
#######################################################
#                                                     #
#                        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   29 (  116),  selected   29 , name T0311AL333_5-D1
# Molecule2: number of CA atoms   64 (  486),  selected   29 , name T0311_D1.pdb
# PARAMETERS: T0311AL333_5-D1.T0311_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:    29        13 - 71          4.06     4.06
  LCS_AVERAGE:     45.31

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22        13 - 36          1.99     4.94
  LONGEST_CONTINUOUS_SEGMENT:    22        17 - 40          1.97     4.60
  LCS_AVERAGE:     31.30

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17        24 - 40          0.60     4.92
  LCS_AVERAGE:     20.42

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:   64
LCS_GDT     I      13     I      13      9   22   29     7    8   11   20   23   24   25   25   26   26   26   26   27   28   28   28   29   29   29   29 
LCS_GDT     Q      14     Q      14      9   22   29     7   11   18   20   23   24   25   25   26   26   26   26   27   28   28   28   29   29   29   29 
LCS_GDT     E      15     E      15      9   22   29     7    8   18   20   23   24   25   25   26   26   26   26   27   28   28   28   29   29   29   29 
LCS_GDT     S      16     S      16      9   22   29     7    8    9   13   23   24   25   25   26   26   26   26   27   28   28   28   29   29   29   29 
LCS_GDT     L      17     L      17      9   22   29     7    8    9   15   23   24   25   25   26   26   26   26   27   28   28   28   29   29   29   29 
LCS_GDT     D      18     D      18      9   22   29     7    8   12   20   23   24   25   25   26   26   26   26   27   28   28   28   29   29   29   29 
LCS_GDT     E      19     E      19      9   22   29     7    8    9   13   23   24   25   25   26   26   26   26   27   28   28   28   29   29   29   29 
LCS_GDT     L      20     L      20      9   22   29     4    8    9   10   15   24   25   25   26   26   26   26   27   28   28   28   29   29   29   29 
LCS_GDT     N      21     N      21      9   22   29     4    6    9    9   12   15   21   24   26   26   26   26   27   28   28   28   29   29   29   29 
LCS_GDT     L      24     L      24     17   22   29    10   17   18   20   23   24   25   25   26   26   26   26   27   28   28   28   29   29   29   29 
LCS_GDT     R      25     R      25     17   22   29    10   17   18   20   23   24   25   25   26   26   26   26   27   28   28   28   29   29   29   29 
LCS_GDT     E      26     E      26     17   22   29    10   17   18   20   23   24   25   25   26   26   26   26   27   28   28   28   29   29   29   29 
LCS_GDT     F      27     F      27     17   22   29    10   17   18   20   23   24   25   25   26   26   26   26   27   28   28   28   29   29   29   29 
LCS_GDT     A      28     A      28     17   22   29    10   17   18   20   23   24   25   25   26   26   26   26   27   28   28   28   29   29   29   29 
LCS_GDT     R      29     R      29     17   22   29    10   17   18   20   23   24   25   25   26   26   26   26   27   28   28   28   29   29   29   29 
LCS_GDT     A      30     A      30     17   22   29    10   17   18   20   23   24   25   25   26   26   26   26   27   28   28   28   29   29   29   29 
LCS_GDT     M      31     M      31     17   22   29    10   17   18   20   23   24   25   25   26   26   26   26   27   28   28   28   29   29   29   29 
LCS_GDT     E      32     E      32     17   22   29    10   17   18   20   23   24   25   25   26   26   26   26   27   28   28   28   29   29   29   29 
