
#######################################################
#                                                     #
#                        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   31 (  124),  selected   31 , name T0363AL333_4-D1
# Molecule2: number of CA atoms   46 (  372),  selected   31 , name T0363_D1.pdb
# PARAMETERS: T0363AL333_4-D1.T0363_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:    21        13 - 35          4.98     9.65
  LCS_AVERAGE:     42.43

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9        24 - 34          1.94    10.65
  LONGEST_CONTINUOUS_SEGMENT:     9        27 - 35          1.80    10.96
  LCS_AVERAGE:     14.24

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        27 - 34          0.84    10.46
  LCS_AVERAGE:     11.43

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:   46
LCS_GDT     N      11     N      11      3    6   17     0    3    4    5    6    8    9   10   11   12   15   16   18   21   21   21   23   25   26   28 
LCS_GDT     Q      12     Q      12      5    6   17     3    4    5    5    6    8    9   13   15   16   17   18   19   21   22   23   24   25   27   28 
LCS_GDT     I      13     I      13      5    6   21     3    4    5    5    6    8    9   13   15   16   17   18   19   21   22   23   24   25   27   28 
LCS_GDT     N      14     N      14      5    6   21     3    4    5    6    6    8    9   13   15   16   17   18   19   21   22   23   24   25   27   28 
LCS_GDT     I      15     I      15      5    6   21     3    4    5    5    6    8    9   13   15   16   17   18   19   21   22   23   25   25   27   28 
LCS_GDT     E      16     E      16      5    6   21     3    4    5    5    6    8    8   10   12   14   17   18   19   21   22   23   24   25   27   28 
LCS_GDT     I      17     I      17      5    5   21     3    6    8    8    9    9   11   13   15   16   17   18   19   21   22   23   25   25   27   28 
LCS_GDT     A      18     A      18      5    6   21     3    4    8    8    9    9   11   13   15   16   17   18   19   21   22   23   25   25   27   28 
LCS_GDT     Y      19     Y      19      5    6   21     3    6    8    8    9    9   11   13   15   16   17   18   19   21   22   23   25   25   27   28 
LCS_GDT     A      20     A      20      5    6   21     3    6    8    8    9    9   11   13   15   16   17   18   19   21   22   23   25   25   27   28 
LCS_GDT     F      21     F      21      5    6   21     3    4    8    8    9    9   11   13   15   16   17   18   19   21   22   23   25   25   27   28 
LCS_GDT     P      22     P      22      4    6   21     3    4    4    4    6    8    9   13   15   16   17   18   19   21   22   23   25   25   27   28 
LCS_GDT     E      23     E      23      4    6   21     3    4    4    4    6    8    9   11   13   16   17   18   19   21   22   23   25   25   27   28 
LCS_GDT     R      24     R      24      3    9   21     3    3    3    3    5    8    9   12   15   16   17   18   19   21   22   23   25   25   27   28 
LCS_GDT     L      27     L      27      8    9   21     5    7    8    8    8    9    9   10   15   16   17   18   19   21   22   23   25   25   27   28 
LCS_GDT     K      28     K      28      8    9   21     5    7    8    8    8    9    9   10   12   15   17   18   19   21   22   23   25   25   27   28 
LCS_GDT     S      29     S      29      8    9   21     4    7    8    8    8    9    9    9   11   13   15   17   18   20   22   22   25   25   27   28 
LCS_GDT     F      30     F      30      8    9   21     5    7    8    8    8    9    9   10   11   13   15   17   18   21   22   23   25   25   27   28 
LCS_GDT     Q      31     Q      31      8    9   21     5    7    8    8    8    9    9    9   11   13   15   16   18   19   21   22   25   25   26   27 
