
#######################################################
#                                                     #
#                        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   35 (  140),  selected   26 , name T0327AL044_1
# Molecule2: number of CA atoms   73 ( 1169),  selected   26 , name T0327.pdb
# PARAMETERS: T0327AL044_1.T0327.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:    16        51 - 67          4.96    11.93
  LCS_AVERAGE:     19.92

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        59 - 64          1.42    18.14
  LCS_AVERAGE:      6.06

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        59 - 62          0.73    20.10
  LONGEST_CONTINUOUS_SEGMENT:     4        64 - 67          0.60    19.87
  LCS_AVERAGE:      4.37

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:   73
LCS_GDT     Y      45     Y      45      3    3    8     3    5    5    5    5    6    7    9    9   11   13   14   16   17   18   19   19   20   22   22 
LCS_GDT     I      46     I      46      3    3    8     3    5    5    5    5    5    6    9    9   10   12   14   16   17   18   19   19   20   22   22 
LCS_GDT     I      47     I      47      3    3    8     3    3    3    3    3    3    3    3    4    6    8   10   11   15   17   18   19   20   22   22 
LCS_GDT     Y      51     Y      51      3    4   16     0    3    3    4    4    4    7   10   11   11   12   13   14   15   17   18   19   20   21   21 
LCS_GDT     S      52     S      52      3    4   16     3    4    4    5    7    7    8   10   11   11   12   13   14   15   17   18   19   20   21   21 
LCS_GDT     D      53     D      53      3    4   16     3    3    3    4    7    7    8   10   11   11   12   13   14   15   17   18   19   20   21   21 
LCS_GDT     D      54     D      54      3    4   16     3    3    3    4    4    5    5    7    9   10   12   13   14   15   17   18   19   20   21   21 
LCS_GDT     R      55     R      55      3    4   16     3    3    3    4    4    5    5    6    9   10   11   12   14   15   17   18   19   20   22   22 
LCS_GDT     H      57     H      57      3    4   16     1    4    4    5    7    7    8   10   11   11   12   13   14   15   17   18   19   20   22   22 
LCS_GDT     L      58     L      58      3    4   16     2    4    4    5    7    7    8   10   11   11   12   13   14   17   18   19   19   20   22   22 
LCS_GDT     Y      59     Y      59      4    6   16     3    4    4    6    7    7    8   10   11   11   12   14   16   17   18   19   19   20   22   22 
LCS_GDT     K      60     K      60      4    6   16     3    4    4    6    6    6    6    7    8    8   10   11   14   15   17   19   19   20   22   22 
LCS_GDT     L      61     L      61      4    6   16     3    4    4    6    6    6    6    7    8   10   12   14   16   17   18   19   19   20   22   22 
LCS_GDT     G      62     G      62      4    6   16     3    4    4    6    7    7    8   10   11   11   13   14   16   17   18   19   19   20   22   22 
LCS_GDT     P      63     P      63      3    6   16     3    3    4    6    6    6    8   10   11   11   13   14   16   17   18   19   19   20   22   22 
LCS_GDT     E      64     E      64      4    6   16     3    4    4    6    7    7    8   10   11   11   13   14   16   17   18   19   19   20   22   22 
LCS_GDT     L      65     L      65      4    5   16     3    4    4    4    5    6    7   10   11   11   13   14   16   17   18   19   19   20   22   22 
LCS_GDT     T      66     T      66      4    5   16     3    4    4    4    5    6    7   10   11   11   13   14   16   17   18   19   19   20   22   22 
LCS_GDT     E      67     E      67      4    5   16     0    4    4    4    5    6    7    8    9   11   13   14   16   17   18   19   19   20   22   22 
LCS_GDT     K      68     K      68      3    5   14     3    5    5    5    5    6    7    8    9   11   13   14   16   17   18   19   19   20   22   22 