LCS_GDT     I      33     I      33     17   22   29    10   17   18   20   23   24   25   25   26   26   26   26   27   28   28   28   29   29   29   29 
LCS_GDT     A      34     A      34     17   22   29     7   17   18   20   23   24   25   25   26   26   26   26   27   28   28   28   29   29   29   29 
LCS_GDT     P      35     P      35     17   22   29     4   17   18   20   23   24   25   25   26   26   26   26   27   28   28   28   29   29   29   29 
LCS_GDT     S      36     S      36     17   22   29    10   17   18   20   23   24   25   25   26   26   26   26   27   28   28   28   29   29   29   29 
LCS_GDT     T      37     T      37     17   22   29     9   17   18   20   23   24   25   25   26   26   26   26   27   28   28   28   29   29   29   29 
LCS_GDT     A      38     A      38     17   22   29     5   17   18   20   23   24   25   25   26   26   26   26   27   28   28   28   29   29   29   29 
LCS_GDT     S      39     S      39     17   22   29     5   17   18   20   23   24   25   25   26   26   26   26   27   28   28   28   29   29   29   29 
LCS_GDT     R      40     R      40     17   22   29     5   17   18   20   23   24   25   25   26   26   26   26   27   28   28   28   29   29   29   29 
LCS_GDT     N      69     N      69      3    3   29     3    3    3    3    3    3    3    7    7    9    9   10   12   12   12   21   29   29   29   29 
LCS_GDT     L      70     L      70      3    3   29     3    3    3    3    3    3    3    7    7    9    9   24   26   28   28   28   29   29   29   29 
LCS_GDT     Q      71     Q      71      3    3   29     3    3    3    3    3    4    5    7   13   19   25   26   27   28   28   28   29   29   29   29 
LCS_AVERAGE  LCS_A:  32.35  (  20.42   31.30   45.31 )

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     10     17     18     20     23     24     25     25     26     26     26     26     27     28     28     28     29     29     29     29 
GDT PERCENT_CA  15.62  26.56  28.12  31.25  35.94  37.50  39.06  39.06  40.62  40.62  40.62  40.62  42.19  43.75  43.75  43.75  45.31  45.31  45.31  45.31
GDT RMS_LOCAL    0.28   0.60   0.70   0.87   1.44   1.60   1.76   1.76   2.01   2.01   2.01   2.01   3.01   3.48   3.48   3.48   4.06   4.06   4.06   4.06
GDT RMS_ALL_CA   4.81   4.92   4.98   4.97   4.78   4.74   4.75   4.75   4.77   4.77   4.77   4.77   4.24   4.11   4.11   4.11   4.06   4.06   4.06   4.06

#      Molecule1      Molecule2       DISTANCE
LGA    I      13      I      13          1.657
LGA    Q      14      Q      14          1.827
LGA    E      15      E      15          1.702
LGA    S      16      S      16          2.611
LGA    L      17      L      17          2.788
LGA    D      18      D      18          2.326
LGA    E      19      E      19          3.142
LGA    L      20      L      20          3.907
LGA    N      21      N      21          5.423
LGA    L      24      L      24          0.903
LGA    R      25      R      25          1.605
LGA    E      26      E      26          1.410
LGA    F      27      F      27          0.849
LGA    A      28      A      28          0.724
LGA    R      29      R      29          1.052
LGA    A      30      A      30          1.106
LGA    M      31      M      31          0.591
LGA    E      32      E      32          0.552
LGA    I      33      I      33          0.514
LGA    A      34      A      34          0.274
LGA    P      35      P      35          1.019
LGA    S      36      S      36          1.675
LGA    T      37      T      37          1.460
LGA    A      38      A      38          1.694
