
#######################################################
#                                                     #
#                        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_1-D1
# Molecule2: number of CA atoms  124 (  963),  selected   29 , name T0356_D1.pdb
# PARAMETERS: T0356AL044_1-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         4.68    10.43
  LCS_AVERAGE:     18.46

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       319 - 327         1.76    13.26
  LCS_AVERAGE:      5.98

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       314 - 319         0.81    22.78
  LONGEST_CONTINUOUS_SEGMENT:     6       315 - 320         0.96    22.58
  LCS_AVERAGE:      3.81

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     4    5    7    8    9   12   15   16   18   20   21   22   22   22   22   22   24   24   24   24 
LCS_GDT     A     315     A     315      6    8   24     4    5    7    8    9   12   15   16   18   20   21   22   22   22   23   23   24   24   24   24 
LCS_GDT     I     316     I     316      6    8   24     4    5    7    8    9   12   15   16   18   20   21   22   22   22   23   23   24   24   24   24 
LCS_GDT     Y     317     Y     317      6    8   24     4    5    7    8   10   12   15   16   18   20   21   22   22   22   23   23   24   24   24   24 
LCS_GDT     H     318     H     318      6    8   24     3    5    7    8    9   12   15   16   18   20   21   22   22   22   23   23   24   24   24   24 
LCS_GDT     S     319     S     319      6    9   24     3    5    7    9   10   10   11   16   18   20   21   22   22   22   23   23   24   24   24   24 
LCS_GDT     T     320     T     320      6    9   24     3    3    7    9   10   12   15   16   18   20   21   22   22   22   23   23   24   24   24   24 
LCS_GDT     Y     321     Y     321      5    9   24     3    3    5    9   10   12   15   16   18   20   21   22   22   22   23   23   24   24   24   24 
LCS_GDT     T     322     T     322      5    9   24     2    5    6    9   10   12   15   16   18   20   21   22   22   22   23   23   24   24   24   24 
LCS_GDT     G     323     G     323      5    9   24     3    5    6    9   10   10   15   16   18   20   21   22   22   22   23   23   24   24   24   24 
LCS_GDT     R     324     R     324      4    9   24     3    4    5    7    7   10   11   15   18   20   21   22   22   22   23   23   24   24   24   24 
LCS_GDT     P     325     P     325      4    9   24     3    5    6    9   10   12   15   16   18   20   21   22   22   22   23   23   24   24   24   24 
LCS_GDT     P     326     P     326      4    9   24     2    5    6    9   10   12   15   16   18   20   21   22   22   22   23   23   24   24   24   24 
LCS_GDT     D     327     D     327      4    9   24     3    4    6    9   10   12   15   16   18   20   21   22   22   22   23   23   24   24   24   24 
LCS_GDT     E     328     E     328      3    8   24     3    4    6    8    8   10   15   16   18   20   21   22   22   22   23   23   24   24   24   24 
LCS_GDT     P     329     P     329      4    8   24     3    3    5    6    9   12   15   16   18   20   21   22   22   22   23   23   24   24   24   24 
LCS_GDT     A     330     A     330      4    6   24     3    3    5    5    7    9   11   14   17   20   21   22   22   22   23   23   24   24   24   24 
LCS_GDT     V     331     V     331      4    6   24     3    3    5    5    7    9   11   11   18   18   21   22   22   22   23   23   24   24   24   24 
LCS_GDT     L     332     L     332      4    6   24     3    5    6    9   10   12   15   16   18   20   21   22   22   22   23   23   24   24   24   24 
LCS_GDT     G     333     G     333      4    6   24     0    4    4    5    6    7   10   14   17   20   21   22   22   22   23   23   24   24   24   24 
LCS_GDT     A     335     A     335      4    6   24     4    4    4    6    8    9   12   16   18   20   21   22   22   22   23   23   24   24   24   24 
LCS_GDT     L     336     L     336      4    6   24     4    4    4    6    7    9   11   11   12   16   17   22   22   22   23   23   24   24   24   24 
LCS_GDT     N     337     N     337      4    6   24     4    4    4    6    6    9   11   11   12   13   14   17   19   21   23   23   24   24   24   24 
LCS_GDT     E     338     E     338      4    6   24     4    4    4    6    7    9   11   11   12   13   14   17   19   21   23   23   24   24   24   24 
LCS_GDT     P     342     P     342      5    6   18     5    5    5    5    5    6    8   10   11   12   13   13   16   17   18   20   21   21   21   22 
LCS_GDT     I     343     I     343      5    6   18     5    5    5    5    5    6    8   10   11   12   13   13   14   15   18   20   21   21   21   22 
LCS_GDT     L     344     L     344      5    6   18     5    5    5    5    5    6    8   10   11   12   13   15   16   17   18   20   21   21   21   22 
LCS_GDT     Q     345     Q     345      5    6   18     5    5    5    5    5    6    8   10   11   12   13   15   16   17   18   20   21   21   21   22 
LCS_GDT     K     346     K     346      5    6   16     5    5    5    5    5    6    8   10   11   12   13   13   14   14   16   20   20   20   21   21 
LCS_AVERAGE  LCS_A:   9.42  (   3.81    5.98   18.46 )