LCS_GDT     V      32     V      32      8    9   21     5    7    8    8    8    9    9   11   13   15   15   17   19   21   22   23   25   25   27   28 
LCS_GDT     D      33     D      33      8    9   21     3    7    8    8    8    9   11   12   13   15   15   17   19   21   22   23   25   25   27   28 
LCS_GDT     E      34     E      34      8    9   21     3    6    8    8    9    9   11   13   15   16   17   18   19   21   22   23   25   25   27   28 
LCS_GDT     G      35     G      35      5    9   21     3    6    8    8    9    9   11   13   15   16   17   18   19   21   22   23   25   25   27   28 
LCS_GDT     I      36     I      36      5    6   18     3    6    8    8    9    9   11   13   15   16   17   18   19   21   22   23   25   25   27   28 
LCS_GDT     T      37     T      37      5    6   16     3    4    5    8    9    9   11   12   14   15   17   17   19   21   22   23   25   25   27   28 
LCS_GDT     V      38     V      38      5    6   16     3    4    5    6    6    9   11   12   13   14   15   17   18   21   21   23   25   25   27   28 
LCS_GDT     Q      39     Q      39      3    6   16     3    3    3    4    6    9   11   12   13   14   14   15   18   19   21   22   25   25   27   28 
LCS_GDT     T      40     T      40      3    3   16     3    3    3    3    3    4    9   12   13   14   14   15   18   19   21   22   25   25   27   28 
LCS_GDT     A      41     A      41      3    3   16     0    3    3    3    3    4    4    6   11   12   13   15   18   19   21   22   25   25   27   28 
LCS_GDT     I      42     I      42      3    3   16     0    3    3    3    3    3    7   10   11   12   14   15   18   19   21   22   25   25   26   28 
LCS_GDT     T      43     T      43      3    3   16     0    3    3    3    3    4    7   10   11   12   13   14   15   19   19   20   23   25   26   27 
LCS_AVERAGE  LCS_A:  22.70  (  11.43   14.24   42.43 )

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      7      8      8      9      9     11     13     15     16     17     18     19     21     22     23     25     25     27     28 
GDT PERCENT_CA  10.87  15.22  17.39  17.39  19.57  19.57  23.91  28.26  32.61  34.78  36.96  39.13  41.30  45.65  47.83  50.00  54.35  54.35  58.70  60.87
GDT RMS_LOCAL    0.34   0.54   0.84   0.84   1.30   1.30   2.04   3.25   3.49   3.64   3.82   4.01   4.19   4.60   4.96   5.22   6.31   5.60   6.38   6.70
GDT RMS_ALL_CA  10.51  10.56  10.46  10.46   8.05   8.05   8.55   8.27   8.42   8.56   8.63   8.61   8.41   8.22   8.95   8.31   8.36   8.31   7.72   7.55

#      Molecule1      Molecule2       DISTANCE
LGA    N      11      N      11          8.348
LGA    Q      12      Q      12          3.732
LGA    I      13      I      13          3.782
LGA    N      14      N      14          2.803
LGA    I      15      I      15          3.926
LGA    E      16      E      16          6.364
LGA    I      17      I      17          3.749
LGA    A      18      A      18          3.999
LGA    Y      19      Y      19          1.888
LGA    A      20      A      20          2.806
LGA    F      21      F      21          1.661
LGA    P      22      P      22          3.807
LGA    E      23      E      23          5.768
LGA    R      24      R      24          4.301
LGA    L      27      L      27          4.593
LGA    K      28      K      28          6.158
LGA    S      29      S      29          9.636
LGA    F      30      F      30          9.095
LGA    Q      31      Q      31         12.282
LGA    V      32      V      32          8.843
LGA    D      33      D      33          9.203
LGA    E      34      E      34          3.427
LGA    G      35      G      35          3.134
LGA    I      36      I      36          3.412
LGA    T      37      T      37          6.421
LGA    V      38      V      38          8.592
