
#######################################################
#                                                     #
#                        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 T0356AL044_2-D1
# Molecule2: number of CA atoms  124 (  963),  selected   29 , name T0356_D1.pdb
# PARAMETERS: T0356AL044_2-D1.T0356_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:    24       314 - 338         4.58    10.32
  LCS_AVERAGE:     18.44

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       319 - 327         1.89    12.51
  LCS_AVERAGE:      5.90

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       314 - 319         0.78    23.03
  LONGEST_CONTINUOUS_SEGMENT:     6       315 - 320         0.97    22.49
  LCS_AVERAGE:      3.67

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:  124
LCS_GDT     D     314     D     314      6    8   24     5    5    7    7    8   11   14   17   19   21   22   22   22   22   22   24   24   24   24   24 
LCS_GDT     A     315     A     315      6    8   24     5    5    7    7    8   11   14   17   19   21   22   22   22   22   23   24   24   24   24   24 
LCS_GDT     I     316     I     316      6    8   24     5    5    7    7    8   11   14   17   19   21   22   22   22   22   23   24   24   24   24   24 
LCS_GDT     Y     317     Y     317      6    8   24     5    5    7    7    9   11   14   17   19   21   22   22   22   22   23   24   24   24   24   24 
LCS_GDT     H     318     H     318      6    8   24     5    5    7    7    8   10   14   17   19   21   22   22   22   22   23   24   24   24   24   24 
LCS_GDT     S     319     S     319      6    9   24     3    3    7    7    9   10   14   17   19   21   22   22   22   22   23   24   24   24   24   24 
LCS_GDT     T     320     T     320      6    9   24     3    4    7    7    9   11   14   17   19   21   22   22   22   22   23   24   24   24   24   24 
LCS_GDT     Y     321     Y     321      5    9   24     3    4    5    7    9   11   14   17   19   21   22   22   22   22   23   24   24   24   24   24 
LCS_GDT     T     322     T     322      5    9   24     3    5    6    7    9   11   14   17   19   21   22   22   22   22   23   24   24   24   24   24 
LCS_GDT     G     323     G     323      5    9   24     3    5    6    7    9   11   14   17   19   21   22   22   22   22   23   24   24   24   24   24 
LCS_GDT     R     324     R     324      4    9   24     3    3    4    7    7   10   11   15   19   21   22   22   22   22   23   24   24   24   24   24 
LCS_GDT     P     325     P     325      4    9   24     3    5    6    7    9   11   14   17   19   21   22   22   22   22   23   24   24   24   24   24 
LCS_GDT     P     326     P     326      4    9   24     3    5    6    7    9   11   14   17   19   21   22   22   22   22   23   24   24   24   24   24 
LCS_GDT     D     327     D     327      4    9   24     3    5    6    7    9   11   14   17   19   21   22   22   22   22   23   24   24   24   24   24 
LCS_GDT     E     328     E     328      3    7   24     3    3    4    5    8    8   14   17   19   21   22   22   22   22   23   24   24   24   24   24 
LCS_GDT     P     329     P     329      3    6   24     3    3    4    6    7    9   14   16   17   21   22   22   22   22   23   24   24   24   24   24 
LCS_GDT     A     330     A     330      3    6   24     3    3    4    5    7    9   12   15   19   21   22   22   22   22   23   24   24   24   24   24 
LCS_GDT     V     331     V     331      3    6   24     3    3    4    6    7    9    9   17   19   21   22   22   22   22   23   24   24   24   24   24 
LCS_GDT     L     332     L     332      3    6   24     3    3    4    7    9   11   14   17   19   21   22   22   22   22   23   24   24   24   24   24 
LCS_GDT     G     333     G     333      3    6   24     0    3    3    5    5    7    7    9   18   21   22   22   22   22   23   24   24   24   24   24 
LCS_GDT     A     335     A     335      4    6   24     4    4    4    6    7    9   12   17   19   21   22   22   22   22   23   24   24   24   24   24 
LCS_GDT     L     336     L     336      4    6   24     4    4    6    6    7    9   11   12   15   21   22   22   22   22   23   24   24   24   24   24 
LCS_GDT     N     337     N     337      4    6   24     4    4    4    6    7    9    9   11   12   13   14   15   18   20   23   24   24   24   24   24 
LCS_GDT     E     338     E     338      4    6   24     4    4    4    6    7    9    9   11   12   13   14   16   17   20   23   24   24   24   24   24 
LCS_GDT     P     342     P     342      5    6   18     5    5    5    5    5    6    7    9   11   11   11   13   14   16   17   18   19   20   21   22 
LCS_GDT     I     343     I     343      5    6   18     5    5    5    5    5    6    7    9   11   11   11   13   13   14   16   18   19   19   21   22 
LCS_GDT     L     344     L     344      5    6   18     5    5    5    5    5    6    7    9   11   11   13   15   15   16   17   18   19   19   21   22 
LCS_GDT     Q     345     Q     345      5    6   18     5    5    5    5    5    6    7    9   11   11   12   15   15   16   17   18   19   19   21   22 
LCS_GDT     K     346     K     346      5    6   15     5    5    5    5    5    6    7    9   11   11   11   13   13   14   14   15   19   19   20   21 
LCS_AVERAGE  LCS_A:   9.33  (   3.67    5.90   18.44 )

