
#######################################################
#                                                     #
#                        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 T0324AL242_3-D2
# Molecule2: number of CA atoms   65 (  494),  selected   27 , name T0324_D2.pdb
# PARAMETERS: T0324AL242_3-D2.T0324_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          4.64     9.08
  LCS_AVERAGE:     23.08

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7        18 - 24          1.68    14.25
  LCS_AVERAGE:      7.75

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        18 - 22          0.70    17.33
  LONGEST_CONTINUOUS_SEGMENT:     5        19 - 23          0.95    15.50
  LONGEST_CONTINUOUS_SEGMENT:     5        30 - 34          0.22    14.04
  LCS_AVERAGE:      6.10

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:   65
LCS_GDT     S      17     S      17      3    3   18     3    3    3    3    4    6    6    8   13   13   14   16   16   18   20   21   21   22   24   24 
LCS_GDT     Q      18     Q      18      5    7   18     4    5    6    6    6    7    8   10   13   13   15   17   17   18   20   21   21   22   24   24 
LCS_GDT     P      19     P      19      5    7   18     4    5    6    6    6    7    8   10   12   13   15   17   17   18   20   21   21   22   24   24 
LCS_GDT     A      20     A      20      5    7   18     4    5    6    6    6    7    8   10   12   13   15   17   17   18   20   21   21   22   24   24 
LCS_GDT     Y      21     Y      21      5    7   18     4    5    6    6    6    7    7   10   13   13   15   17   17   18   20   21   21   22   24   24 
LCS_GDT     T      22     T      22      5    7   18     3    5    6    6    6    7    8   10   13   13   15   17   17   18   20   21   21   22   24   24 
LCS_GDT     T      23     T      23      5    7   18     3    4    6    6    6    7    7    9   13   13   15   17   17   18   20   21   21   22   24   24 
LCS_GDT     V      24     V      24      3    7   18     3    3    3    5    6    7    8   10   13   13   15   17   17   18   20   21   21   22   24   24 
LCS_GDT     M      25     M      25      3    4   18     3    3    3    4    4    5    6    9   10   12   13   17   17   17   20   21   21   22   24   24 
LCS_GDT     R      26     R      26      3    4   18     3    3    3    4    5    6    6    7    9   11   14   17   17   18   20   21   21   22   24   24 
LCS_GDT     E      27     E      27      3    4   18     3    3    4    5    5    7    8   10   12   13   15   17   17   18   20   21   21   22   24   24 
LCS_GDT     V      28     V      28      3    3   18     3    3    4    4    4    6    7    9   12   13   15   17   17   18   19   21   21   22   24   24 
LCS_GDT     L      29     L      29      3    5   18     3    3    4    4    4    6    8   10   12   13   15   17   17   18   19   20   21   22   24   24 
LCS_GDT     A      30     A      30      5    5   18     5    5    5    5    6    7    8   10   12   13   15   17   17   18   19   20   21   22   24   24 
LCS_GDT     T      31     T      31      5    5   18     5    5    5    5    6    7    8   10   12   13   15   17   17   18   19   20   21   22   24   24 
LCS_GDT     Y      32     Y      32      5    5   18     5    5    5    5    6    7    8   10   12   13   15   17   17   18   19   20   21   22   24   24 
LCS_GDT     G      33     G      33      5    5   18     5    5    5    5    6    7    8   10   12   13   15   17   17   18   19   20   21   22   24   24 
LCS_GDT     K      34     K      34      5    5   18     5    5    5    5    5    7    8   10   12   13   15   17   17   18   19   20   21   22   24   24 
LCS_GDT     V      73     V      73      3    3    9     0    3    4    4    4    4    6    6    8   11   12   13   16   17   20   21   21   22   24   24 
LCS_GDT     M      74     M      74      3    5    9     0    3    4    4    4    6    6    7   10   12   13   16   16   17   20   21   21   22   24   24 
LCS_GDT     A      75     A      75      4    5    9     3    4    4    4    4    6    8   10   13   13   14   16   16   17   20   21   21   22   24   24 
LCS_GDT     S      76     S      76      4    5    9     3    4    4    4    5    6    8   10   13   13   14   16   16   18   20   21   21   22   24   24 
LCS_GDT     H      77     H      77      4    5    9     3    4    4    4    5    7    8   10   13   13   14   16   16   17   20   21   21   22   24   24 
LCS_GDT     Y      78     Y      78      4    5    9     3    4    4    4    5    7    7    9   13   13   13   16   16   17   20   21   21   22   24   24 
LCS_GDT     D      79     D      79      3    4    9     3    3    4    4    5    7    8   10   13   13   14   16   16   17   20   21   21   21   22   22 
LCS_GDT     Q      80     Q      80      3    4    9     3    3    4    4    4    7    7   10   13   13   14   16   16   17   20   21   21   21   21   22 
LCS_GDT     I      81     I      81      3    3    9     3    3    3    3    5    7    8   10   13   13   14   16   16   17   20   21   21   21   21   22 
LCS_AVERAGE  LCS_A:  12.31  (   6.10    7.75   23.08 )