LGA    S      39      S      39          1.574
LGA    R      40      R      40          1.523
LGA    N      69      N      69         14.963
LGA    L      70      L      70         12.179
LGA    Q      71      Q      71         13.189

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   29   64    4.0     25    1.76    35.156    35.300     1.342

LGA_LOCAL      RMSD =  1.763  Number of atoms =   25  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.746  Number of atoms =   29 
Std_ALL_ATOMS  RMSD =  4.059  (standard rmsd on all 29 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.835743 * X  +   0.464857 * Y  +   0.292304 * Z  +   5.156013
  Y_new =   0.402499 * X  +  -0.880688 * Y  +   0.249767 * Z  +  17.430706
  Z_new =   0.373534 * X  +  -0.091089 * Y  +  -0.923133 * Z  +  19.087975 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.043237    0.098356  [ DEG:  -174.3646      5.6354 ]
  Theta =  -0.382816   -2.758776  [ DEG:   -21.9338   -158.0662 ]
  Phi   =   0.448825   -2.692768  [ DEG:    25.7158   -154.2842 ]
 
# 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: T0311AL333_5-D1                               
REMARK     2: T0311_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0311AL333_5-D1.T0311_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   29   64   4.0   25   1.76  35.300     4.06
REMARK  ---------------------------------------------------------- 
MOLECULE T0311AL333_5-D1
REMARK Aligment from pdb entry: 1d1l_A
ATOM     25  N   ILE    13      32.210   3.268  11.719  1.00  0.00              
ATOM     26  CA  ILE    13      31.431   2.093  12.174  1.00  0.00              
ATOM     27  C   ILE    13      31.325   2.054  13.718  1.00  0.00              
ATOM     28  O   ILE    13      30.239   2.010  14.344  1.00  0.00              
ATOM     29  N   GLN    14      32.471   2.148  14.371  1.00  0.00              
ATOM     30  CA  GLN    14      32.524   2.166  15.835  1.00  0.00              
ATOM     31  C   GLN    14      31.646   3.246  16.478  1.00  0.00              
ATOM     32  O   GLN    14      30.882   2.971  17.384  1.00  0.00              
ATOM     33  N   GLU    15      31.738   4.505  16.067  1.00  0.00              
ATOM     34  CA  GLU    15      30.899   5.511  16.714  1.00  0.00              
ATOM     35  C   GLU    15      29.431   5.244  16.451  1.00  0.00              
ATOM     36  O   GLU    15      28.572   5.539  17.255  1.00  0.00              
ATOM     37  N   SER    16      29.140   4.819  15.223  1.00  0.00              
ATOM     38  CA  SER    16      27.744   4.564  14.853  1.00  0.00              
ATOM     39  C   SER    16      27.153   3.469  15.771  1.00  0.00              
ATOM     40  O   SER    16      26.076   3.604  16.321  1.00  0.00              
ATOM     41  N   LEU    17      27.857   2.330  15.862  1.00  0.00              
ATOM     42  CA  LEU    17      27.368   1.213  16.681  1.00  0.00              
ATOM     43  C   LEU    17      27.206   1.607  18.131  1.00  0.00              
ATOM     44  O   LEU    17      26.268   1.182  18.809  1.00  0.00              
ATOM     45  N   ASP    18      28.152   2.434  18.606  1.00  0.00              
ATOM     46  CA  ASP    18      28.146   2.896  19.984  1.00  0.00              
ATOM     47  C   ASP    18      26.935   3.773  20.294  1.00  0.00              
ATOM     48  O   ASP    18      26.190   3.604  21.263  1.00  0.00              
ATOM     49  N   GLU    19      26.626   4.664  19.393  1.00  0.00              
ATOM     50  CA  GLU    19      25.458   5.449  19.633  1.00  0.00              
ATOM     51  C   GLU    19      24.159   4.728  19.382  1.00  0.00              