LCS_GDT     G      69     G      69      3    3   14     3    5    5    5    5    6    7    9    9   11   13   14   16   17   18   19   19   20   22   22 
LCS_GDT     E      70     E      70      3    3   14     3    5    5    5    5    6    7    9    9   11   13   14   16   17   18   19   19   20   22   22 
LCS_GDT     N      71     N      71      3    4   14     3    3    3    3    4    4    6    9    9   11   13   14   16   17   18   19   19   20   22   22 
LCS_GDT     Y      72     Y      72      3    4   14     3    3    3    3    4    4    6    9    9   11   13   14   16   17   18   19   19   20   22   22 
LCS_GDT     L      73     L      73      3    4   14     3    3    3    3    4    4    6    9    9   11   13   14   16   17   18   19   19   20   22   22 
LCS_GDT     G      77     G      77      0    4   14     0    0    3    3    5    6    7    8    9   11   13   14   16   17   18   19   19   20   22   22 
LCS_AVERAGE  LCS_A:  10.12  (   4.37    6.06   19.92 )

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      3      5      5      6      7      7      8     10     11     11     13     14     16     17     18     19     19     20     22     22 
GDT PERCENT_CA   4.11   6.85   6.85   8.22   9.59   9.59  10.96  13.70  15.07  15.07  17.81  19.18  21.92  23.29  24.66  26.03  26.03  27.40  30.14  30.14
GDT RMS_LOCAL    0.02   0.72   0.72   1.42   1.80   1.80   2.11   2.75   3.02   3.02   3.90   4.07   4.55   4.80   5.13   5.45   5.45   6.02   6.63   6.63
GDT RMS_ALL_CA  23.66  16.46  16.46  18.14  14.85  14.85  14.73  13.55  13.19  13.19  12.28  12.17  11.60  11.11  10.51  10.43  10.43  10.19   9.18   9.18

#      Molecule1      Molecule2       DISTANCE
LGA    Y      45      Y      45         11.800
LGA    I      46      I      46         12.529
LGA    I      47      I      47         12.897
LGA    Y      51      Y      51          3.662
LGA    S      52      S      52          3.118
LGA    D      53      D      53          3.854
LGA    D      54      D      54          7.599
LGA    R      55      R      55          8.423
LGA    H      57      H      57          0.877
LGA    L      58      L      58          1.957
LGA    Y      59      Y      59          1.399
LGA    K      60      K      60          7.709
LGA    L      61      L      61          6.776
LGA    G      62      G      62          3.352
LGA    P      63      P      63          3.362
LGA    E      64      E      64          0.869
LGA    L      65      L      65          3.829
LGA    T      66      T      66          4.258
LGA    E      67      E      67         10.798
LGA    K      68      K      68         13.283
LGA    G      69      G      69         13.788
LGA    E      70      E      70         19.691
LGA    N      71      N      71         25.578
LGA    Y      72      Y      72         25.653
LGA    L      73      L      73         28.135
LGA    G      77      G      77         27.445

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   35   73    4.0     10    2.75    13.699    11.470     0.350

LGA_LOCAL      RMSD =  2.755  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 13.193  Number of atoms =   26 
Std_ALL_ATOMS  RMSD =  8.390  (standard rmsd on all 26 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.406136 * X  +   0.077065 * Y  +  -0.910557 * Z  +  57.754074
  Y_new =   0.782266 * X  +  -0.485737 * Y  +  -0.390025 * Z  + -83.451469
  Z_new =  -0.472348 * X  +  -0.870701 * Y  +   0.136990 * Z  +  63.169781 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.414743    1.726850  [ DEG:   -81.0588     98.9412 ]
  Theta =   0.491953    2.649640  [ DEG:    28.1868    151.8132 ]
  Phi   =   2.049669   -1.091924  [ DEG:   117.4374    -62.5626 ]
 
