
#######################################################
#                                                     #
#                        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   32 (  128),  selected   32 , name T0374AL509_1
# Molecule2: number of CA atoms  160 ( 2486),  selected   32 , name T0374.pdb
# PARAMETERS: T0374AL509_1.T0374.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:    32        58 - 158         3.84     3.84
  LCS_AVERAGE:     20.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22       115 - 158         0.71     4.07
  LCS_AVERAGE:     10.90

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22       115 - 158         0.71     4.07
  LCS_AVERAGE:     10.41

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:  160
LCS_GDT     D      58     D      58      7    7   32    12   24   29   29   29   29   29   29   29   29   29   29   29   30   30   30   30   31   31   31 
LCS_GDT     G      59     G      59      7    7   32     6   24   29   29   29   29   29   29   29   29   29   29   29   30   30   30   30   31   31   31 
LCS_GDT     Q      60     Q      60      7    7   32    13   24   29   29   29   29   29   29   29   29   29   29   29   30   30   30   30   31   31   31 
LCS_GDT     V      61     V      61      7    7   32    13   24   29   29   29   29   29   29   29   29   29   29   29   30   30   30   30   31   31   31 
LCS_GDT     L      62     L      62      7    7   32    13   24   29   29   29   29   29   29   29   29   29   29   29   30   30   30   30   31   31   31 
LCS_GDT     G      63     G      63      7    7   32    14   24   29   29   29   29   29   29   29   29   29   29   29   30   30   30   30   31   31   31 
LCS_GDT     F      64     F      64      7    7   32     3   24   29   29   29   29   29   29   29   29   29   29   29   30   30   30   30   31   31   31 
LCS_GDT     E     106     E     106      0    0   32     0    0    0    0    0    5    7    7    8    8    8    8    8    8   14   18   30   30   30   31 
LCS_GDT     K     109     K     109      0    4   32     0    2    4    4    4    4    6    8   14   21   21   22   22   24   26   27   30   31   31   31 
LCS_GDT     A     110     A     110      0   21   32     0    2    4    4    4    6   14   16   20   21   21   25   27   30   30   30   30   31   31   31 
LCS_GDT     I     115     I     115     22   22   32     7   17   29   29   29   29   29   29   29   29   29   29   29   30   30   30   30   31   31   31 
LCS_GDT     S     116     S     116     22   22   32     8   24   29   29   29   29   29   29   29   29   29   29   29   30   30   30   30   31   31   31 
LCS_GDT     C     117     C     117     22   22   32    13   24   29   29   29   29   29   29   29   29   29   29   29   30   30   30   30   31   31   31 
LCS_GDT     F     118     F     118     22   22   32    14   24   29   29   29   29   29   29   29   29   29   29   29   30   30   30   30   31   31   31 
LCS_GDT     N     119     N     119     22   22   32    10   21   29   29   29   29   29   29   29   29   29   29   29   30   30   30   30   31   31   31 
LCS_GDT     A     120     A     120     22   22   32    10   20   29   29   29   29   29   29   29   29   29   29   29   30   30   30   30   31   31   31 
LCS_GDT     N     121     N     121     22   22   32    14   24   29   29   29   29   29   29   29   29   29   29   29   30   30   30   30   31   31   31 
LCS_GDT     A     122     A     122     22   22   32    14   24   29   29   29   29   29   29   29   29   29   29   29   30   30   30   30   31   31   31 
LCS_GDT     A     123     A     123     22   22   32    14   24   29   29   29   29   29   29   29   29   29   29   29   30   30   30   30   31   31   31 
LCS_GDT     G     124     G     124     22   22   32    14   24   29   29   29   29   29   29   29   29   29   29   29   30   30   30   30   31   31   31 