LGA    Q      39      Q      39         11.329
LGA    T      40      T      40         13.351
LGA    A      41      A      41         13.304
LGA    I      42      I      42         16.005
LGA    T      43      T      43         22.121

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   31   46    4.0     13    3.25    27.717    24.392     0.388

LGA_LOCAL      RMSD =  3.254  Number of atoms =   13  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  8.420  Number of atoms =   31 
Std_ALL_ATOMS  RMSD =  7.432  (standard rmsd on all 31 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.362418 * X  +  -0.034554 * Y  +   0.931375 * Z  +  17.895945
  Y_new =  -0.911484 * X  +  -0.221741 * Y  +   0.346451 * Z  +  14.195814
  Z_new =   0.194553 * X  +  -0.974493 * Y  +  -0.111859 * Z  +   7.488457 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.685083    1.456510  [ DEG:   -96.5481     83.4519 ]
  Theta =  -0.195802   -2.945791  [ DEG:   -11.2186   -168.7814 ]
  Phi   =  -1.192349    1.949243  [ DEG:   -68.3166    111.6834 ]
 
# 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: T0363AL333_4-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363AL333_4-D1.T0363_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   31   46   4.0   13   3.25  24.392     7.43
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL333_4-D1
REMARK Aligment from pdb entry: 1jt8_A
ATOM     41  N   ASN    11      11.532   0.931   4.145  1.00  0.00              
ATOM     42  CA  ASN    11      11.817  -0.522   4.369  1.00  0.00              
ATOM     43  C   ASN    11      12.848  -0.683   5.493  1.00  0.00              
ATOM     44  O   ASN    11      12.633  -1.427   6.434  1.00  0.00              
ATOM     45  N   GLN    12      13.963   0.008   5.401  1.00  0.00              
ATOM     46  CA  GLN    12      15.015  -0.097   6.460  1.00  0.00              
ATOM     47  C   GLN    12      15.158   1.247   7.197  1.00  0.00              
ATOM     48  O   GLN    12      16.201   1.548   7.752  1.00  0.00              
ATOM     49  N   ILE    13      14.113   2.053   7.212  1.00  0.00              
ATOM     50  CA  ILE    13      14.170   3.379   7.911  1.00  0.00              
ATOM     51  C   ILE    13      15.203   4.297   7.235  1.00  0.00              
ATOM     52  O   ILE    13      15.909   3.898   6.325  1.00  0.00              
ATOM     53  N   ASN    14      15.290   5.529   7.681  1.00  0.00              
ATOM     54  CA  ASN    14      16.270   6.490   7.084  1.00  0.00              
ATOM     55  C   ASN    14      17.147   7.091   8.191  1.00  0.00              
ATOM     56  O   ASN    14      16.916   6.873   9.369  1.00  0.00              
ATOM     57  N   ILE    15      18.151   7.846   7.817  1.00  0.00              
ATOM     58  CA  ILE    15      19.053   8.468   8.820  1.00  0.00              
ATOM     59  C   ILE    15      18.790   9.984   8.820  1.00  0.00              
ATOM     60  O   ILE    15      18.210  10.505   7.881  1.00  0.00              
ATOM     61  N   GLU    16      19.182  10.708   9.855  1.00  0.00              
ATOM     62  CA  GLU    16      18.885  12.200   9.836  1.00  0.00              
ATOM     63  C   GLU    16      20.178  12.975  10.037  1.00  0.00              
ATOM     64  O   GLU    16      20.838  12.785  11.034  1.00  0.00              
ATOM     65  N   ILE    17      23.615  19.139   6.837  1.00  0.00              
ATOM     66  CA  ILE    17      24.559  19.302   5.692  1.00  0.00              
ATOM     67  C   ILE    17      25.407  20.568   5.847  1.00  0.00              
ATOM     68  O   ILE    17      24.999  21.559   6.442  1.00  0.00              
ATOM     69  N   ALA    18      26.585  20.513   5.283  1.00  0.00              
ATOM     70  CA  ALA    18      27.533  21.663   5.320  1.00  0.00              