ATOM     52  O   GLU    19      23.219   4.966  20.121  1.00  0.00              
ATOM     53  N   LEU    20      24.040   3.934  18.297  1.00  0.00              
ATOM     54  CA  LEU    20      22.801   3.193  18.015  1.00  0.00              
ATOM     55  C   LEU    20      22.697   1.722  18.453  1.00  0.00              
ATOM     56  O   LEU    20      21.655   1.100  18.387  1.00  0.00              
ATOM     57  N   ASN    21      23.742   1.075  18.866  1.00  0.00              
ATOM     58  CA  ASN    21      23.529  -0.325  19.202  1.00  0.00              
ATOM     59  C   ASN    21      23.882  -1.255  18.038  1.00  0.00              
ATOM     60  O   ASN    21      23.573  -0.989  16.902  1.00  0.00              
ATOM     61  N   LEU    24      24.524  -2.354  18.338  1.00  0.00              
ATOM     62  CA  LEU    24      24.943  -3.321  17.325  1.00  0.00              
ATOM     63  C   LEU    24      23.782  -3.863  16.524  1.00  0.00              
ATOM     64  O   LEU    24      23.833  -4.109  15.319  1.00  0.00              
ATOM     65  N   ARG    25      22.690  -4.036  17.217  1.00  0.00              
ATOM     66  CA  ARG    25      21.566  -4.602  16.557  1.00  0.00              
ATOM     67  C   ARG    25      21.041  -3.725  15.428  1.00  0.00              
ATOM     68  O   ARG    25      20.789  -4.125  14.275  1.00  0.00              
ATOM     69  N   GLU    26      20.805  -2.498  15.788  1.00  0.00              
ATOM     70  CA  GLU    26      20.285  -1.603  14.787  1.00  0.00              
ATOM     71  C   GLU    26      21.282  -1.397  13.652  1.00  0.00              
ATOM     72  O   GLU    26      20.953  -1.163  12.497  1.00  0.00              
ATOM     73  N   PHE    27      22.553  -1.418  13.996  1.00  0.00              
ATOM     74  CA  PHE    27      23.558  -1.239  12.949  1.00  0.00              
ATOM     75  C   PHE    27      23.462  -2.380  11.914  1.00  0.00              
ATOM     76  O   PHE    27      23.496  -2.193  10.675  1.00  0.00              
ATOM     77  N   ALA    28      23.371  -3.614  12.455  1.00  0.00              
ATOM     78  CA  ALA    28      23.341  -4.824  11.586  1.00  0.00              
ATOM     79  C   ALA    28      22.140  -4.748  10.642  1.00  0.00              
ATOM     80  O   ALA    28      22.126  -4.975   9.412  1.00  0.00              
ATOM     81  N   ARG    29      21.057  -4.426  11.298  1.00  0.00              
ATOM     82  CA  ARG    29      19.828  -4.289  10.595  1.00  0.00              
ATOM     83  C   ARG    29      19.903  -3.213   9.529  1.00  0.00              
ATOM     84  O   ARG    29      19.546  -3.496   8.426  1.00  0.00              
ATOM     85  N   ALA    30      20.389  -2.002   9.878  1.00  0.00              
ATOM     86  CA  ALA    30      20.603  -0.884   8.971  1.00  0.00              
ATOM     87  C   ALA    30      21.447  -1.290   7.773  1.00  0.00              
ATOM     88  O   ALA    30      21.198  -0.895   6.647  1.00  0.00              
ATOM     89  N   MET    31      22.471  -2.089   7.998  1.00  0.00              
ATOM     90  CA  MET    31      23.308  -2.484   6.864  1.00  0.00              
ATOM     91  C   MET    31      22.860  -3.811   6.234  1.00  0.00              
ATOM     92  O   MET    31      23.375  -4.237   5.210  1.00  0.00              
ATOM     93  N   GLU    32      21.983  -4.526   6.911  1.00  0.00              
ATOM     94  CA  GLU    32      21.596  -5.816   6.411  1.00  0.00              
ATOM     95  C   GLU    32      22.685  -6.879   6.547  1.00  0.00              
