    4     3    4    4    6    6    6    7    7    9   10   12   14   15   17   18   19   19   20   20   22 
LCS_GDT     M      20     M      20      4    4    4     3    4    4    4    4    4    7    7    8   10   10   11   12   14   18   19   19   20   20   22 
LCS_GDT     D      69     D      69      4    4   14     3    3    4    4    4    5    5    6    8    9   11   13   13   14   14   15   15   15   16   16 
LCS_GDT     K      70     K      70      4    4   14     3    3    4    4    4    5    5    6    8    9   11   13   13   14   14   15   15   15   16   16 
LCS_GDT     F      71     F      71      4    4   14     3    3    4    4    4    5    5    8    9   10   11   13   13   14   14   15   15   15   16   16 
LCS_GDT     D      72     D      72      4    4   14     2    3    4    4    4    5    5    8    9   10   11   13   13   14   14   15   15   15   16   16 
LCS_GDT     K      73     K      73      3    4   14     3    3    3    4    4    4    5    8    9   10   10   13   13   14   14   15   15   15   16   16 
LCS_GDT     A      74     A      74      3    4   14     3    3    3    4    4    4    5    7    9   10   10   12   13   14   14   15   17   20   20   22 
LCS_GDT     K      75     K      75      3    4   14     3    3    3    4    4    6    6    8    9   10   11   13   13   14   14   15   17   20   20   22 
LCS_GDT     E      76     E      76      3    3   14     3    3    3    5    5    6    6    8    9   10   11   13   13   14   17   18   19   20   20   22 
LCS_GDT     T      77     T      77      3    5   14     3    3    4    5    5    6    6    8    9   10   11   14   15   17   18   19   19   20   20   22 
LCS_GDT     Y      78     Y      78      4    5   14     4    4    4    5    5    6    6    7    9   10   11   13   15   17   18   19   19   20   20   22 
LCS_GDT     I      79     I      79      4    5   14     4    4    4    4    4    5    5    6    7   10   10   14   15   17   18   19   19   20   20   22 
LCS_GDT     A      80     A      80      4    5   14     4    4    4    4    4    5    5    6    9   10   12   14   15   17   18   19   19   20   20   22 
LCS_GDT     L      81     L      81      4    5   14     4    4    4    5    5    6    6    8    9   10   12   14   15   17   18   19   19   20   20   22 
LCS_GDT     F      82     F      82      3    4   14     3    3    3    5    5    6    6    8    9   10   12   14   15   17   18   19   19   20   20   22 
LCS_GDT     R      83     R      83      3    4   14     1    3    5    6    6    6    7    7    9   10   12   14   15   17   18   19   19   20   20   22 
LCS_GDT     E      84     E      84      3    4   14     3    3    5    6    6    6    7    7    9   10   12   14   15   17   18   19   19   20   20   22 
LCS_GDT     R      85     R      85      3    4   14     3    3    5    6    6    6    7    7    9   10   12   14   15   17   18   19   19   20   20   22 
LCS_GDT     A      86     A      86      4    5   14     3    4    4    5    6    6    7    7    8   10   11   14   15   17   18   19   19   20   20   22 
LCS_GDT     R      87     R      87      4    5   14     3    4    4    5    6    6    7    7    9   10   12   14   15   17   18   19   19   20   20   22 
LCS_GDT     R      88     R      88      4    5   14     3    4    4    5    6    6    7    7    8   10   12   14   15   17   18   19   19   20   20   22 
LCS_GDT     E      89     E      89      4    5   14     3    4    4    5    6    6    7    7    8   10   12   12   15   17   18   19   19   20   20   22 
LCS_GDT     D      90     D      90      3    5   14     3    3    3    3    4    5    5    6    8    9   10   12   13   17   18   19   19   20   20   22 
LCS_GDT     I      91     I      91      3    3   13     3    3    3    3    6    6    7    7    8   10   10   11   15   17   18   19   19   20   20   22 
LCS_AVERAGE  LCS_A:   9.43  (   4.99    5.97   17.34 )