LCS_GDT     L     125     L     125     22   22   32    14   24   29   29   29   29   29   29   29   29   29   29   29   30   30   30   30   31   31   31 
LCS_GDT     L     126     L     126     22   22   32    14   24   29   29   29   29   29   29   29   29   29   29   29   30   30   30   30   31   31   31 
LCS_GDT     L     127     L     127     22   22   32    14   24   29   29   29   29   29   29   29   29   29   29   29   30   30   30   30   31   31   31 
LCS_GDT     Y     128     Y     128     22   22   32    14   24   29   29   29   29   29   29   29   29   29   29   29   30   30   30   30   31   31   31 
LCS_GDT     T     129     T     129     22   22   32    14   24   29   29   29   29   29   29   29   29   29   29   29   30   30   30   30   31   31   31 
LCS_GDT     Q     130     Q     130     22   22   32    14   24   29   29   29   29   29   29   29   29   29   29   29   30   30   30   30   31   31   31 
LCS_GDT     L     131     L     131     22   22   32    14   24   29   29   29   29   29   29   29   29   29   29   29   30   30   30   30   31   31   31 
LCS_GDT     G     132     G     132     22   22   32    14   24   29   29   29   29   29   29   29   29   29   29   29   30   30   30   30   31   31   31 
LCS_GDT     Y     133     Y     133     22   22   32    14   24   29   29   29   29   29   29   29   29   29   29   29   30   30   30   30   31   31   31 
LCS_GDT     K     156     K     156     22   22   32    12   24   29   29   29   29   29   29   29   29   29   29   29   30   30   30   30   31   31   31 
LCS_GDT     P     157     P     157     22   22   32     3   18   29   29   29   29   29   29   29   29   29   29   29   30   30   30   30   31   31   31 
LCS_GDT     L     158     L     158     22   22   32     3   10   29   29   29   29   29   29   29   29   29   29   29   30   30   30   30   31   31   31 
LCS_AVERAGE  LCS_A:  13.77  (  10.41   10.90   20.00 )

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     14     24     29     29     29     29     29     29     29     29     29     29     29     30     30     30     30     31     31     31 
GDT PERCENT_CA   8.75  15.00  18.13  18.13  18.13  18.13  18.13  18.13  18.13  18.13  18.13  18.13  18.13  18.75  18.75  18.75  18.75  19.38  19.38  19.38
GDT RMS_LOCAL    0.20   0.56   0.77   0.77   0.77   0.77   0.77   0.77   0.77   0.77   0.77   0.77   0.77   2.01   2.01   2.01   2.01   3.04   3.04   3.04
GDT RMS_ALL_CA   3.90   3.96   3.98   3.98   3.98   3.98   3.98   3.98   3.98   3.98   3.98   3.98   3.98   3.91   3.91   3.91   3.91   3.91   3.91   3.91

#      Molecule1      Molecule2       DISTANCE
LGA    D      58      D      58          0.477
LGA    G      59      G      59          0.773
LGA    Q      60      Q      60          0.728
LGA    V      61      V      61          0.852
LGA    L      62      L      62          0.550
LGA    G      63      G      63          1.062
LGA    F      64      F      64          0.787
LGA    E     106      E     106         13.640
LGA    K     109      K     109         13.932
LGA    A     110      A     110         10.508
LGA    I     115      I     115          1.245
LGA    S     116      S     116          0.899
LGA    C     117      C     117          0.550
LGA    F     118      F     118          0.229
LGA    N     119      N     119          1.167
LGA    A     120      A     120          1.459
LGA    N     121      N     121          0.701
LGA    A     122      A     122          0.482
LGA    A     123      A     123          0.531
LGA    G     124      G     124          0.480
LGA    L     125      L     125          0.337
LGA    L     126      L     126          0.217
LGA    L     127      L     127          0.438
LGA    Y     128      Y     128          0.342
LGA    T     129      T     129          0.312
LGA    Q     130      Q     130          0.374
LGA    L     131      L     131          0.638
LGA    G     132      G     132          0.681
LGA    Y     133      Y     133          0.440