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      9     10     12     15     16     18     20     21     22     22     22     23     23     24     24     24     24 
GDT PERCENT_CA   4.03   4.03   5.65   7.26   8.06   9.68  12.10  12.90  14.52  16.13  16.94  17.74  17.74  17.74  18.55  18.55  19.35  19.35  19.35  19.35
GDT RMS_LOCAL    0.30   0.30   1.02   1.46   1.81   2.33   2.63   2.75   3.04   3.36   3.52   3.80   3.80   3.80   4.61   4.61   4.68   4.68   4.68   4.68
GDT RMS_ALL_CA  24.42  24.42  22.94  13.11  12.91  12.45  12.36  12.42  11.92  11.48  11.61  11.16  11.16  11.16  10.21  10.21  10.43  10.43  10.43  10.43

#      Molecule1      Molecule2       DISTANCE
LGA    D     314      D     314          3.768
LGA    A     315      A     315          1.923
LGA    I     316      I     316          3.456
LGA    Y     317      Y     317          2.541
LGA    H     318      H     318          2.992
LGA    S     319      S     319          3.990
LGA    T     320      T     320          2.733
LGA    Y     321      Y     321          1.835
LGA    T     322      T     322          2.162
LGA    G     323      G     323          3.342
LGA    R     324      R     324          4.802
LGA    P     325      P     325          2.494
LGA    P     326      P     326          1.550
LGA    D     327      D     327          2.032
LGA    E     328      E     328          3.594
LGA    P     329      P     329          2.999
LGA    A     330      A     330          6.192
LGA    V     331      V     331          6.507
LGA    L     332      L     332          1.681
LGA    G     333      G     333          6.458
LGA    A     335      A     335          4.799
LGA    L     336      L     336          8.408
LGA    N     337      N     337         12.715
LGA    E     338      E     338         13.067
LGA    P     342      P     342         20.520
LGA    I     343      I     343         24.035
LGA    L     344      L     344         26.000
LGA    Q     345      Q     345         28.604
LGA    K     346      K     346         32.142

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   29  124    4.0     16    2.75    10.685    10.189     0.560

LGA_LOCAL      RMSD =  2.755  Number of atoms =   16  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 12.067  Number of atoms =   29 
Std_ALL_ATOMS  RMSD =  8.851  (standard rmsd on all 29 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.074067 * X  +  -0.996538 * Y  +   0.037758 * Z  +  92.614624
  Y_new =   0.750991 * X  +   0.080648 * Y  +   0.655369 * Z  +  19.519634
  Z_new =  -0.656146 * X  +  -0.020186 * Y  +   0.754364 * Z  +  59.851013 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.026752    3.114841  [ DEG:    -1.5328    178.4672 ]
  Theta =   0.715700    2.425893  [ DEG:    41.0066    138.9934 ]
  Phi   =   1.472488   -1.669105  [ DEG:    84.3674    -95.6326 ]
 