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      5      6      6      6      7      8      9     10     12     14     15     17     18     19     19     20     20     22 
GDT PERCENT_CA   5.56   5.56   6.94   8.33   8.33   8.33   9.72  11.11  12.50  13.89  16.67  19.44  20.83  23.61  25.00  26.39  26.39  27.78  27.78  30.56
GDT RMS_LOCAL    0.20   0.20   1.23   1.40   1.40   1.40   2.01   3.37   3.60   3.62   4.26   4.70   4.94   5.26   5.39   5.65   5.65   6.01   6.01   7.01
GDT RMS_ALL_CA  18.24  18.24  13.46  13.45  13.45  13.45  15.75  15.07  15.40  13.88  14.90  14.30  14.39  14.52  14.63  14.24  14.24  13.82  13.82  12.75

#      Molecule1      Molecule2       DISTANCE
LGA    V      17      V      17         21.044
LGA    E      18      E      18         26.539
LGA    S      19      S      19         25.357
LGA    M      20      M      20         27.365
LGA    D      69      D      69          8.882
LGA    K      70      K      70          9.714
LGA    F      71      F      71          3.088
LGA    D      72      D      72          3.903
LGA    K      73      K      73          3.934
LGA    A      74      A      74          6.752
LGA    K      75      K      75          3.953
LGA    E      76      E      76          2.615
LGA    T      77      T      77          3.646
LGA    Y      78      Y      78          4.529
LGA    I      79      I      79          9.257
LGA    A      80      A      80          8.370
LGA    L      81      L      81          3.327
LGA    F      82      F      82          2.975
LGA    R      83      R      83          7.895
LGA    E      84      E      84         12.392
LGA    R      85      R      85         16.923
LGA    A      86      A      86         20.855
LGA    R      87      R      87         25.187
LGA    R      88      R      88         24.543
LGA    E      89      E      89         24.220
LGA    D      90      D      90         17.144
LGA    I      91      I      91         17.804

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   27   72    4.0      8    3.37    12.847    10.769     0.230

LGA_LOCAL      RMSD =  3.371  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 15.398  Number of atoms =   27 
Std_ALL_ATOMS  RMSD = 10.892  (standard rmsd on all 27 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.114218 * X  +   0.950078 * Y  +   0.290354 * Z  +  18.154339
  Y_new =   0.179529 * X  +  -0.307194 * Y  +   0.934559 * Z  +  47.536724
  Z_new =   0.977100 * X  +  -0.054617 * Y  +  -0.205654 * Z  +  14.245036 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.882008    0.259585  [ DEG:  -165.1269     14.8731 ]
  Theta =  -1.356375   -1.785218  [ DEG:   -77.7145   -102.2855 ]
  Phi   =   1.004175   -2.137418  [ DEG:    57.5350   -122.4650 ]
 
# 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: T0330AL242_4-D2                               
REMARK     2: T0330_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0330AL242_4-D2.T0330_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   27   72   4.0    8   3.37  10.769    10.89
REMARK  ---------------------------------------------------------- 
MOLECULE T0330AL242_4-D2
REMARK Aligment from pdb entry: 1u7p_A
ATOM     65  N   VAL    17      27.983  50.268   7.700  1.00  0.00              
ATOM     66  CA  VAL    17      28.620  50.702   6.462  1.00  0.00              
ATOM     67  C   VAL    17      28.412  52.191   6.266  1.00  0.00              
ATOM     68  O   VAL    17      27.638  52.811   6.997  1.00  0.00              
ATOM     69  N   GLU    18      29.117  52.758   5.288  1.00  0.00              
ATOM     70  CA  GLU    18      28.958  54.168   4.940  1.00  0.00              
ATOM     71  C   GLU    18      27.970  54.178   3.778  1.00  0.00              
ATOM     72  O   GLU    18      28.198  53.515   2.764  1.00  0.00              
ATOM     73  N   SER    19      26.877  54.917   3.923  1.00  0.00              
ATOM     74  CA  SER    19      25.871  54.973   2.872  1.00  0.00              