LGA    K     156      K     156          0.444
LGA    P     157      P     157          1.052
LGA    L     158      L     158          1.534

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   32  160    4.0     29    0.77    17.500    16.137     3.350

LGA_LOCAL      RMSD =  0.766  Number of atoms =   29  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.983  Number of atoms =   32 
Std_ALL_ATOMS  RMSD =  3.842  (standard rmsd on all 32 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.196659 * X  +   0.192344 * Y  +   0.961420 * Z  + -46.544575
  Y_new =   0.687888 * X  +  -0.725803 * Y  +   0.004498 * Z  +  52.071205
  Z_new =   0.698667 * X  +   0.660465 * Y  +  -0.275047 * Z  + -31.469177 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.965398   -1.176195  [ DEG:   112.6090    -67.3910 ]
  Theta =  -0.773533   -2.368060  [ DEG:   -44.3202   -135.6798 ]
  Phi   =   1.292336   -1.849257  [ DEG:    74.0454   -105.9546 ]
 
# 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: T0374AL509_1                                  
REMARK     2: T0374.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0374AL509_1.T0374.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   32  160   4.0   29   0.77  16.137     3.84
REMARK  ---------------------------------------------------------- 
MOLECULE T0374AL509_1
REMARK Aligment from pdb entry: 1tiq_A
ATOM      1  N   ASP    58      19.548  30.855   1.975  1.00  0.00              
ATOM      2  CA  ASP    58      19.268  31.924   1.025  1.00  0.00              
ATOM      3  C   ASP    58      17.865  31.793   0.433  1.00  0.00              
ATOM      4  O   ASP    58      17.658  32.045  -0.751  1.00  0.00              
ATOM      5  N   GLY    59      16.913  31.398   1.278  1.00  0.00              
ATOM      6  CA  GLY    59      15.510  31.233   0.889  1.00  0.00              
ATOM      7  C   GLY    59      15.245  30.000   0.029  1.00  0.00              
ATOM      8  O   GLY    59      14.123  29.788  -0.428  1.00  0.00              
ATOM      9  N   GLN    60      16.275  29.188  -0.186  1.00  0.00              
ATOM     10  CA  GLN    60      16.139  27.973  -0.988  1.00  0.00              
ATOM     11  C   GLN    60      16.119  26.720  -0.116  1.00  0.00              
ATOM     12  O   GLN    60      16.948  26.571   0.777  1.00  0.00              
ATOM     13  N   VAL    61      15.165  25.826  -0.376  1.00  0.00              
ATOM     14  CA  VAL    61      15.047  24.587   0.389  1.00  0.00              
ATOM     15  C   VAL    61      16.290  23.722   0.201  1.00  0.00              
ATOM     16  O   VAL    61      16.638  23.340  -0.921  1.00  0.00              
ATOM     17  N   LEU    62      16.953  23.401   1.309  1.00  0.00              
ATOM     18  CA  LEU    62      18.178  22.612   1.265  1.00  0.00              
ATOM     19  C   LEU    62      18.073  21.202   1.843  1.00  0.00              
ATOM     20  O   LEU    62      18.942  20.371   1.599  1.00  0.00              
ATOM     21  N   GLY    63      17.025  20.928   2.611  1.00  0.00              
ATOM     22  CA  GLY    63      16.885  19.602   3.184  1.00  0.00              
ATOM     23  C   GLY    63      15.843  19.559   4.278  1.00  0.00              
ATOM     24  O   GLY    63      15.142  20.538   4.510  1.00  0.00              
ATOM     25  N   PHE    64      15.714  18.421   4.947  1.00  0.00              
ATOM     26  CA  PHE    64      14.731  18.321   6.015  1.00  0.00              
ATOM     27  C   PHE    64      15.104  17.251   7.022  1.00  0.00              
ATOM     28  O   PHE    64      16.006  16.442   6.795  1.00  0.00              
ATOM     29  N   GLU   106      13.604   9.953  18.274  1.00  0.00              
ATOM     30  CA  GLU   106      14.271   9.355  17.130  1.00  0.00              
ATOM     31  C   GLU   106      14.426  10.340  15.973  1.00  0.00              