# 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_1-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356AL044_1-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   16   2.75  10.189     8.85
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL044_1-D1
REMARK Aligment from pdb entry: 1jwq_A
ATOM     93  N   ASP   314      78.941  73.657  95.805  1.00  0.00              
ATOM     94  CA  ASP   314      78.485  72.655  94.855  1.00  0.00              
ATOM     95  C   ASP   314      77.034  72.279  95.048  1.00  0.00              
ATOM     96  O   ASP   314      76.594  71.993  96.159  1.00  0.00              
ATOM     97  N   ALA   315      76.290  72.268  93.954  1.00  0.00              
ATOM     98  CA  ALA   315      74.887  71.902  94.025  1.00  0.00              
ATOM     99  C   ALA   315      74.549  70.886  92.952  1.00  0.00              
ATOM    100  O   ALA   315      75.242  70.773  91.939  1.00  0.00              
ATOM    101  N   ILE   316      73.492  70.125  93.199  1.00  0.00              
ATOM    102  CA  ILE   316      73.035  69.131  92.243  1.00  0.00              
ATOM    103  C   ILE   316      71.600  69.507  91.921  1.00  0.00              
ATOM    104  O   ILE   316      70.772  69.686  92.816  1.00  0.00              
ATOM    105  N   TYR   317      71.316  69.653  90.637  1.00  0.00              
ATOM    106  CA  TYR   317      69.988  70.042  90.207  1.00  0.00              
ATOM    107  C   TYR   317      69.219  68.875  89.616  1.00  0.00              
ATOM    108  O   TYR   317      69.723  68.172  88.750  1.00  0.00              
ATOM    109  N   HIS   318      68.012  68.654  90.122  1.00  0.00              
ATOM    110  CA  HIS   318      67.139  67.613  89.590  1.00  0.00              
ATOM    111  C   HIS   318      66.103  68.483  88.890  1.00  0.00              
ATOM    112  O   HIS   318      65.164  68.978  89.511  1.00  0.00              
ATOM    113  N   SER   319      66.303  68.685  87.592  1.00  0.00              
ATOM    114  CA  SER   319      65.446  69.563  86.804  1.00  0.00              
ATOM    115  C   SER   319      63.961  69.241  86.794  1.00  0.00              
ATOM    116  O   SER   319      63.135  70.137  86.931  1.00  0.00              
ATOM    117  N   THR   320      63.633  67.967  86.626  1.00  0.00              
ATOM    118  CA  THR   320      62.243  67.552  86.598  1.00  0.00              
ATOM    119  C   THR   320      62.175  66.041  86.646  1.00  0.00              
ATOM    120  O   THR   320      63.214  65.378  86.657  1.00  0.00              
ATOM    121  N   TYR   321      60.964  65.490  86.662  1.00  0.00              
ATOM    122  CA  TYR   321      60.781  64.039  86.729  1.00  0.00              
ATOM    123  C   TYR   321      60.529  63.383  85.383  1.00  0.00              
ATOM    124  O   TYR   321      59.587  63.734  84.677  1.00  0.00              
ATOM    125  N   THR   322      61.378  62.418  85.042  1.00  0.00              
ATOM    126  CA  THR   322      61.255  61.690  83.789  1.00  0.00              
ATOM    127  C   THR   322      60.215  60.585  83.926  1.00  0.00              
ATOM    128  O   THR   322      59.858  59.936  82.946  1.00  0.00              
ATOM    129  N   GLY   323      59.750  60.376  85.154  1.00  0.00              
ATOM    130  CA  GLY   323      58.755  59.349  85.450  1.00  0.00              
ATOM    131  C   GLY   323      57.328  59.849  85.233  1.00  0.00              
ATOM    132  O   GLY   323      56.367  59.082  85.333  1.00  0.00              
ATOM    133  N   ARG   324      57.196  61.142  84.951  1.00  0.00              
ATOM    134  CA  ARG   324      55.899  61.754  84.688  1.00  0.00              
ATOM    135  C   ARG   324      55.838  61.987  83.180  1.00  0.00              
ATOM    136  O   ARG   324      56.726  62.610  82.608  1.00  0.00              
ATOM    137  N   PRO   325      54.796  61.469  82.541  1.00  0.00              
ATOM    138  CA  PRO   325      54.644  61.591  81.095  1.00  0.00              
ATOM    139  C   PRO   325      54.774  63.009  80.550  1.00  0.00              
ATOM    140  O   PRO   325      55.564  63.259  79.637  1.00  0.00              
ATOM    141  N   PRO   326      53.995  63.936  81.096  1.00  0.00              
ATOM    142  CA  PRO   326      54.040  65.319  80.628  1.00  0.00              
ATOM    143  C   PRO   326      55.385  65.980  80.909  1.00  0.00              
ATOM    144  O   PRO   326      55.951  66.649  80.043  1.00  0.00              
ATOM    145  N   ASP   327      55.898  65.784  82.119  1.00  0.00              
ATOM    146  CA  ASP   327      57.166  66.387  82.495  1.00  0.00              
ATOM    147  C   ASP   327      58.339  65.842  81.684  1.00  0.00              
ATOM    148  O   ASP   327      59.247  66.591  81.321  1.00  0.00              