ATOM     75  C   SER    19      26.379  55.633   1.582  1.00  0.00              
ATOM     76  O   SER    19      25.820  55.409   0.510  1.00  0.00              
ATOM     77  N   MET    20      27.445  56.427   1.677  1.00  0.00              
ATOM     78  CA  MET    20      27.987  57.095   0.494  1.00  0.00              
ATOM     79  C   MET    20      29.135  56.311  -0.145  1.00  0.00              
ATOM     80  O   MET    20      29.759  56.785  -1.095  1.00  0.00              
ATOM     81  N   ASP    69      29.395  55.108   0.357  1.00  0.00              
ATOM     82  CA  ASP    69      30.500  54.310  -0.155  1.00  0.00              
ATOM     83  C   ASP    69      30.235  52.837  -0.462  1.00  0.00              
ATOM     84  O   ASP    69      30.506  52.370  -1.569  1.00  0.00              
ATOM     85  N   LYS    70      29.716  52.108   0.518  1.00  0.00              
ATOM     86  CA  LYS    70      29.492  50.675   0.371  1.00  0.00              
ATOM     87  C   LYS    70      28.246  50.208  -0.366  1.00  0.00              
ATOM     88  O   LYS    70      28.125  49.029  -0.690  1.00  0.00              
ATOM     89  N   PHE    71      27.320  51.118  -0.626  1.00  0.00              
ATOM     90  CA  PHE    71      26.090  50.755  -1.308  1.00  0.00              
ATOM     91  C   PHE    71      25.837  51.626  -2.525  1.00  0.00              
ATOM     92  O   PHE    71      26.501  52.639  -2.726  1.00  0.00              
ATOM     93  N   ASP    72      24.866  51.228  -3.336  1.00  0.00              
ATOM     94  CA  ASP    72      24.532  51.970  -4.543  1.00  0.00              
ATOM     95  C   ASP    72      23.023  52.235  -4.574  1.00  0.00              
ATOM     96  O   ASP    72      22.239  51.384  -4.996  1.00  0.00              
ATOM     97  N   LYS    73      22.605  53.421  -4.093  1.00  0.00              
ATOM     98  CA  LYS    73      21.208  53.872  -4.029  1.00  0.00              
ATOM     99  C   LYS    73      20.634  54.097  -5.429  1.00  0.00              
ATOM    100  O   LYS    73      21.381  54.266  -6.385  1.00  0.00              
ATOM    101  N   ALA    74      19.300  54.119  -5.562  1.00  0.00              
ATOM    102  CA  ALA    74      18.298  53.952  -4.503  1.00  0.00              
ATOM    103  C   ALA    74      18.171  52.509  -4.023  1.00  0.00              
ATOM    104  O   ALA    74      18.761  51.588  -4.599  1.00  0.00              
ATOM    105  N   LYS    75      17.381  52.322  -2.971  1.00  0.00              
ATOM    106  CA  LYS    75      17.154  51.002  -2.403  1.00  0.00              
ATOM    107  C   LYS    75      15.705  50.586  -2.637  1.00  0.00              
ATOM    108  O   LYS    75      14.890  51.381  -3.093  1.00  0.00              
ATOM    109  N   GLU    76      15.391  49.334  -2.313  1.00  0.00              
ATOM    110  CA  GLU    76      14.036  48.816  -2.479  1.00  0.00              
ATOM    111  C   GLU    76      13.880  47.505  -1.717  1.00  0.00              
ATOM    112  O   GLU    76      14.850  46.772  -1.528  1.00  0.00              
ATOM    113  N   THR    77      12.658  47.213  -1.282  1.00  0.00              
ATOM    114  CA  THR    77      12.398  45.966  -0.575  1.00  0.00              
ATOM    115  C   THR    77      12.240  44.852  -1.596  1.00  0.00              
ATOM    116  O   THR    77      11.530  45.003  -2.588  1.00  0.00              
ATOM    117  N   TYR    78      12.914  43.737  -1.350  1.00  0.00              
ATOM    118  CA  TYR    78      12.853  42.594  -2.247  1.00  0.00              
ATOM    119  C   TYR    78      11.621  41.757  -1.912  1.00  0.00              
ATOM    120  O   TYR    78      10.937  42.012  -0.920  1.00  0.00              
ATOM    121  N   ILE    79      11.340  40.758  -2.743  1.00  0.00              
ATOM    122  CA  ILE    79      10.186  39.894  -2.529  1.00  0.00              
ATOM    123  C   ILE    79      10.316  39.089  -1.239  1.00  0.00              