# 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: T0327AL044_1                                  
REMARK     2: T0327.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0327AL044_1.T0327.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   35   73   4.0   10   2.75  11.470     8.39
REMARK  ---------------------------------------------------------- 
MOLECULE T0327AL044_1
REMARK Aligment from pdb entry: 1j93_A
ATOM      1  N   TYR    45       7.677  -9.409   4.349  1.00  0.00              
ATOM      2  CA  TYR    45       7.861  -9.333   5.783  1.00  0.00              
ATOM      3  C   TYR    45       9.344  -9.148   6.009  1.00  0.00              
ATOM      4  O   TYR    45      10.164  -9.931   5.534  1.00  0.00              
ATOM      5  N   ILE    46       9.684  -8.098   6.733  1.00  0.00              
ATOM      6  CA  ILE    46      11.069  -7.799   7.027  1.00  0.00              
ATOM      7  C   ILE    46      11.058  -6.898   8.253  1.00  0.00              
ATOM      8  O   ILE    46      10.791  -5.706   8.139  1.00  0.00              
ATOM      9  N   ILE    47      11.320  -7.461   9.429  1.00  0.00              
ATOM     10  CA  ILE    47      11.314  -6.650  10.637  1.00  0.00              
ATOM     11  C   ILE    47      12.504  -5.703  10.634  1.00  0.00              
ATOM     12  O   ILE    47      13.546  -6.004  10.055  1.00  0.00              
ATOM     13  N   TYR    51      12.339  -4.554  11.277  1.00  0.00              
ATOM     14  CA  TYR    51      13.411  -3.584  11.318  1.00  0.00              
ATOM     15  C   TYR    51      13.509  -2.858   9.995  1.00  0.00              
ATOM     16  O   TYR    51      14.606  -2.541   9.538  1.00  0.00              
ATOM     17  N   SER    52      12.358  -2.589   9.379  1.00  0.00              
ATOM     18  CA  SER    52      12.315  -1.907   8.090  1.00  0.00              
ATOM     19  C   SER    52      12.005  -0.423   8.239  1.00  0.00              
ATOM     20  O   SER    52      11.799   0.283   7.250  1.00  0.00              
ATOM     21  N   ASP    53      11.988   0.041   9.484  1.00  0.00              
ATOM     22  CA  ASP    53      11.706   1.434   9.774  1.00  0.00              
ATOM     23  C   ASP    53      12.409   2.471   8.917  1.00  0.00              
ATOM     24  O   ASP    53      11.875   3.557   8.690  1.00  0.00              
ATOM     25  N   ASP    54      13.603   2.160   8.432  1.00  0.00              
ATOM     26  CA  ASP    54      14.315   3.124   7.611  1.00  0.00              
ATOM     27  C   ASP    54      14.229   2.827   6.126  1.00  0.00              
ATOM     28  O   ASP    54      14.767   3.576   5.305  1.00  0.00              
ATOM     29  N   ARG    55      13.538   1.740   5.783  1.00  0.00              
ATOM     30  CA  ARG    55      13.389   1.320   4.393  1.00  0.00              
ATOM     31  C   ARG    55      11.979   1.439   3.846  1.00  0.00              
ATOM     32  O   ARG    55      11.734   1.146   2.680  1.00  0.00              
ATOM     33  N   HIS    57      11.047   1.860   4.684  1.00  0.00              
ATOM     34  CA  HIS    57       9.659   1.952   4.269  1.00  0.00              
ATOM     35  C   HIS    57       9.429   2.475   2.865  1.00  0.00              
ATOM     36  O   HIS    57       8.811   1.799   2.045  1.00  0.00              
ATOM     37  N   LEU    58       9.936   3.661   2.572  1.00  0.00              
ATOM     38  CA  LEU    58       9.730   4.250   1.258  1.00  0.00              
ATOM     39  C   LEU    58      10.157   3.387   0.080  1.00  0.00              
ATOM     40  O   LEU    58       9.606   3.533  -1.011  1.00  0.00              
ATOM     41  N   TYR    59      11.119   2.486   0.272  1.00  0.00              
ATOM     42  CA  TYR    59      11.538   1.657  -0.849  1.00  0.00              
ATOM     43  C   TYR    59      10.835   0.316  -0.946  1.00  0.00              
ATOM     44  O   TYR    59      10.866  -0.317  -1.998  1.00  0.00              