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      5      5      6      6      6      7      8     10     13     13     15     17     17     18     20     21     21     22     24     24 
GDT PERCENT_CA   7.69   7.69   9.23   9.23   9.23  10.77  12.31  15.38  20.00  20.00  23.08  26.15  26.15  27.69  30.77  32.31  32.31  33.85  36.92  36.92
GDT RMS_LOCAL    0.22   0.22   1.04   1.04   1.04   1.68   2.29   2.74   3.44   3.44   3.85   4.34   4.34   4.66   5.37   5.55   5.40   5.67   6.36   6.36
GDT RMS_ALL_CA  14.04  14.04  15.96  15.96  15.96  14.25   8.91   8.84  16.16  16.16   9.18   9.50   9.50   8.60  12.10  11.31   8.23   8.14   7.82   7.82

#      Molecule1      Molecule2       DISTANCE
LGA    S      17      S      17          7.137
LGA    Q      18      Q      18          1.465
LGA    P      19      P      19          0.956
LGA    A      20      A      20          3.607
LGA    Y      21      Y      21          5.694
LGA    T      22      T      22          7.047
LGA    T      23      T      23          6.053
LGA    V      24      V      24          3.977
LGA    M      25      M      25          7.596
LGA    R      26      R      26          7.742
LGA    E      27      E      27          2.216
LGA    V      28      V      28          5.278
LGA    L      29      L      29          4.633
LGA    A      30      A      30          3.100
LGA    T      31      T      31          3.987
LGA    Y      32      Y      32          2.765
LGA    G      33      G      33          1.426
LGA    K      34      K      34          2.338
LGA    V      73      V      73         12.332
LGA    M      74      M      74         10.141
LGA    A      75      A      75          9.979
LGA    S      76      S      76          7.293
LGA    H      77      H      77          9.890
LGA    Y      78      Y      78         15.267
LGA    D      79      D      79         17.941
LGA    Q      80      Q      80         18.283
LGA    I      81      I      81         16.614

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   27   65    4.0     10    2.74    16.154    13.989     0.352

LGA_LOCAL      RMSD =  2.737  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  8.787  Number of atoms =   27 
Std_ALL_ATOMS  RMSD =  7.553  (standard rmsd on all 27 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.151931 * X  +   0.061857 * Y  +   0.986454 * Z  +  12.347342
  Y_new =   0.943179 * X  +   0.307477 * Y  +   0.125985 * Z  +  24.670414
  Z_new =  -0.295518 * X  +   0.949543 * Y  +  -0.105057 * Z  +   1.324304 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.680988   -1.460604  [ DEG:    96.3135    -83.6865 ]
  Theta =   0.299998    2.841595  [ DEG:    17.1886    162.8114 ]
  Phi   =   1.730508   -1.411085  [ DEG:    99.1508    -80.8492 ]
 