ATOM    149  N   GLU   328      58.329  64.543  81.398  1.00  0.00              
ATOM    150  CA  GLU   328      59.402  63.958  80.598  1.00  0.00              
ATOM    151  C   GLU   328      59.433  64.638  79.229  1.00  0.00              
ATOM    152  O   GLU   328      60.494  65.016  78.737  1.00  0.00              
ATOM    153  N   PRO   329      58.263  64.779  78.613  1.00  0.00              
ATOM    154  CA  PRO   329      58.171  65.422  77.303  1.00  0.00              
ATOM    155  C   PRO   329      58.727  66.840  77.388  1.00  0.00              
ATOM    156  O   PRO   329      59.474  67.285  76.515  1.00  0.00              
ATOM    157  N   ALA   330      60.917  68.086  79.597  1.00  0.00              
ATOM    158  CA  ALA   330      62.363  68.107  79.788  1.00  0.00              
ATOM    159  C   ALA   330      63.118  67.877  78.484  1.00  0.00              
ATOM    160  O   ALA   330      64.244  68.348  78.326  1.00  0.00              
ATOM    161  N   VAL   331      62.506  67.157  77.548  1.00  0.00              
ATOM    162  CA  VAL   331      63.165  66.918  76.273  1.00  0.00              
ATOM    163  C   VAL   331      62.708  67.878  75.189  1.00  0.00              
ATOM    164  O   VAL   331      62.941  67.649  74.003  1.00  0.00              
ATOM    165  N   LEU   332      62.063  68.961  75.608  1.00  0.00              
ATOM    166  CA  LEU   332      61.610  69.990  74.682  1.00  0.00              
ATOM    167  C   LEU   332      62.756  70.991  74.549  1.00  0.00              
ATOM    168  O   LEU   332      63.275  71.490  75.549  1.00  0.00              
ATOM    169  N   GLY   333      63.152  71.276  73.314  1.00  0.00              
ATOM    170  CA  GLY   333      64.250  72.201  73.060  1.00  0.00              
ATOM    171  C   GLY   333      64.117  73.575  73.689  1.00  0.00              
ATOM    172  O   GLY   333      65.075  74.083  74.270  1.00  0.00              
ATOM    173  N   ALA   335      62.941  74.183  73.576  1.00  0.00              
ATOM    174  CA  ALA   335      62.741  75.510  74.141  1.00  0.00              
ATOM    175  C   ALA   335      62.877  75.480  75.658  1.00  0.00              
ATOM    176  O   ALA   335      63.463  76.382  76.253  1.00  0.00              
ATOM    177  N   LEU   336      62.332  74.438  76.275  1.00  0.00              
ATOM    178  CA  LEU   336      62.411  74.272  77.722  1.00  0.00              
ATOM    179  C   LEU   336      63.877  74.238  78.136  1.00  0.00              
ATOM    180  O   LEU   336      64.298  74.973  79.029  1.00  0.00              
ATOM    181  N   ASN   337      64.650  73.384  77.474  1.00  0.00              
ATOM    182  CA  ASN   337      66.071  73.245  77.780  1.00  0.00              
ATOM    183  C   ASN   337      66.822  74.562  77.654  1.00  0.00              
ATOM    184  O   ASN   337      67.617  74.916  78.521  1.00  0.00              
ATOM    185  N   GLU   338      66.571  75.293  76.575  1.00  0.00              
ATOM    186  CA  GLU   338      67.253  76.564  76.372  1.00  0.00              
ATOM    187  C   GLU   338      66.933  77.567  77.467  1.00  0.00              
ATOM    188  O   GLU   338      67.812  78.282  77.943  1.00  0.00              
ATOM    189  N   PRO   342      65.668  77.611  77.865  1.00  0.00              
ATOM    190  CA  PRO   342      65.215  78.524  78.902  1.00  0.00              
ATOM    191  C   PRO   342      65.851  78.164  80.246  1.00  0.00              
ATOM    192  O   PRO   342      66.336  79.030  80.978  1.00  0.00              
ATOM    193  N   ILE   343      65.848  76.874  80.557  1.00  0.00              
ATOM    194  CA  ILE   343      66.409  76.380  81.806  1.00  0.00              
ATOM    195  C   ILE   343      67.924  76.534  81.823  1.00  0.00              
ATOM    196  O   ILE   343      68.502  76.882  82.849  1.00  0.00              
ATOM    197  N   LEU   344      68.560  76.285  80.681  1.00  0.00              
ATOM    198  CA  LEU   344      70.007  76.419  80.580  1.00  0.00              
ATOM    199  C   LEU   344      70.393  77.859  80.887  1.00  0.00              
ATOM    200  O   LEU   344      71.414  78.120  81.526  1.00  0.00              
ATOM    201  N   GLN   345      69.578  78.801  80.425  1.00  0.00              
ATOM    202  CA  GLN   345      69.870  80.205  80.682  1.00  0.00              
ATOM    203  C   GLN   345      69.697  80.491  82.166  1.00  0.00              
ATOM    204  O   GLN   345      70.459  81.260  82.749  1.00  0.00              
ATOM    205  N   LYS   346      68.689  79.870  82.770  1.00  0.00              
ATOM    206  CA  LYS   346      68.447  80.066  84.188  1.00  0.00              
ATOM    207  C   LYS   346      69.615  79.546  85.006  1.00  0.00              
ATOM    208  O   LYS   346      70.058  80.190  85.958  1.00  0.00              
END
