
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  ------------ 10/2009               #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

!!!   License for LGA program has expired  !!!
#   For updated version of the LGA program   #
# please contact Adam Zemla:  adamz@llnl.gov #

# Molecule1: number of CA atoms   68 (  513),  selected   68 , name one
# Molecule2: number of CA atoms  401 ( 3055),  selected   68 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    68     306_A - 373_A       2.84     2.84
  LCS_AVERAGE:     16.96

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    54     316_A - 369_A       1.99     3.30
  LCS_AVERAGE:     12.84

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24     308_A - 331_A       0.94     5.29
  LONGEST_CONTINUOUS_SEGMENT:    24     320_A - 343_A       0.98     3.77
  LCS_AVERAGE:      5.50

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   68
LCS_GDT     RESIDUE       RESIDUE       SEGMENT_SIZE    GLOBAL DISTANCE TEST COLUMNS: number of residues under the threshold assigned to each residue pair
LCS_GDT   NAME NUMBER   NAME NUMBER    1.0  2.0  5.0    0.5  1.0  1.5  2.0  2.5  3.0  3.5  4.0  4.5  5.0  5.5  6.0  6.5  7.0  7.5  8.0  8.5  9.0  9.5 10.0
LCS_GDT     G   306_A     G   306_A      3    3   68      0    3    4    4    4    8   10   14   17   22   34   49   67   68   68   68   68   68   68   68 
LCS_GDT     A   307_A     A   307_A      3   37   68      3    3    4    4    6    8   10   17   25   27   34   49   55   68   68   68   68   68   68   68 
LCS_GDT     T   308_A     T   308_A     24   44   68     15   19   26   33   44   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     P   309_A     P   309_A     24   44   68     15   19   26   38   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     E   310_A     E   310_A     24   44   68     15   19   26   33   45   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     E   311_A     E   311_A     24   44   68     15   19   26   33   44   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     I   312_A     I   312_A     24   44   68     15   19   26   33   44   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     A   313_A     A   313_A     24   44   68     15   19   26   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     E   314_A     E   314_A     24   44   68     15   19   26   33   44   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     A   315_A     A   315_A     24   44   68     15   19   26   33   44   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     Q   316_A     Q   316_A     24   54   68     15   19   26   36   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     W   317_A     W   317_A     24   54   68     15   20   26   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     A   318_A     A   318_A     24   54   68     15   19   26   33   44   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     I   319_A     I   319_A     24   54   68     15   19   26   33   46   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     S   320_A     S   320_A     24   54   68     15   19   26   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     R   321_A     R   321_A     24   54   68     15   20   26   37   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     L   322_A     L   322_A     24   54   68     15   19   26   33   46   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     L   323_A     L   323_A     24   54   68     14   19   26   39   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     A   324_A     A   324_A     24   54   68     15   20   26   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     T   325_A     T   325_A     24   54   68     12   20   26   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     A   326_A     A   326_A     24   54   68     13   20   25   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     A   327_A     A   327_A     24   54   68     15   20   26   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     A   328_A     A   328_A     24   54   68     15   20   26   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     E   329_A     E   329_A     24   54   68     15   20   26   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     L   330_A     L   330_A     24   54   68     15   20   26   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     S   331_A     S   331_A     24   54   68     15   20   26   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     A   332_A     A   332_A     24   54   68     15   20   26   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     L   333_A     L   333_A     24   54   68     15   20   26   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     E   334_A     E   334_A     24   54   68     15   20   26   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     R   335_A     R   335_A     24   54   68     15   20   26   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     V   336_A     V   336_A     24   54   68     15   20   26   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     L   337_A     L   337_A     24   54   68     15   20   26   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     E   338_A     E   338_A     24   54   68     15   20   26   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     T   339_A     T   339_A     24   54   68     15   20   26   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     L   340_A     L   340_A     24   54   68     15   20   26   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     L   341_A     L   341_A     24   54   68     15   20   26   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     K   342_A     K   342_A     24   54   68      4   20   26   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     H   343_A     H   343_A     24   54   68      6   17   26   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     V   344_A     V   344_A     21   54   68      4   15   24   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     A   345_A     A   345_A      5   54   68      4    5   12   23   45   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     E   346_A     E   346_A     23   54   68      4    4   21   38   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     A   347_A     A   347_A     23   54   68      4    4   22   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     D   348_A     D   348_A     23   54   68     13   17   26   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     K   349_A     K   349_A     23   54   68     13   17   26   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     A   350_A     A   350_A     23   54   68     13   17   26   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     R   351_A     R   351_A     23   54   68     13   17   24   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     V   352_A     V   352_A     23   54   68     13   17   24   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     E   353_A     E   353_A     23   54   68     13   17   26   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     A   354_A     A   354_A     23   54   68     13   17   24   40   48   57   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     A   355_A     A   355_A     23   54   68     13   17   24   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     L   356_A     L   356_A     23   54   68     13   17   24   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     A   357_A     A   357_A     23   54   68     11   17   24   40   48   57   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     R   358_A     R   358_A     23   54   68     11   17   24   40   48   53   60   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     V   359_A     V   359_A     23   54   68     13   17   24   40   48   57   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     E   360_A     E   360_A     23   54   68     13   17   26   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     T   361_A     T   361_A     23   54   68     11   17   24   40   48   57   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     T   362_A     T   362_A     23   54   68     13   17   24   40   48   54   62   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     R   363_A     R   363_A     23   54   68     13   17   24   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     A   364_A     A   364_A     23   54   68      6   17   26   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     G   365_A     G   365_A     23   54   68      6   19   26   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     L   366_A     L   366_A     23   54   68      6   17   26   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     I   367_A     I   367_A     23   54   68      6   17   24   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     D   368_A     D   368_A     23   54   68      6   20   26   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     I   369_A     I   369_A     21   54   68      6   13   22   40   48   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     F   370_A     F   370_A     15   53   68      4    9   14   24   33   48   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     R   371_A     R   371_A     15   53   68      4   13   18   29   47   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     E   372_A     E   372_A     12   50   68      4    8   12   19   40   58   63   65   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_GDT     A   373_A     A   373_A     12   37   68      4    5   12   12   20   26   41   55   66   66   66   66   67   68   68   68   68   68   68   68 
LCS_AVERAGE  LCS_A:  11.77  (   5.50   12.84   16.96 )