# 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: T0324AL242_3-D2                               
REMARK     2: T0324_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0324AL242_3-D2.T0324_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   27   65   4.0   10   2.74  13.989     7.55
REMARK  ---------------------------------------------------------- 
MOLECULE T0324AL242_3-D2
REMARK Aligment from pdb entry: 1u7p_A
ATOM     65  N   SER    17      20.282  23.734  10.438  1.00  0.00              
ATOM     66  CA  SER    17      21.311  23.008  11.174  1.00  0.00              
ATOM     67  C   SER    17      22.616  23.031  10.403  1.00  0.00              
ATOM     68  O   SER    17      22.645  23.455   9.247  1.00  0.00              
ATOM     69  N   GLN    18      23.690  22.589  11.055  1.00  0.00              
ATOM     70  CA  GLN    18      24.996  22.485  10.407  1.00  0.00              
ATOM     71  C   GLN    18      25.093  21.034   9.946  1.00  0.00              
ATOM     72  O   GLN    18      24.948  20.115  10.754  1.00  0.00              
ATOM     73  N   PRO    19      25.331  20.828   8.657  1.00  0.00              
ATOM     74  CA  PRO    19      25.422  19.475   8.124  1.00  0.00              
ATOM     75  C   PRO    19      26.625  18.690   8.669  1.00  0.00              
ATOM     76  O   PRO    19      26.626  17.461   8.642  1.00  0.00              
ATOM     77  N   ALA    20      27.636  19.392   9.180  1.00  0.00              
ATOM     78  CA  ALA    20      28.818  18.718   9.716  1.00  0.00              
ATOM     79  C   ALA    20      28.735  18.506  11.229  1.00  0.00              
ATOM     80  O   ALA    20      29.691  18.034  11.845  1.00  0.00              
ATOM     81  N   TYR    21      27.588  18.829  11.819  1.00  0.00              
ATOM     82  CA  TYR    21      27.433  18.707  13.262  1.00  0.00              
ATOM     83  C   TYR    21      26.166  18.038  13.790  1.00  0.00              
ATOM     84  O   TYR    21      26.238  17.094  14.577  1.00  0.00              
ATOM     85  N   THR    22      25.009  18.533  13.366  1.00  0.00              
ATOM     86  CA  THR    22      23.733  18.029  13.859  1.00  0.00              
ATOM     87  C   THR    22      23.177  16.748  13.257  1.00  0.00              
ATOM     88  O   THR    22      22.220  16.184  13.782  1.00  0.00              
ATOM     89  N   THR    23      23.762  16.290  12.162  1.00  0.00              
ATOM     90  CA  THR    23      23.283  15.084  11.509  1.00  0.00              
ATOM     91  C   THR    23      24.395  14.073  11.300  1.00  0.00              
ATOM     92  O   THR    23      25.571  14.381  11.472  1.00  0.00              
ATOM     93  N   VAL    24      24.016  12.859  10.921  1.00  0.00              
ATOM     94  CA  VAL    24      24.984  11.796  10.697  1.00  0.00              
ATOM     95  C   VAL    24      24.733  11.161   9.326  1.00  0.00              
ATOM     96  O   VAL    24      23.880  10.284   9.181  1.00  0.00              
ATOM     97  N   MET    25      25.463  11.630   8.297  1.00  0.00              
ATOM     98  CA  MET    25      25.377  11.163   6.906  1.00  0.00              
ATOM     99  C   MET    25      25.883   9.725   6.772  1.00  0.00              
ATOM    100  O   MET    25      26.614   9.243   7.628  1.00  0.00              
ATOM    101  N   ARG    26      25.512   9.030   5.687  1.00  0.00              
ATOM    102  CA  ARG    26      24.662   9.492   4.584  1.00  0.00              
ATOM    103  C   ARG    26      23.187   9.580   4.963  1.00  0.00              
ATOM    104  O   ARG    26      22.778   9.154   6.049  1.00  0.00              
ATOM    105  N   GLU    27      22.390  10.124   4.049  1.00  0.00              
ATOM    106  CA  GLU    27      20.959  10.270   4.262  1.00  0.00              
ATOM    107  C   GLU    27      20.202   9.351   3.307  1.00  0.00              
ATOM    108  O   GLU    27      20.794   8.748   2.418  1.00  0.00              
ATOM    109  N   VAL    28      18.889   9.258   3.495  1.00  0.00              
ATOM    110  CA  VAL    28      18.049   8.421   2.642  1.00  0.00              
ATOM    111  C   VAL    28      16.580   8.770   2.848  1.00  0.00              
ATOM    112  O   VAL    28      16.189   9.219   3.926  1.00  0.00              
ATOM    113  N   LEU    29      15.770   8.563   1.815  1.00  0.00              
ATOM    114  CA  LEU    29      14.342   8.831   1.925  1.00  0.00              
ATOM    115  C   LEU    29      13.677   7.650   2.611  1.00  0.00              
