
#######################################################
#                                                     #
#                        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   19 (  151),  selected   19 , name T0348TS186_4
# Molecule2: number of CA atoms   61 (  465),  selected   19 , name T0348.pdb
# PARAMETERS: T0348TS186_4.T0348.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:    14        43 - 56          4.47     9.71
  LONGEST_CONTINUOUS_SEGMENT:    14        44 - 57          4.54     8.95
  LONGEST_CONTINUOUS_SEGMENT:    14        45 - 58          4.92     8.43
  LONGEST_CONTINUOUS_SEGMENT:    14        46 - 59          4.84     9.87
  LCS_AVERAGE:     22.43

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        48 - 55          1.83    10.89
  LONGEST_CONTINUOUS_SEGMENT:     8        49 - 56          1.65    11.88
  LCS_AVERAGE:      9.06

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        49 - 53          0.43    11.89
  LCS_AVERAGE:      5.87

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:   61
LCS_GDT     P      43     P      43      3    3   14     0    3    3    3    3    4    4    4    5    6    8   11   13   13   14   14   14   14   15   15 
LCS_GDT     M      44     M      44      3    3   14     0    3    3    3    3    4    4    4    5    6   10   12   13   13   14   14   14   14   16   16 
LCS_GDT     M      45     M      45      3    3   14     0    3    3    3    3    4    4    4    7   10   12   12   13   13   14   14   14   15   16   16 
LCS_GDT     L      46     L      46      3    3   14     0    3    3    3    4    4    4    9    9   10   12   12   13   13   14   14   14   15   16   16 
LCS_GDT     E      47     E      47      3    3   14     1    3    3    3    4    4    5    9   10   10   12   12   13   13   14   14   14   15   16   16 
LCS_GDT     S      48     S      48      3    8   14     1    3    3    5    7    8    9    9   10   11   12   12   13   13   14   14   14   15   16   16 
LCS_GDT     E      49     E      49      5    8   14     5    6    6    7    7    8    9    9   10   11   12   12   13   13   14   14   14   15   16   16 
LCS_GDT     A      50     A      50      5    8   14     5    6    6    7    7    8    9    9   10   11   12   12   13   13   14   14   14   15   16   16 
LCS_GDT     R      51     R      51      5    8   14     5    6    6    7    7    8    9    9   10   11   12   12   13   13   14   14   14   15   16   16 
LCS_GDT     E      52     E      52      5    8   14     5    6    6    7    7    8    9    9   10   11   12   12   13   13   14   14   14   15   16   16 
LCS_GDT     L      53     L      53      5    8   14     5    6    6    7    7    8    9    9   10   11   12   12   13   13   14   14   14   15   16   16 
LCS_GDT     A      54     A      54      4    8   14     3    3    6    7    7    8    9    9   10   11   12   12   13   13   14   14   14   15   16   16 
LCS_GDT     P      55     P      55      3    8   14     5    6    6    6    7    8    9    9   10   11   12   12   13   13   14   14   14   15   16   16 
LCS_GDT     E      56     E      56      3    8   14     3    3    6    7    7    8    9    9   10   11   12   12   13   13   14   14   14   15   16   16 
LCS_GDT     E      57     E      57      3    4   14     3    3    3    4    4    5    6    9   10   11   11   11   12   13   13   13   14   15   16   16 