ATOM    124  O   ILE    79       9.313  38.703  -0.639  1.00  0.00              
ATOM    125  N   ALA    80      11.553  38.840  -0.816  1.00  0.00              
ATOM    126  CA  ALA    80      11.802  38.075   0.403  1.00  0.00              
ATOM    127  C   ALA    80      11.830  38.957   1.650  1.00  0.00              
ATOM    128  O   ALA    80      12.273  38.527   2.714  1.00  0.00              
ATOM    129  N   LEU    81      11.362  40.194   1.510  1.00  0.00              
ATOM    130  CA  LEU    81      11.323  41.111   2.641  1.00  0.00              
ATOM    131  C   LEU    81      12.590  41.900   2.936  1.00  0.00              
ATOM    132  O   LEU    81      12.570  42.825   3.743  1.00  0.00              
ATOM    133  N   PHE    82      13.694  41.542   2.289  1.00  0.00              
ATOM    134  CA  PHE    82      14.952  42.235   2.523  1.00  0.00              
ATOM    135  C   PHE    82      15.018  43.596   1.830  1.00  0.00              
ATOM    136  O   PHE    82      14.226  43.897   0.937  1.00  0.00              
ATOM    137  N   ARG    83      15.958  44.426   2.266  1.00  0.00              
ATOM    138  CA  ARG    83      16.170  45.727   1.649  1.00  0.00              
ATOM    139  C   ARG    83      17.372  45.513   0.739  1.00  0.00              
ATOM    140  O   ARG    83      18.361  44.895   1.138  1.00  0.00              
ATOM    141  N   GLU    84      17.283  46.007  -0.486  1.00  0.00              
ATOM    142  CA  GLU    84      18.374  45.820  -1.431  1.00  0.00              
ATOM    143  C   GLU    84      18.746  47.110  -2.141  1.00  0.00              
ATOM    144  O   GLU    84      17.940  48.034  -2.227  1.00  0.00              
ATOM    145  N   ARG    85      19.972  47.162  -2.651  1.00  0.00              
ATOM    146  CA  ARG    85      20.440  48.326  -3.387  1.00  0.00              
ATOM    147  C   ARG    85      20.587  47.894  -4.846  1.00  0.00              
ATOM    148  O   ARG    85      20.372  46.724  -5.172  1.00  0.00              
ATOM    149  N   ALA    86      20.947  48.829  -5.716  1.00  0.00              
ATOM    150  CA  ALA    86      21.091  48.551  -7.144  1.00  0.00              
ATOM    151  C   ALA    86      21.987  47.366  -7.511  1.00  0.00              
ATOM    152  O   ALA    86      21.836  46.784  -8.586  1.00  0.00              
ATOM    153  N   ARG    87      22.919  47.010  -6.635  1.00  0.00              
ATOM    154  CA  ARG    87      23.824  45.900  -6.918  1.00  0.00              
ATOM    155  C   ARG    87      23.421  44.600  -6.234  1.00  0.00              
ATOM    156  O   ARG    87      24.239  43.692  -6.074  1.00  0.00              
ATOM    157  N   ARG    88      22.154  44.520  -5.839  1.00  0.00              
ATOM    158  CA  ARG    88      21.645  43.320  -5.200  1.00  0.00              
ATOM    159  C   ARG    88      22.189  43.014  -3.816  1.00  0.00              
ATOM    160  O   ARG    88      22.077  41.881  -3.342  1.00  0.00              
ATOM    161  N   GLU    89      22.776  44.009  -3.159  1.00  0.00              
ATOM    162  CA  GLU    89      23.316  43.801  -1.820  1.00  0.00              
ATOM    163  C   GLU    89      22.214  43.747  -0.771  1.00  0.00              
ATOM    164  O   GLU    89      21.241  44.494  -0.830  1.00  0.00              
ATOM    165  N   ASP    90      22.380  42.856   0.193  1.00  0.00              
ATOM    166  CA  ASP    90      21.418  42.736   1.272  1.00  0.00              
ATOM    167  C   ASP    90      21.796  43.839   2.257  1.00  0.00              
ATOM    168  O   ASP    90      22.889  43.815   2.814  1.00  0.00              
ATOM    169  N   ILE    91      20.907  44.806   2.459  1.00  0.00              
ATOM    170  CA  ILE    91      21.185  45.911   3.375  1.00  0.00              
ATOM    171  C   ILE    91      20.548  45.622   4.730  1.00  0.00              
ATOM    172  O   ILE    91      19.344  45.413   4.811  1.00  0.00              
END