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      5      7      7      9     11     14     17     19     21     22     22     22     22     23     24     24     24     24     24 
GDT PERCENT_CA   4.03   4.03   5.65   5.65   7.26   8.87  11.29  13.71  15.32  16.94  17.74  17.74  17.74  17.74  18.55  19.35  19.35  19.35  19.35  19.35
GDT RMS_LOCAL    0.25   0.25   1.01   1.01   1.78   2.39   2.65   3.02   3.24   3.48   3.62   3.62   3.62   3.62   4.55   4.58   4.58   4.58   4.58   4.58
GDT RMS_ALL_CA  26.55  26.55  23.00  23.00  12.74  11.21  11.45  11.64  11.44  11.27  10.98  10.98  10.98  10.98  10.14  10.32  10.32  10.32  10.32  10.32

#      Molecule1      Molecule2       DISTANCE
LGA    D     314      D     314          2.840
LGA    A     315      A     315          2.434
LGA    I     316      I     316          2.960
LGA    Y     317      Y     317          2.901
LGA    H     318      H     318          3.422
LGA    S     319      S     319          3.716
LGA    T     320      T     320          2.431
LGA    Y     321      Y     321          1.242
LGA    T     322      T     322          2.441
LGA    G     323      G     323          3.269
LGA    R     324      R     324          4.728
LGA    P     325      P     325          2.435
LGA    P     326      P     326          2.564
LGA    D     327      D     327          2.232
LGA    E     328      E     328          3.985
LGA    P     329      P     329          5.319
LGA    A     330      A     330          4.842
LGA    V     331      V     331          3.743
LGA    L     332      L     332          3.586
LGA    G     333      G     333          5.592
LGA    A     335      A     335          3.857
LGA    L     336      L     336          6.801
LGA    N     337      N     337         11.603
LGA    E     338      E     338         12.122
LGA    P     342      P     342         19.333
LGA    I     343      I     343         22.774
LGA    L     344      L     344         25.226
LGA    Q     345      Q     345         27.658
LGA    K     346      K     346         31.109

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   29  124    4.0     17    3.02    10.685    10.069     0.545

LGA_LOCAL      RMSD =  3.018  Number of atoms =   17  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 11.523  Number of atoms =   29 
Std_ALL_ATOMS  RMSD =  8.834  (standard rmsd on all 29 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.048497 * X  +   0.504692 * Y  +   0.861936 * Z  +  59.290253
  Y_new =  -0.987483 * X  +  -0.153895 * Y  +   0.034550 * Z  + 151.021576
  Z_new =   0.150084 * X  +  -0.849472 * Y  +   0.505838 * Z  +  82.466904 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.033712    2.107881  [ DEG:   -59.2273    120.7727 ]
  Theta =  -0.150654   -2.990939  [ DEG:    -8.6318   -171.3682 ]
  Phi   =  -1.619869    1.521724  [ DEG:   -92.8116     87.1884 ]
 