LCS_GDT     E      58     E      58      3    4   14     3    3    3    4    4    5    6    6    7    7    9   10   12   13   13   13   14   15   16   16 
LCS_GDT     V      59     V      59      3    4   14     3    3    3    4    4    5    6    6    7   11   11   11   12   13   13   13   14   15   16   16 
LCS_GDT     K      60     K      60      3    3   13     3    3    3    3    3    5    6    6    7    7    8   10   10   13   13   13   13   13   14   15 
LCS_GDT     L      61     L      61      3    3    9     3    3    3    3    4    5    5    6    7    7    8    8    8    8    8    9   10   11   11   11 
LCS_AVERAGE  LCS_A:  12.45  (   5.87    9.06   22.43 )

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      6      6      7      7      8      9      9     10     11     12     12     13     13     14     14     14     15     16     16 
GDT PERCENT_CA   8.20   9.84   9.84  11.48  11.48  13.11  14.75  14.75  16.39  18.03  19.67  19.67  21.31  21.31  22.95  22.95  22.95  24.59  26.23  26.23
GDT RMS_LOCAL    0.31   0.41   0.41   1.34   1.34   1.65   2.03   2.03   2.66   3.47   3.47   3.47   3.98   3.98   4.47   4.47   4.47   5.41   5.75   5.75
GDT RMS_ALL_CA  11.92  11.91  11.91  12.16  12.16  11.88  11.77  11.77  10.78  11.81   9.41   9.41   9.38   9.38   9.71   9.71   9.71   8.16   8.23   8.23

#      Molecule1      Molecule2       DISTANCE
LGA    P      43      P      43         26.497
LGA    M      44      M      44         20.054
LGA    M      45      M      45         15.719
LGA    L      46      L      46          9.798
LGA    E      47      E      47          6.669
LGA    S      48      S      48          3.149
LGA    E      49      E      49          2.527
LGA    A      50      A      50          0.531
LGA    R      51      R      51          1.250
LGA    E      52      E      52          1.172
LGA    L      53      L      53          1.574
LGA    A      54      A      54          2.467
LGA    P      55      P      55          2.387
LGA    E      56      E      56          1.834
LGA    E      57      E      57          8.627
LGA    E      58      E      58         12.787
LGA    V      59      V      59         11.239
LGA    K      60      K      60         16.818
LGA    L      61      L      61         21.321

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   19   61    4.0      9    2.03    14.754    13.561     0.422

LGA_LOCAL      RMSD =  2.032  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 11.767  Number of atoms =   19 
Std_ALL_ATOMS  RMSD =  8.014  (standard rmsd on all 19 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.756998 * X  +  -0.331349 * Y  +   0.563171 * Z  +  14.716537
  Y_new =  -0.376033 * X  +  -0.483946 * Y  +  -0.790187 * Z  + 105.301620
  Z_new =   0.534372 * X  +  -0.809941 * Y  +   0.241748 * Z  +  89.659401 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.280738    1.860855  [ DEG:   -73.3809    106.6191 ]
  Theta =  -0.563764   -2.577828  [ DEG:   -32.3013   -147.6987 ]
  Phi   =  -2.680555    0.461038  [ DEG:  -153.5845     26.4155 ]
 
# 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: T0348TS186_4                                  
REMARK     2: T0348.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0348TS186_4.T0348.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   19   61   4.0    9   2.03  13.561     8.01
REMARK  ---------------------------------------------------------- 