ATOM    116  O   LEU    29      13.927   6.497   2.266  1.00  0.00              
ATOM    117  N   ALA    30      12.834   7.945   3.591  1.00  0.00              
ATOM    118  CA  ALA    30      12.131   6.910   4.332  1.00  0.00              
ATOM    119  C   ALA    30      10.875   6.506   3.565  1.00  0.00              
ATOM    120  O   ALA    30      10.523   7.128   2.561  1.00  0.00              
ATOM    121  N   THR    31      10.203   5.461   4.036  1.00  0.00              
ATOM    122  CA  THR    31       8.992   4.978   3.384  1.00  0.00              
ATOM    123  C   THR    31       7.873   6.014   3.438  1.00  0.00              
ATOM    124  O   THR    31       6.993   6.029   2.578  1.00  0.00              
ATOM    125  N   TYR    32       7.910   6.878   4.449  1.00  0.00              
ATOM    126  CA  TYR    32       6.890   7.910   4.608  1.00  0.00              
ATOM    127  C   TYR    32       7.229   9.189   3.843  1.00  0.00              
ATOM    128  O   TYR    32       6.621  10.234   4.066  1.00  0.00              
ATOM    129  N   GLY    33       8.209   9.100   2.948  1.00  0.00              
ATOM    130  CA  GLY    33       8.597  10.253   2.148  1.00  0.00              
ATOM    131  C   GLY    33       9.599  11.217   2.767  1.00  0.00              
ATOM    132  O   GLY    33      10.116  12.096   2.082  1.00  0.00              
ATOM    133  N   LYS    34       9.876  11.061   4.057  1.00  0.00              
ATOM    134  CA  LYS    34      10.813  11.949   4.728  1.00  0.00              
ATOM    135  C   LYS    34      12.272  11.632   4.402  1.00  0.00              
ATOM    136  O   LYS    34      12.593  10.559   3.890  1.00  0.00              
ATOM    137  N   VAL    73      13.153  12.585   4.683  1.00  0.00              
ATOM    138  CA  VAL    73      14.580  12.386   4.482  1.00  0.00              
ATOM    139  C   VAL    73      15.109  12.069   5.874  1.00  0.00              
ATOM    140  O   VAL    73      14.751  12.733   6.849  1.00  0.00              
ATOM    141  N   MET    74      15.947  11.049   5.971  1.00  0.00              
ATOM    142  CA  MET    74      16.476  10.658   7.269  1.00  0.00              
ATOM    143  C   MET    74      17.980  10.445   7.236  1.00  0.00              
ATOM    144  O   MET    74      18.555  10.196   6.179  1.00  0.00              
ATOM    145  N   ALA    75      18.608  10.542   8.403  1.00  0.00              
ATOM    146  CA  ALA    75      20.042  10.323   8.515  1.00  0.00              
ATOM    147  C   ALA    75      20.229   9.022   9.294  1.00  0.00              
ATOM    148  O   ALA    75      19.249   8.416   9.737  1.00  0.00              
ATOM    149  N   SER    76      21.475   8.595   9.459  1.00  0.00              
ATOM    150  CA  SER    76      21.785   7.349  10.159  1.00  0.00              
ATOM    151  C   SER    76      21.171   7.189  11.552  1.00  0.00              
ATOM    152  O   SER    76      20.994   6.066  12.026  1.00  0.00              
ATOM    153  N   HIS    77      20.854   8.298  12.211  1.00  0.00              
ATOM    154  CA  HIS    77      20.280   8.230  13.551  1.00  0.00              
ATOM    155  C   HIS    77      18.766   8.404  13.571  1.00  0.00              
ATOM    156  O   HIS    77      18.182   8.728  14.608  1.00  0.00              
ATOM    157  N   TYR    78      18.141   8.183  12.419  1.00  0.00              
ATOM    158  CA  TYR    78      16.697   8.292  12.320  1.00  0.00              
ATOM    159  C   TYR    78      16.116   9.686  12.470  1.00  0.00              
ATOM    160  O   TYR    78      14.919   9.836  12.727  1.00  0.00              
ATOM    161  N   ASP    79      16.946  10.712  12.311  1.00  0.00              
ATOM    162  CA  ASP    79      16.466  12.085  12.429  1.00  0.00              
ATOM    163  C   ASP    79      15.686  12.515  11.194  1.00  0.00              
ATOM    164  O   ASP    79      16.042  12.183  10.067  1.00  0.00              
ATOM    165  N   GLN    80      14.618  13.263  11.421  1.00  0.00              
ATOM    166  CA  GLN    80      13.815  13.768  10.324  1.00  0.00              
ATOM    167  C   GLN    80      14.555  15.012   9.838  1.00  0.00              
ATOM    168  O   GLN    80      14.696  15.973  10.587  1.00  0.00              
ATOM    169  N   ILE    81      15.039  14.987   8.600  1.00  0.00              
ATOM    170  CA  ILE    81      15.773  16.127   8.052  1.00  0.00              
ATOM    171  C   ILE    81      14.830  16.983   7.214  1.00  0.00              
ATOM    172  O   ILE    81      14.224  16.490   6.271  1.00  0.00              
END