ATOM     45  N   LYS    60      10.189  -0.131   0.123  1.00  0.00              
ATOM     46  CA  LYS    60       9.519  -1.428   0.067  1.00  0.00              
ATOM     47  C   LYS    60       8.509  -1.529  -1.086  1.00  0.00              
ATOM     48  O   LYS    60       8.507  -2.500  -1.849  1.00  0.00              
ATOM     49  N   LEU    61       7.642  -0.519  -1.236  1.00  0.00              
ATOM     50  CA  LEU    61       6.658  -0.560  -2.322  1.00  0.00              
ATOM     51  C   LEU    61       7.290  -0.724  -3.698  1.00  0.00              
ATOM     52  O   LEU    61       6.696  -1.306  -4.600  1.00  0.00              
ATOM     53  N   GLY    62       8.500  -0.212  -3.863  1.00  0.00              
ATOM     54  CA  GLY    62       9.166  -0.306  -5.151  1.00  0.00              
ATOM     55  C   GLY    62       9.437  -1.748  -5.575  1.00  0.00              
ATOM     56  O   GLY    62       9.765  -2.001  -6.729  1.00  0.00              
ATOM     57  N   PRO    63       9.292  -2.691  -4.647  1.00  0.00              
ATOM     58  CA  PRO    63       9.515  -4.105  -4.964  1.00  0.00              
ATOM     59  C   PRO    63       8.328  -4.598  -5.764  1.00  0.00              
ATOM     60  O   PRO    63       8.441  -5.552  -6.526  1.00  0.00              
ATOM     61  N   GLU    64       7.187  -3.941  -5.577  1.00  0.00              
ATOM     62  CA  GLU    64       5.988  -4.330  -6.290  1.00  0.00              
ATOM     63  C   GLU    64       5.087  -5.253  -5.486  1.00  0.00              
ATOM     64  O   GLU    64       4.020  -5.642  -5.954  1.00  0.00              
ATOM     65  N   LEU    65       5.506  -5.603  -4.275  1.00  0.00              
ATOM     66  CA  LEU    65       4.711  -6.493  -3.439  1.00  0.00              
ATOM     67  C   LEU    65       3.347  -5.884  -3.176  1.00  0.00              
ATOM     68  O   LEU    65       3.221  -4.676  -3.051  1.00  0.00              
ATOM     69  N   THR    66       2.323  -6.727  -3.095  1.00  0.00              
ATOM     70  CA  THR    66       0.960  -6.265  -2.847  1.00  0.00              
ATOM     71  C   THR    66       0.744  -5.815  -1.409  1.00  0.00              
ATOM     72  O   THR    66      -0.071  -4.927  -1.148  1.00  0.00              
ATOM     73  N   GLU    67       1.453  -6.429  -0.470  1.00  0.00              
ATOM     74  CA  GLU    67       1.302  -6.046   0.924  1.00  0.00              
ATOM     75  C   GLU    67       2.616  -6.059   1.700  1.00  0.00              
ATOM     76  O   GLU    67       3.462  -6.932   1.510  1.00  0.00              
ATOM     77  N   LYS    68       2.791  -5.054   2.550  1.00  0.00              
ATOM     78  CA  LYS    68       3.990  -4.925   3.365  1.00  0.00              
ATOM     79  C   LYS    68       3.649  -5.159   4.825  1.00  0.00              
ATOM     80  O   LYS    68       2.756  -4.520   5.386  1.00  0.00              
ATOM     81  N   GLY    69       4.363  -6.095   5.432  1.00  0.00              
ATOM     82  CA  GLY    69       4.150  -6.418   6.828  1.00  0.00              
ATOM     83  C   GLY    69       5.018  -5.456   7.619  1.00  0.00              
ATOM     84  O   GLY    69       6.239  -5.489   7.509  1.00  0.00              
ATOM     85  N   GLU    70       4.379  -4.588   8.396  1.00  0.00              
ATOM     86  CA  GLU    70       5.088  -3.604   9.208  1.00  0.00              
ATOM     87  C   GLU    70       5.370  -4.153  10.606  1.00  0.00              
ATOM     88  O   GLU    70       4.531  -4.867  11.161  1.00  0.00              
ATOM     89  N   ASN    71       6.532  -3.828  11.180  1.00  0.00              
ATOM     90  CA  ASN    71       6.839  -4.300  12.527  1.00  0.00              
ATOM     91  C   ASN    71       6.273  -3.267  13.482  1.00  0.00              
ATOM     92  O   ASN    71       5.772  -2.244  13.044  1.00  0.00              