MOLECULE T0348TS186_4
PFRMAT TS
TARGET T0348
MODEL  4
PARENT 1g3j_B
ATOM      1  N   PRO    43     -10.331  28.885  71.400  1.00  0.00
ATOM      2  CA  PRO    43      -9.002  28.421  70.906  1.00  0.00
ATOM      3  C   PRO    43      -8.971  28.375  69.384  1.00  0.00
ATOM      4  O   PRO    43     -10.009  28.240  68.736  1.00  0.00
ATOM      5  CB  PRO    43      -8.849  27.025  71.513  1.00  0.00
ATOM      6  CG  PRO    43      -9.738  27.038  72.711  1.00  0.00
ATOM      7  CD  PRO    43     -10.930  27.875  72.335  1.00  0.00
ATOM      8  N   MET    44      -7.774  28.504  68.821  1.00  0.00
ATOM      9  CA  MET    44      -7.593  28.472  67.374  1.00  0.00
ATOM     10  C   MET    44      -7.102  27.099  66.926  1.00  0.00
ATOM     11  O   MET    44      -6.517  26.351  67.713  1.00  0.00
ATOM     12  CB  MET    44      -6.565  29.518  66.939  1.00  0.00
ATOM     13  CG  MET    44      -7.002  30.954  67.178  1.00  0.00
ATOM     14  SD  MET    44      -5.728  32.152  66.738  1.00  0.00
ATOM     15  CE  MET    44      -5.942  32.236  64.962  1.00  0.00
ATOM     16  N   MET    45      -7.351  26.772  65.663  1.00  0.00
ATOM     17  CA  MET    45      -6.939  25.494  65.097  1.00  0.00
ATOM     18  C   MET    45      -5.415  25.483  64.945  1.00  0.00
ATOM     19  O   MET    45      -4.835  26.412  64.380  1.00  0.00
ATOM     20  CB  MET    45      -7.582  25.282  63.725  1.00  0.00
ATOM     21  CG  MET    45      -9.087  25.071  63.772  1.00  0.00
ATOM     22  SD  MET    45      -9.550  23.552  64.626  1.00  0.00
ATOM     23  CE  MET    45      -9.023  22.320  63.436  1.00  0.00
ATOM     24  N   LEU    46      -9.288  26.410  51.506  1.00  0.00
ATOM     25  CA  LEU    46      -8.502  25.729  52.525  1.00  0.00
ATOM     26  C   LEU    46      -7.130  26.369  52.648  1.00  0.00
ATOM     27  O   LEU    46      -6.611  26.932  51.687  1.00  0.00
ATOM     28  CB  LEU    46      -8.319  24.254  52.163  1.00  0.00
ATOM     29  CG  LEU    46      -9.585  23.395  52.156  1.00  0.00
ATOM     30  CD1 LEU    46      -9.280  21.992  51.656  1.00  0.00
ATOM     31  CD2 LEU    46     -10.167  23.285  53.558  1.00  0.00
ATOM     32  N   GLU    47      -6.546  26.281  53.836  1.00  0.00
ATOM     33  CA  GLU    47      -5.220  26.833  54.056  1.00  0.00
ATOM     34  C   GLU    47      -4.157  25.883  53.508  1.00  0.00
ATOM     35  O   GLU    47      -4.253  24.667  53.682  1.00  0.00
ATOM     36  CB  GLU    47      -4.967  27.039  55.551  1.00  0.00
ATOM     37  CG  GLU    47      -5.872  28.075  56.196  1.00  0.00
ATOM     38  CD  GLU    47      -5.571  28.277  57.668  1.00  0.00
ATOM     39  OE1 GLU    47      -4.679  27.577  58.193  1.00  0.00
ATOM     40  OE2 GLU    47      -6.226  29.134  58.297  1.00  0.00
ATOM     41  N   SER    48      -3.174  26.445  52.809  1.00  0.00
ATOM     42  CA  SER    48      -2.062  25.669  52.264  1.00  0.00
ATOM     43  C   SER    48      -1.283  25.123  53.453  1.00  0.00
ATOM     44  O   SER    48      -1.297  25.725  54.525  1.00  0.00
ATOM     45  CB  SER    48      -1.163  26.556  51.400  1.00  0.00
ATOM     46  OG  SER    48      -0.502  27.531  52.187  1.00  0.00
ATOM     47  N   GLU    49      -0.603  23.994  53.265  1.00  0.00
ATOM     48  CA  GLU    49       0.180  23.387  54.342  1.00  0.00
ATOM     49  C   GLU    49       1.426  22.673  53.843  1.00  0.00
ATOM     50  O   GLU    49       1.396  22.001  52.816  1.00  0.00