ATOM     32  O   GLU   106      13.522  11.129  15.697  1.00  0.00              
ATOM     33  N   LYS   109      18.894  20.649  15.916  1.00  0.00              
ATOM     34  CA  LYS   109      17.508  21.042  16.104  1.00  0.00              
ATOM     35  C   LYS   109      16.802  19.834  16.714  1.00  0.00              
ATOM     36  O   LYS   109      15.964  19.983  17.604  1.00  0.00              
ATOM     37  N   ALA   110      17.141  18.637  16.234  1.00  0.00              
ATOM     38  CA  ALA   110      16.537  17.410  16.770  1.00  0.00              
ATOM     39  C   ALA   110      16.934  17.258  18.234  1.00  0.00              
ATOM     40  O   ALA   110      16.137  16.810  19.057  1.00  0.00              
ATOM     41  N   ILE   115      18.988   6.812  16.414  1.00  0.00              
ATOM     42  CA  ILE   115      18.659   6.697  15.005  1.00  0.00              
ATOM     43  C   ILE   115      19.179   5.377  14.466  1.00  0.00              
ATOM     44  O   ILE   115      20.031   4.726  15.076  1.00  0.00              
ATOM     45  N   SER   116      18.648   4.991  13.317  1.00  0.00              
ATOM     46  CA  SER   116      19.082   3.776  12.671  1.00  0.00              
ATOM     47  C   SER   116      19.765   4.221  11.390  1.00  0.00              
ATOM     48  O   SER   116      19.274   5.138  10.722  1.00  0.00              
ATOM     49  N   CYS   117      20.903   3.613  11.057  1.00  0.00              
ATOM     50  CA  CYS   117      21.616   3.967   9.825  1.00  0.00              
ATOM     51  C   CYS   117      22.262   2.767   9.144  1.00  0.00              
ATOM     52  O   CYS   117      22.963   1.977   9.771  1.00  0.00              
ATOM     53  N   PHE   118      21.992   2.631   7.849  1.00  0.00              
ATOM     54  CA  PHE   118      22.537   1.538   7.042  1.00  0.00              
ATOM     55  C   PHE   118      24.057   1.500   7.187  1.00  0.00              
ATOM     56  O   PHE   118      24.736   2.506   6.967  1.00  0.00              
ATOM     57  N   ASN   119      24.591   0.341   7.555  1.00  0.00              
ATOM     58  CA  ASN   119      26.030   0.200   7.760  1.00  0.00              
ATOM     59  C   ASN   119      26.891   0.657   6.575  1.00  0.00              
ATOM     60  O   ASN   119      28.024   1.085   6.774  1.00  0.00              
ATOM     61  N   ALA   120      26.351   0.581   5.357  1.00  0.00              
ATOM     62  CA  ALA   120      27.089   0.992   4.158  1.00  0.00              
ATOM     63  C   ALA   120      27.157   2.513   3.987  1.00  0.00              
ATOM     64  O   ALA   120      27.954   3.018   3.198  1.00  0.00              
ATOM     65  N   ASN   121      26.311   3.240   4.705  1.00  0.00              
ATOM     66  CA  ASN   121      26.305   4.693   4.594  1.00  0.00              
ATOM     67  C   ASN   121      27.422   5.279   5.466  1.00  0.00              
ATOM     68  O   ASN   121      27.173   5.853   6.528  1.00  0.00              
ATOM     69  N   ALA   122      28.660   5.124   5.000  1.00  0.00              
ATOM     70  CA  ALA   122      29.830   5.610   5.721  1.00  0.00              
ATOM     71  C   ALA   122      29.827   7.110   5.958  1.00  0.00              
ATOM     72  O   ALA   122      30.273   7.562   7.008  1.00  0.00              
ATOM     73  N   ALA   123      29.341   7.878   4.988  1.00  0.00              
ATOM     74  CA  ALA   123      29.294   9.331   5.140  1.00  0.00              
ATOM     75  C   ALA   123      28.403   9.706   6.320  1.00  0.00              
ATOM     76  O   ALA   123      28.784  10.520   7.165  1.00  0.00              
ATOM     77  N   GLY   124      27.216   9.113   6.394  1.00  0.00              
ATOM     78  CA  GLY   124      26.310   9.446   7.495  1.00  0.00              
ATOM     79  C   GLY   124      26.830   8.979   8.853  1.00  0.00              
ATOM     80  O   GLY   124      26.658   9.673   9.858  1.00  0.00              