ATOM     71  C   ALA    18      28.300  21.733   3.991  1.00  0.00              
ATOM     72  O   ALA    18      28.733  20.714   3.460  1.00  0.00              
ATOM     73  N   TYR    19      28.486  22.930   3.468  1.00  0.00              
ATOM     74  CA  TYR    19      29.244  23.115   2.187  1.00  0.00              
ATOM     75  C   TYR    19      29.043  24.541   1.657  1.00  0.00              
ATOM     76  O   TYR    19      27.929  24.980   1.431  1.00  0.00              
ATOM     77  N   ALA    20      30.124  25.256   1.447  1.00  0.00              
ATOM     78  CA  ALA    20      30.030  26.654   0.917  1.00  0.00              
ATOM     79  C   ALA    20      30.553  26.695  -0.528  1.00  0.00              
ATOM     80  O   ALA    20      30.117  27.508  -1.323  1.00  0.00              
ATOM     81  N   PHE    21      31.486  25.827  -0.868  1.00  0.00              
ATOM     82  CA  PHE    21      32.048  25.810  -2.258  1.00  0.00              
ATOM     83  C   PHE    21      30.911  25.643  -3.276  1.00  0.00              
ATOM     84  O   PHE    21      30.742  26.460  -4.163  1.00  0.00              
ATOM     85  N   PRO    22      30.129  24.594  -3.148  1.00  0.00              
ATOM     86  CA  PRO    22      28.997  24.368  -4.098  1.00  0.00              
ATOM     87  C   PRO    22      29.500  23.627  -5.339  1.00  0.00              
ATOM     88  O   PRO    22      29.664  24.210  -6.395  1.00  0.00              
ATOM     89  N   GLU    23      29.739  22.340  -5.217  1.00  0.00              
ATOM     90  CA  GLU    23      30.226  21.539  -6.383  1.00  0.00              
ATOM     91  C   GLU    23      29.219  20.419  -6.691  1.00  0.00              
ATOM     92  O   GLU    23      29.594  19.312  -7.043  1.00  0.00              
ATOM     93  N   ARG    24      27.937  20.704  -6.554  1.00  0.00              
ATOM     94  CA  ARG    24      26.872  19.680  -6.825  1.00  0.00              
ATOM     95  C   ARG    24      26.886  18.572  -5.748  1.00  0.00              
ATOM     96  O   ARG    24      26.103  17.640  -5.810  1.00  0.00              
ATOM     97  N   LEU    27      27.759  18.665  -4.765  1.00  0.00              
ATOM     98  CA  LEU    27      27.815  17.624  -3.691  1.00  0.00              
ATOM     99  C   LEU    27      28.071  18.300  -2.333  1.00  0.00              
ATOM    100  O   LEU    27      28.613  19.389  -2.260  1.00  0.00              
ATOM    101  N   LYS    28      27.669  17.661  -1.262  1.00  0.00              
ATOM    102  CA  LYS    28      27.860  18.242   0.108  1.00  0.00              
ATOM    103  C   LYS    28      28.239  17.153   1.098  1.00  0.00              
ATOM    104  O   LYS    28      28.169  15.970   0.807  1.00  0.00              
ATOM    105  N   SER    29      28.636  17.549   2.273  1.00  0.00              
ATOM    106  CA  SER    29      29.029  16.536   3.322  1.00  0.00              
ATOM    107  C   SER    29      28.044  16.559   4.494  1.00  0.00              
ATOM    108  O   SER    29      27.759  17.604   5.056  1.00  0.00              
ATOM    109  N   PHE    30      27.513  15.409   4.862  1.00  0.00              
ATOM    110  CA  PHE    30      26.540  15.353   5.983  1.00  0.00              
ATOM    111  C   PHE    30      27.013  14.447   7.118  1.00  0.00              
ATOM    112  O   PHE    30      27.638  13.417   6.923  1.00  0.00              
ATOM    113  N   GLN    31      26.613  14.819   8.298  1.00  0.00              
ATOM    114  CA  GLN    31      26.892  14.018   9.531  1.00  0.00              
ATOM    115  C   GLN    31      25.512  13.693  10.086  1.00  0.00              
ATOM    116  O   GLN    31      24.639  14.546  10.070  1.00  0.00              
ATOM    117  N   VAL    32      25.253  12.480  10.496  1.00  0.00              