ATOM     51  CB  GLU    49      -0.656  22.373  55.117  1.00  0.00
ATOM     52  CG  GLU    49      -1.811  22.947  55.885  1.00  0.00
ATOM     53  CD  GLU    49      -2.587  21.875  56.604  1.00  0.00
ATOM     54  OE1 GLU    49      -1.973  21.134  57.402  1.00  0.00
ATOM     55  OE2 GLU    49      -3.804  21.765  56.365  1.00  0.00
ATOM     56  N   ALA    50       2.488  22.757  54.637  1.00  0.00
ATOM     57  CA  ALA    50       3.768  22.128  54.315  1.00  0.00
ATOM     58  C   ALA    50       3.816  20.682  54.783  1.00  0.00
ATOM     59  O   ALA    50       3.260  20.344  55.826  1.00  0.00
ATOM     60  CB  ALA    50       4.910  22.875  54.989  1.00  0.00
ATOM     61  N   ARG    51       4.450  19.825  53.988  1.00  0.00
ATOM     62  CA  ARG    51       4.623  18.421  54.340  1.00  0.00
ATOM     63  C   ARG    51       6.088  18.336  54.755  1.00  0.00
ATOM     64  O   ARG    51       6.986  18.567  53.939  1.00  0.00
ATOM     65  CB  ARG    51       4.317  17.526  53.139  1.00  0.00
ATOM     66  CG  ARG    51       2.878  17.606  52.655  1.00  0.00
ATOM     67  CD  ARG    51       2.667  16.767  51.405  1.00  0.00
ATOM     68  NE  ARG    51       1.300  16.871  50.900  1.00  0.00
ATOM     69  CZ  ARG    51       0.841  16.205  49.846  1.00  0.00
ATOM     70  NH1 ARG    51      -0.417  16.363  49.459  1.00  0.00
ATOM     71  NH2 ARG    51       1.641  15.381  49.182  1.00  0.00
ATOM     72  N   GLU    52       6.325  18.041  56.031  1.00  0.00
ATOM     73  CA  GLU    52       7.683  17.966  56.558  1.00  0.00
ATOM     74  C   GLU    52       8.406  16.693  56.136  1.00  0.00
ATOM     75  O   GLU    52       8.196  15.632  56.721  1.00  0.00
ATOM     76  CB  GLU    52       7.666  17.994  58.088  1.00  0.00
ATOM     77  CG  GLU    52       9.046  18.049  58.723  1.00  0.00
ATOM     78  CD  GLU    52       8.996  17.943  60.234  1.00  0.00
ATOM     79  OE1 GLU    52       7.878  17.911  60.792  1.00  0.00
ATOM     80  OE2 GLU    52      10.075  17.890  60.862  1.00  0.00
ATOM     81  N   LEU    53       9.233  16.793  55.099  1.00  0.00
ATOM     82  CA  LEU    53      10.001  15.647  54.629  1.00  0.00
ATOM     83  C   LEU    53      11.377  15.716  55.279  1.00  0.00
ATOM     84  O   LEU    53      11.997  16.781  55.314  1.00  0.00
ATOM     85  CB  LEU    53      10.141  15.683  53.107  1.00  0.00
ATOM     86  CG  LEU    53       8.839  15.630  52.304  1.00  0.00
ATOM     87  CD1 LEU    53       9.121  15.751  50.814  1.00  0.00
ATOM     88  CD2 LEU    53       8.112  14.316  52.546  1.00  0.00
ATOM     89  N   ALA    54      11.849  14.589  55.798  1.00  0.00
ATOM     90  CA  ALA    54      13.152  14.535  56.454  1.00  0.00
ATOM     91  C   ALA    54      13.719  13.126  56.394  1.00  0.00
ATOM     92  O   ALA    54      14.056  12.537  57.420  1.00  0.00
ATOM     93  CB  ALA    54      13.027  14.943  57.915  1.00  0.00
ATOM     94  N   PRO    55      13.841  12.601  55.178  1.00  0.00
ATOM     95  CA  PRO    55      14.357  11.255  54.970  1.00  0.00
ATOM     96  C   PRO    55      15.844  11.229  54.607  1.00  0.00
ATOM     97  O   PRO    55      16.237  11.602  53.501  1.00  0.00
ATOM     98  CB  PRO    55      13.513  10.709  53.817  1.00  0.00
ATOM     99  CG  PRO    55      13.132  11.918  53.028  1.00  0.00
ATOM    100  CD  PRO    55      13.128  13.065  53.999  1.00  0.00