ATOM     96  O   GLU    32      22.697  -7.788   5.739  1.00  0.00              
ATOM     97  N   ILE    33      23.608  -6.800   7.542  1.00  0.00              
ATOM     98  CA  ILE    33      24.627  -7.832   7.694  1.00  0.00              
ATOM     99  C   ILE    33      24.322  -8.750   8.863  1.00  0.00              
ATOM    100  O   ILE    33      23.441  -8.482   9.673  1.00  0.00              
ATOM    101  N   ALA    34      25.022  -9.879   8.910  1.00  0.00              
ATOM    102  CA  ALA    34      24.890 -10.817  10.013  1.00  0.00              
ATOM    103  C   ALA    34      25.517 -10.123  11.213  1.00  0.00              
ATOM    104  O   ALA    34      26.674  -9.639  11.141  1.00  0.00              
ATOM    105  N   PRO    35      24.770 -10.029  12.297  1.00  0.00              
ATOM    106  CA  PRO    35      25.157  -9.211  13.454  1.00  0.00              
ATOM    107  C   PRO    35      26.561  -9.319  13.950  1.00  0.00              
ATOM    108  O   PRO    35      27.181  -8.320  14.366  1.00  0.00              
ATOM    109  N   SER    36      27.065 -10.556  13.967  1.00  0.00              
ATOM    110  CA  SER    36      28.366 -10.725  14.582  1.00  0.00              
ATOM    111  C   SER    36      29.503 -10.136  13.756  1.00  0.00              
ATOM    112  O   SER    36      30.585  -9.827  14.278  1.00  0.00              
ATOM    113  N   THR    37      29.256  -9.907  12.475  1.00  0.00              
ATOM    114  CA  THR    37      30.256  -9.269  11.601  1.00  0.00              
ATOM    115  C   THR    37      30.627  -7.859  12.050  1.00  0.00              
ATOM    116  O   THR    37      31.724  -7.382  11.823  1.00  0.00              
ATOM    117  N   ALA    38      29.677  -7.182  12.673  1.00  0.00              
ATOM    118  CA  ALA    38      29.858  -5.833  13.177  1.00  0.00              
ATOM    119  C   ALA    38      30.940  -5.816  14.257  1.00  0.00              
ATOM    120  O   ALA    38      31.967  -5.124  14.236  1.00  0.00              
ATOM    121  N   SER    39      30.664  -6.659  15.231  1.00  0.00              
ATOM    122  CA  SER    39      31.503  -6.809  16.376  1.00  0.00              
ATOM    123  C   SER    39      32.937  -7.165  15.965  1.00  0.00              
ATOM    124  O   SER    39      33.934  -6.592  16.375  1.00  0.00              
ATOM    125  N   ARG    40      33.066  -8.123  15.091  1.00  0.00              
ATOM    126  CA  ARG    40      34.372  -8.473  14.582  1.00  0.00              
ATOM    127  C   ARG    40      35.101  -7.355  13.805  1.00  0.00              
ATOM    128  O   ARG    40      36.317  -7.302  13.839  1.00  0.00              
ATOM    129  N   ASN    69      34.410  -6.510  13.030  1.00  0.00              
ATOM    130  CA  ASN    69      35.100  -5.483  12.249  1.00  0.00              
ATOM    131  C   ASN    69      35.659  -4.399  13.166  1.00  0.00              
ATOM    132  O   ASN    69      36.747  -3.852  12.970  1.00  0.00              
ATOM    133  N   LEU    70      34.874  -4.117  14.196  1.00  0.00              
ATOM    134  CA  LEU    70      35.246  -3.158  15.232  1.00  0.00              
ATOM    135  C   LEU    70      36.522  -3.633  15.966  1.00  0.00              
ATOM    136  O   LEU    70      37.622  -3.066  15.829  1.00  0.00              
ATOM    137  N   GLN    71      36.360  -4.742  16.693  1.00  0.00              
ATOM    138  CA  GLN    71      37.431  -5.332  17.438  1.00  0.00              
ATOM    139  C   GLN    71      38.671  -5.488  16.586  1.00  0.00              
ATOM    140  O   GLN    71      39.762  -5.425  17.112  1.00  0.00              
END