ATOM    118  CA  VAL    32      23.861  12.183  10.929  1.00  0.00              
ATOM    119  C   VAL    32      23.759  11.288  12.160  1.00  0.00              
ATOM    120  O   VAL    32      24.644  10.515  12.493  1.00  0.00              
ATOM    121  N   ASP    33      22.603  11.355  12.768  1.00  0.00              
ATOM    122  CA  ASP    33      22.265  10.521  13.913  1.00  0.00              
ATOM    123  C   ASP    33      21.552   9.300  13.344  1.00  0.00              
ATOM    124  O   ASP    33      21.418   9.147  12.114  1.00  0.00              
ATOM    125  N   GLU    34      21.168   8.408  14.214  1.00  0.00              
ATOM    126  CA  GLU    34      20.613   7.108  13.779  1.00  0.00              
ATOM    127  C   GLU    34      21.854   6.307  13.306  1.00  0.00              
ATOM    128  O   GLU    34      21.765   5.341  12.572  1.00  0.00              
ATOM    129  N   GLY    35      23.025   6.717  13.822  1.00  0.00              
ATOM    130  CA  GLY    35      24.330   6.033  13.546  1.00  0.00              
ATOM    131  C   GLY    35      24.794   6.142  12.088  1.00  0.00              
ATOM    132  O   GLY    35      25.059   5.124  11.473  1.00  0.00              
ATOM    133  N   ILE    36      24.937   7.329  11.515  1.00  0.00              
ATOM    134  CA  ILE    36      25.433   7.365  10.102  1.00  0.00              
ATOM    135  C   ILE    36      26.319   8.576   9.800  1.00  0.00              
ATOM    136  O   ILE    36      26.185   9.641  10.373  1.00  0.00              
ATOM    137  N   THR    37      27.166   8.402   8.821  1.00  0.00              
ATOM    138  CA  THR    37      28.052   9.502   8.317  1.00  0.00              
ATOM    139  C   THR    37      28.094   9.315   6.803  1.00  0.00              
ATOM    140  O   THR    37      28.482   8.260   6.311  1.00  0.00              
ATOM    141  N   VAL    38      27.622  10.279   6.055  1.00  0.00              
ATOM    142  CA  VAL    38      27.560  10.078   4.580  1.00  0.00              
ATOM    143  C   VAL    38      27.785  11.359   3.789  1.00  0.00              
ATOM    144  O   VAL    38      27.651  12.459   4.293  1.00  0.00              
ATOM    145  N   GLN    39      28.046  11.197   2.518  1.00  0.00              
ATOM    146  CA  GLN    39      28.186  12.375   1.614  1.00  0.00              
ATOM    147  C   GLN    39      26.816  12.513   0.936  1.00  0.00              
ATOM    148  O   GLN    39      26.291  11.551   0.400  1.00  0.00              
ATOM    149  N   THR    40      26.192  13.657   1.016  1.00  0.00              
ATOM    150  CA  THR    40      24.817  13.795   0.445  1.00  0.00              
ATOM    151  C   THR    40      24.835  14.374  -0.964  1.00  0.00              
ATOM    152  O   THR    40      25.621  15.246  -1.291  1.00  0.00              
ATOM    153  N   ALA    41      23.944  13.879  -1.795  1.00  0.00              
ATOM    154  CA  ALA    41      23.847  14.362  -3.200  1.00  0.00              
ATOM    155  C   ALA    41      22.440  14.913  -3.463  1.00  0.00              
ATOM    156  O   ALA    41      21.465  14.467  -2.880  1.00  0.00              
ATOM    157  N   ILE    42      22.336  15.881  -4.338  1.00  0.00              
ATOM    158  CA  ILE    42      21.007  16.484  -4.659  1.00  0.00              
ATOM    159  C   ILE    42      20.789  16.447  -6.188  1.00  0.00              
ATOM    160  O   ILE    42      21.743  16.387  -6.944  1.00  0.00              
ATOM    161  N   THR    43      19.535  16.481  -6.598  1.00  0.00              
ATOM    162  CA  THR    43      19.162  16.449  -8.032  1.00  0.00              
ATOM    163  C   THR    43      19.447  17.800  -8.708  1.00  0.00              
ATOM    164  O   THR    43      19.718  18.786  -8.052  1.00  0.00              
END