ATOM    101  N   GLU    56      16.659  10.799  55.566  1.00  0.00
ATOM    102  CA  GLU    56      18.102  10.675  55.383  1.00  0.00
ATOM    103  C   GLU    56      18.318   9.310  54.749  1.00  0.00
ATOM    104  O   GLU    56      19.038   9.168  53.762  1.00  0.00
ATOM    105  CB  GLU    56      18.813  10.730  56.740  1.00  0.00
ATOM    106  CG  GLU    56      20.328  10.625  56.659  1.00  0.00
ATOM    107  CD  GLU    56      21.006  10.666  58.023  1.00  0.00
ATOM    108  OE1 GLU    56      20.428  10.168  59.016  1.00  0.00
ATOM    109  OE2 GLU    56      22.135  11.192  58.098  1.00  0.00
ATOM    110  N   GLU    57      17.671   8.320  55.361  1.00  0.00
ATOM    111  CA  GLU    57      17.696   6.929  54.934  1.00  0.00
ATOM    112  C   GLU    57      18.793   6.319  54.082  1.00  0.00
ATOM    113  O   GLU    57      19.092   6.783  52.980  1.00  0.00
ATOM    114  CB  GLU    57      16.459   6.603  54.095  1.00  0.00
ATOM    115  CG  GLU    57      16.366   5.149  53.665  1.00  0.00
ATOM    116  CD  GLU    57      15.101   4.851  52.884  1.00  0.00
ATOM    117  OE1 GLU    57      14.290   5.782  52.691  1.00  0.00
ATOM    118  OE2 GLU    57      14.922   3.690  52.464  1.00  0.00
ATOM    119  N   GLU    58      19.352   5.228  54.596  1.00  0.00
ATOM    120  CA  GLU    58      20.389   4.447  53.923  1.00  0.00
ATOM    121  C   GLU    58      21.765   5.035  53.640  1.00  0.00
ATOM    122  O   GLU    58      21.916   5.970  52.852  1.00  0.00
ATOM    123  CB  GLU    58      19.836   3.840  52.626  1.00  0.00
ATOM    124  CG  GLU    58      19.464   2.366  52.719  1.00  0.00
ATOM    125  CD  GLU    58      18.265   2.105  53.610  1.00  0.00
ATOM    126  OE1 GLU    58      18.399   2.235  54.847  1.00  0.00
ATOM    127  OE2 GLU    58      17.188   1.767  53.070  1.00  0.00
ATOM    128  N   VAL    59      22.764   4.452  54.295  1.00  0.00
ATOM    129  CA  VAL    59      24.165   4.809  54.097  1.00  0.00
ATOM    130  C   VAL    59      24.715   3.472  53.652  1.00  0.00
ATOM    131  O   VAL    59      24.719   2.513  54.423  1.00  0.00
ATOM    132  CB  VAL    59      24.805   5.327  55.399  1.00  0.00
ATOM    133  CG1 VAL    59      26.270   5.665  55.173  1.00  0.00
ATOM    134  CG2 VAL    59      24.091   6.579  55.882  1.00  0.00
ATOM    135  N   LYS    60      25.105   3.390  52.387  1.00  0.00
ATOM    136  CA  LYS    60      25.644   2.158  51.840  1.00  0.00
ATOM    137  C   LYS    60      26.934   1.746  52.557  1.00  0.00
ATOM    138  O   LYS    60      28.038   1.886  52.028  1.00  0.00
ATOM    139  CB  LYS    60      25.962   2.326  50.353  1.00  0.00
ATOM    140  CG  LYS    60      24.737   2.509  49.472  1.00  0.00
ATOM    141  CD  LYS    60      25.124   2.638  48.008  1.00  0.00
ATOM    142  CE  LYS    60      23.901   2.842  47.130  1.00  0.00
ATOM    143  NZ  LYS    60      24.266   2.983  45.693  1.00  0.00
ATOM    144  N   LEU    61      26.766   1.263  53.787  1.00  0.00
ATOM    145  CA  LEU    61      27.866   0.812  54.637  1.00  0.00
ATOM    146  C   LEU    61      28.184  -0.664  54.383  1.00  0.00
ATOM    147  O   LEU    61      27.523  -1.273  53.511  1.00  0.00
ATOM    148  CB  LEU    61      27.504   0.977  56.114  1.00  0.00
ATOM    149  CG  LEU    61      27.146   2.392  56.572  1.00  0.00
ATOM    150  CD1 LEU    61      26.770   2.402  58.046  1.00  0.00
ATOM    151  CD2 LEU    61      28.324   3.334  56.374  1.00  0.00
TER
END