ATOM     81  N   LEU   125      27.450   7.804   8.886  1.00  0.00              
ATOM     82  CA  LEU   125      27.992   7.271  10.134  1.00  0.00              
ATOM     83  C   LEU   125      29.067   8.207  10.677  1.00  0.00              
ATOM     84  O   LEU   125      29.069   8.546  11.864  1.00  0.00              
ATOM     85  N   LEU   126      29.959   8.648   9.797  1.00  0.00              
ATOM     86  CA  LEU   126      31.038   9.554  10.180  1.00  0.00              
ATOM     87  C   LEU   126      30.474  10.875  10.704  1.00  0.00              
ATOM     88  O   LEU   126      30.995  11.439  11.662  1.00  0.00              
ATOM     89  N   LEU   127      29.421  11.366  10.057  1.00  0.00              
ATOM     90  CA  LEU   127      28.763  12.606  10.469  1.00  0.00              
ATOM     91  C   LEU   127      28.193  12.431  11.879  1.00  0.00              
ATOM     92  O   LEU   127      28.476  13.232  12.775  1.00  0.00              
ATOM     93  N   TYR   128      27.412  11.374  12.082  1.00  0.00              
ATOM     94  CA  TYR   128      26.815  11.121  13.395  1.00  0.00              
ATOM     95  C   TYR   128      27.861  10.998  14.510  1.00  0.00              
ATOM     96  O   TYR   128      27.672  11.531  15.606  1.00  0.00              
ATOM     97  N   THR   129      28.953  10.285  14.244  1.00  0.00              
ATOM     98  CA  THR   129      30.004  10.123  15.252  1.00  0.00              
ATOM     99  C   THR   129      30.612  11.477  15.604  1.00  0.00              
ATOM    100  O   THR   129      30.945  11.742  16.762  1.00  0.00              
ATOM    101  N   GLN   130      30.756  12.335  14.603  1.00  0.00              
ATOM    102  CA  GLN   130      31.304  13.665  14.835  1.00  0.00              
ATOM    103  C   GLN   130      30.318  14.428  15.723  1.00  0.00              
ATOM    104  O   GLN   130      30.722  15.216  16.581  1.00  0.00              
ATOM    105  N   LEU   131      29.025  14.181  15.529  1.00  0.00              
ATOM    106  CA  LEU   131      28.009  14.854  16.324  1.00  0.00              
ATOM    107  C   LEU   131      27.816  14.245  17.722  1.00  0.00              
ATOM    108  O   LEU   131      26.916  14.651  18.455  1.00  0.00              
ATOM    109  N   GLY   132      28.645  13.272  18.084  1.00  0.00              
ATOM    110  CA  GLY   132      28.549  12.687  19.411  1.00  0.00              
ATOM    111  C   GLY   132      27.768  11.398  19.583  1.00  0.00              
ATOM    112  O   GLY   132      27.628  10.897  20.705  1.00  0.00              
ATOM    113  N   TYR   133      27.256  10.852  18.488  1.00  0.00              
ATOM    114  CA  TYR   133      26.502   9.603  18.555  1.00  0.00              
ATOM    115  C   TYR   133      27.450   8.406  18.545  1.00  0.00              
ATOM    116  O   TYR   133      28.528   8.476  17.961  1.00  0.00              
ATOM    117  N   LYS   156      22.814   8.717  21.823  1.00  0.00              
ATOM    118  CA  LYS   156      23.512   9.621  22.713  1.00  0.00              
ATOM    119  C   LYS   156      22.586   9.935  23.876  1.00  0.00              
ATOM    120  O   LYS   156      21.386  10.161  23.694  1.00  0.00              
ATOM    121  N   PRO   157      23.153   9.930  25.075  1.00  0.00              
ATOM    122  CA  PRO   157      22.392  10.227  26.273  1.00  0.00              
ATOM    123  C   PRO   157      22.406  11.729  26.492  1.00  0.00              
ATOM    124  O   PRO   157      23.440  12.375  26.349  1.00  0.00              
ATOM    125  N   LEU   158      21.248  12.284  26.822  1.00  0.00              
ATOM    126  CA  LEU   158      21.127  13.719  27.043  1.00  0.00              
ATOM    127  C   LEU   158      21.021  14.041  28.535  1.00  0.00              
ATOM    128  O   LEU   158      21.722  13.453  29.359  1.00  0.00              
END