# 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: T0356AL044_2-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356AL044_2-D1.T0356_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   29  124   4.0   17   3.02  10.069     8.83
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL044_2-D1
REMARK Aligment from pdb entry: 1xov_A
ATOM     97  N   ASP   314      78.007  74.353  96.001  1.00  0.00              
ATOM     98  CA  ASP   314      77.484  73.355  95.102  1.00  0.00              
ATOM     99  C   ASP   314      75.956  73.202  95.181  1.00  0.00              
ATOM    100  O   ASP   314      75.370  73.344  96.273  1.00  0.00              
ATOM    101  N   ALA   315      75.312  72.966  94.043  1.00  0.00              
ATOM    102  CA  ALA   315      73.923  72.647  94.004  1.00  0.00              
ATOM    103  C   ALA   315      73.727  71.485  93.049  1.00  0.00              
ATOM    104  O   ALA   315      74.496  71.315  92.099  1.00  0.00              
ATOM    105  N   ILE   316      72.671  70.717  93.303  1.00  0.00              
ATOM    106  CA  ILE   316      72.363  69.560  92.504  1.00  0.00              
ATOM    107  C   ILE   316      70.967  69.727  92.007  1.00  0.00              
ATOM    108  O   ILE   316      70.001  69.802  92.778  1.00  0.00              
ATOM    109  N   TYR   317      70.839  69.898  90.696  1.00  0.00              
ATOM    110  CA  TYR   317      69.535  70.021  90.090  1.00  0.00              
ATOM    111  C   TYR   317      68.848  68.711  89.797  1.00  0.00              
ATOM    112  O   TYR   317      69.417  67.841  89.171  1.00  0.00              
ATOM    113  N   HIS   318      67.599  68.597  90.212  1.00  0.00              
ATOM    114  CA  HIS   318      66.723  67.515  89.730  1.00  0.00              
ATOM    115  C   HIS   318      65.660  68.154  88.848  1.00  0.00              
ATOM    116  O   HIS   318      64.584  68.638  89.274  1.00  0.00              
ATOM    117  N   SER   319      65.978  68.164  87.571  1.00  0.00              
ATOM    118  CA  SER   319      65.239  68.981  86.625  1.00  0.00              
ATOM    119  C   SER   319      63.737  68.673  86.562  1.00  0.00              
ATOM    120  O   SER   319      62.920  69.594  86.494  1.00  0.00              
ATOM    121  N   THR   320      63.394  67.387  86.487  1.00  0.00              
ATOM    122  CA  THR   320      62.016  66.908  86.446  1.00  0.00              
ATOM    123  C   THR   320      62.108  65.385  86.584  1.00  0.00              
ATOM    124  O   THR   320      63.236  64.869  86.709  1.00  0.00              
ATOM    125  N   TYR   321      60.970  64.710  86.666  1.00  0.00              
ATOM    126  CA  TYR   321      60.954  63.276  86.886  1.00  0.00              
ATOM    127  C   TYR   321      61.007  62.535  85.540  1.00  0.00              
ATOM    128  O   TYR   321      60.396  62.948  84.540  1.00  0.00              
ATOM    129  N   THR   322      61.686  61.388  85.543  1.00  0.00              
ATOM    130  CA  THR   322      61.753  60.530  84.346  1.00  0.00              
ATOM    131  C   THR   322      60.548  59.596  84.188  1.00  0.00              
ATOM    132  O   THR   322      60.357  58.965  83.135  1.00  0.00              
ATOM    133  N   GLY   323      59.723  59.527  85.235  1.00  0.00              
ATOM    134  CA  GLY   323      58.656  58.540  85.351  1.00  0.00              
ATOM    135  C   GLY   323      57.281  59.162  85.562  1.00  0.00              
ATOM    136  O   GLY   323      56.392  58.565  86.180  1.00  0.00              
ATOM    137  N   ARG   324      57.087  60.325  84.945  1.00  0.00              
ATOM    138  CA  ARG   324      55.865  61.054  85.060  1.00  0.00              
ATOM    139  C   ARG   324      55.576  61.624  83.662  1.00  0.00              
ATOM    140  O   ARG   324      56.424  62.248  83.014  1.00  0.00              
ATOM    141  N   PRO   325      54.388  61.359  83.129  1.00  0.00              
ATOM    142  CA  PRO   325      54.088  61.845  81.788  1.00  0.00              
ATOM    143  C   PRO   325      54.024  63.369  81.656  1.00  0.00              
ATOM    144  O   PRO   325      54.362  63.933  80.597  1.00  0.00              
ATOM    145  N   PRO   326      53.499  64.032  82.712  1.00  0.00              
ATOM    146  CA  PRO   326      53.434  65.497  82.690  1.00  0.00              
ATOM    147  C   PRO   326      54.843  66.029  82.420  1.00  0.00              
ATOM    148  O   PRO   326      55.070  66.869  81.569  1.00  0.00              
ATOM    149  N   ASP   327      55.791  65.514  83.172  1.00  0.00              
ATOM    150  CA  ASP   327      57.191  65.968  83.089  1.00  0.00              
ATOM    151  C   ASP   327      57.825  65.634  81.751  1.00  0.00              
ATOM    152  O   ASP   327      58.568  66.415  81.179  1.00  0.00              