ATOM     93  N   TYR    72       6.330  -3.527  14.778  1.00  0.00              
ATOM     94  CA  TYR    72       5.758  -2.609  15.749  1.00  0.00              
ATOM     95  C   TYR    72       6.538  -1.319  16.036  1.00  0.00              
ATOM     96  O   TYR    72       6.012  -0.424  16.708  1.00  0.00              
ATOM     97  N   LEU    73       7.773  -1.208  15.544  1.00  0.00              
ATOM     98  CA  LEU    73       8.562  -0.007  15.805  1.00  0.00              
ATOM     99  C   LEU    73       8.119   1.189  14.957  1.00  0.00              
ATOM    100  O   LEU    73       8.462   2.335  15.256  1.00  0.00              
ATOM    101  N   GLY    77       7.358   0.919  13.902  1.00  0.00              
ATOM    102  CA  GLY    77       6.849   1.969  13.033  1.00  0.00              
ATOM    103  C   GLY    77       5.375   2.172  13.374  1.00  0.00              
ATOM    104  O   GLY    77       4.609   1.214  13.389  1.00  0.00              
ATOM    105  N   THR    78       4.975   3.407  13.661  1.00  0.00              
ATOM    106  CA  THR    78       3.580   3.675  13.979  1.00  0.00              
ATOM    107  C   THR    78       2.720   3.409  12.751  1.00  0.00              
ATOM    108  O   THR    78       3.128   3.704  11.630  1.00  0.00              
ATOM    109  N   TRP    79       1.529   2.849  12.964  1.00  0.00              
ATOM    110  CA  TRP    79       0.643   2.522  11.860  1.00  0.00              
ATOM    111  C   TRP    79       0.363   3.714  10.970  1.00  0.00              
ATOM    112  O   TRP    79       0.437   3.606   9.746  1.00  0.00              
ATOM    113  N   SER    80       0.032   4.850  11.573  1.00  0.00              
ATOM    114  CA  SER    80      -0.255   6.034  10.791  1.00  0.00              
ATOM    115  C   SER    80       0.962   6.416   9.963  1.00  0.00              
ATOM    116  O   SER    80       0.848   6.702   8.773  1.00  0.00              
ATOM    117  N   LYS    81       2.133   6.405  10.588  1.00  0.00              
ATOM    118  CA  LYS    81       3.369   6.767   9.893  1.00  0.00              
ATOM    119  C   LYS    81       3.635   5.825   8.735  1.00  0.00              
ATOM    120  O   LYS    81       3.971   6.254   7.628  1.00  0.00              
ATOM    121  N   ALA    82       3.515   4.531   9.015  1.00  0.00              
ATOM    122  CA  ALA    82       3.750   3.521   8.003  1.00  0.00              
ATOM    123  C   ALA    82       2.775   3.636   6.855  1.00  0.00              
ATOM    124  O   ALA    82       3.175   3.521   5.692  1.00  0.00              
ATOM    125  N   TYR    83       1.502   3.861   7.172  1.00  0.00              
ATOM    126  CA  TYR    83       0.477   3.990   6.145  1.00  0.00              
ATOM    127  C   TYR    83       0.806   5.172   5.238  1.00  0.00              
ATOM    128  O   TYR    83       0.561   5.137   4.024  1.00  0.00              
ATOM    129  N   LYS    84       1.379   6.218   5.826  1.00  0.00              
ATOM    130  CA  LYS    84       1.743   7.400   5.055  1.00  0.00              
ATOM    131  C   LYS    84       3.020   7.192   4.246  1.00  0.00              
ATOM    132  O   LYS    84       3.039   7.425   3.038  1.00  0.00              
ATOM    133  N   THR    85       4.078   6.737   4.919  1.00  0.00              
ATOM    134  CA  THR    85       5.380   6.522   4.291  1.00  0.00              
ATOM    135  C   THR    85       5.404   5.464   3.207  1.00  0.00              
ATOM    136  O   THR    85       6.261   5.502   2.323  1.00  0.00              
ATOM    137  N   ILE    86       4.470   4.522   3.259  1.00  0.00              
ATOM    138  CA  ILE    86       4.431   3.465   2.252  1.00  0.00              
ATOM    139  C   ILE    86       3.684   3.877   0.985  1.00  0.00              
ATOM    140  O   ILE    86       3.817   3.243  -0.061  1.00  0.00              
END