ATOM    153  N   GLU   328      57.523  64.440  81.213  1.00  0.00              
ATOM    154  CA  GLU   328      57.996  64.108  79.869  1.00  0.00              
ATOM    155  C   GLU   328      57.447  65.039  78.797  1.00  0.00              
ATOM    156  O   GLU   328      58.200  65.481  77.920  1.00  0.00              
ATOM    157  N   PRO   329      56.129  65.297  78.811  1.00  0.00              
ATOM    158  CA  PRO   329      55.526  66.231  77.866  1.00  0.00              
ATOM    159  C   PRO   329      56.205  67.579  77.918  1.00  0.00              
ATOM    160  O   PRO   329      56.467  68.184  76.860  1.00  0.00              
ATOM    161  N   ALA   330      59.301  68.559  79.152  1.00  0.00              
ATOM    162  CA  ALA   330      60.690  68.719  78.745  1.00  0.00              
ATOM    163  C   ALA   330      60.868  68.532  77.246  1.00  0.00              
ATOM    164  O   ALA   330      61.873  68.946  76.701  1.00  0.00              
ATOM    165  N   VAL   331      59.891  67.885  76.613  1.00  0.00              
ATOM    166  CA  VAL   331      59.902  67.659  75.152  1.00  0.00              
ATOM    167  C   VAL   331      59.131  68.697  74.324  1.00  0.00              
ATOM    168  O   VAL   331      58.987  68.563  73.116  1.00  0.00              
ATOM    169  N   LEU   332      58.623  69.738  74.964  1.00  0.00              
ATOM    170  CA  LEU   332      58.037  70.851  74.248  1.00  0.00              
ATOM    171  C   LEU   332      59.089  71.593  73.426  1.00  0.00              
ATOM    172  O   LEU   332      60.276  71.612  73.746  1.00  0.00              
ATOM    173  N   GLY   333      58.627  72.230  72.347  1.00  0.00              
ATOM    174  CA  GLY   333      59.574  72.843  71.435  1.00  0.00              
ATOM    175  C   GLY   333      60.353  73.939  72.132  1.00  0.00              
ATOM    176  O   GLY   333      59.783  74.761  72.820  1.00  0.00              
ATOM    177  N   ALA   335      61.672  73.910  71.995  1.00  0.00              
ATOM    178  CA  ALA   335      62.542  74.902  72.611  1.00  0.00              
ATOM    179  C   ALA   335      62.716  74.861  74.118  1.00  0.00              
ATOM    180  O   ALA   335      63.302  75.780  74.694  1.00  0.00              
ATOM    181  N   LEU   336      62.258  73.790  74.756  1.00  0.00              
ATOM    182  CA  LEU   336      62.346  73.706  76.209  1.00  0.00              
ATOM    183  C   LEU   336      63.781  73.602  76.682  1.00  0.00              
ATOM    184  O   LEU   336      64.108  74.157  77.730  1.00  0.00              
ATOM    185  N   ASN   337      64.674  72.892  75.988  1.00  0.00              
ATOM    186  CA  ASN   337      66.031  72.865  76.529  1.00  0.00              
ATOM    187  C   ASN   337      66.649  74.260  76.545  1.00  0.00              
ATOM    188  O   ASN   337      67.376  74.581  77.493  1.00  0.00              
ATOM    189  N   GLU   338      66.389  75.035  75.486  1.00  0.00              
ATOM    190  CA  GLU   338      66.836  76.451  75.469  1.00  0.00              
ATOM    191  C   GLU   338      66.276  77.213  76.651  1.00  0.00              
ATOM    192  O   GLU   338      66.982  77.967  77.326  1.00  0.00              
ATOM    193  N   PRO   342      64.987  77.051  76.887  1.00  0.00              
ATOM    194  CA  PRO   342      64.336  77.758  78.000  1.00  0.00              
ATOM    195  C   PRO   342      64.911  77.352  79.343  1.00  0.00              
ATOM    196  O   PRO   342      64.995  78.168  80.255  1.00  0.00              
ATOM    197  N   ILE   343      65.303  76.093  79.475  1.00  0.00              
ATOM    198  CA  ILE   343      65.907  75.634  80.724  1.00  0.00              
ATOM    199  C   ILE   343      67.310  76.147  80.856  1.00  0.00              
ATOM    200  O   ILE   343      67.737  76.469  81.950  1.00  0.00              
ATOM    201  N   LEU   344      68.050  76.233  79.758  1.00  0.00              
ATOM    202  CA  LEU   344      69.409  76.818  79.830  1.00  0.00              
ATOM    203  C   LEU   344      69.336  78.271  80.317  1.00  0.00              
ATOM    204  O   LEU   344      70.174  78.712  81.109  1.00  0.00              
ATOM    205  N   GLN   345      68.334  78.999  79.846  1.00  0.00              
ATOM    206  CA  GLN   345      68.080  80.383  80.295  1.00  0.00              
ATOM    207  C   GLN   345      67.732  80.449  81.785  1.00  0.00              
ATOM    208  O   GLN   345      68.288  81.222  82.543  1.00  0.00              
ATOM    209  N   LYS   346      66.808  79.605  82.204  1.00  0.00              
ATOM    210  CA  LYS   346      66.398  79.526  83.607  1.00  0.00              
ATOM    211  C   LYS   346      67.563  79.267  84.533  1.00  0.00              
ATOM    212  O   LYS   346      67.686  79.912  85.594  1.00  0.00              
END