GLOBAL_DISTANCE_TEST (summary information about detected largest sets of residues (represented by selected AToms) that can fit under specified thresholds)
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_AT     15     20     26     40     48     58     63     65     66     66     66     66     67     68     68     68     68     68     68     68 
GDT PERCENT_AT   3.74   4.99   6.48   9.98  11.97  14.46  15.71  16.21  16.46  16.46  16.46  16.46  16.71  16.96  16.96  16.96  16.96  16.96  16.96  16.96
GDT RMS_LOCAL    0.27   0.50   0.98   1.49   1.68   2.16   2.27   2.32   2.40   2.40   2.40   2.40   2.63   2.84   2.84   2.84   2.84   2.84   2.84   2.84
GDT RMS_ALL_AT   6.66   4.11   5.86   4.14   3.65   2.90   2.90   2.91   2.89   2.89   2.89   2.89   2.85   2.84   2.84   2.84   2.84   2.84   2.84   2.84

# Checking swapping
#   possible swapping detected:  E   353_A      E   353_A
#   possible swapping detected:  E   360_A      E   360_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G   306_A      G   306_A     9.702     0    0.300   0.300    10.048    0.595    0.595
LGA    A   307_A      A   307_A    10.120     0    0.648   0.587    12.389    3.571    2.857
LGA    T   308_A      T   308_A     3.363     0    0.615   1.301     5.659   46.429   54.014
LGA    P   309_A      P   309_A     1.931     0    0.111   0.315     2.736   70.833   67.143
LGA    E   310_A      E   310_A     2.885     0    0.054   0.956     5.759   55.476   43.069
LGA    E   311_A      E   311_A     3.982     0    0.050   0.056     7.250   46.667   31.534
LGA    I   312_A      I   312_A     2.787     0    0.058   0.091     4.865   62.976   51.726
LGA    A   313_A      A   313_A     1.988     0    0.022   0.032     2.801   68.810   66.476
LGA    E   314_A      E   314_A     3.253     0    0.020   0.414     8.614   55.476   34.074
LGA    A   315_A      A   315_A     3.485     0    0.007   0.011     4.400   55.357   51.714
LGA    Q   316_A      Q   316_A     2.456     0    0.063   1.139     9.732   66.786   39.577
LGA    W   317_A      W   317_A     2.346     0    0.023   1.589     7.949   66.786   45.442
LGA    A   318_A      A   318_A     3.065     0    0.031   0.031     4.108   57.262   53.238
LGA    I   319_A      I   319_A     2.550     0    0.051   0.065     4.531   64.881   52.679
LGA    S   320_A      S   320_A     2.111     0    0.013   0.098     3.022   66.786   62.381
LGA    R   321_A      R   321_A     2.576     0    0.050   1.291     5.522   60.952   49.091
LGA    L   322_A      L   322_A     2.138     0    0.082   1.382     7.027   70.833   49.167
LGA    L   323_A      L   323_A     2.007     0    0.020   0.070     3.429   68.810   61.190
LGA    A   324_A      A   324_A     2.407     0    0.046   0.051     2.819   66.786   64.857
LGA    T   325_A      T   325_A     2.034     0    0.026   0.085     2.685   70.833   68.299
LGA    A   326_A      A   326_A     1.311     0    0.019   0.026     1.409   81.429   81.429
LGA    A   327_A      A   327_A     1.506     0    0.019   0.019     1.629   75.000   74.571
LGA    A   328_A      A   328_A     1.762     0    0.023   0.021     1.994   72.857   72.857
LGA    E   329_A      E   329_A     1.574     0    0.037   0.176     1.577   75.000   79.630
LGA    L   330_A      L   330_A     1.307     0    0.043   0.058     1.912   81.429   78.214
LGA    S   331_A      S   331_A     1.015     0    0.035   0.088     1.129   81.429   84.444
LGA    A   332_A      A   332_A     1.434     0    0.023   0.026     1.679   77.143   76.286
LGA    L   333_A      L   333_A     1.557     0    0.070   0.093     2.381   77.143   73.988
LGA    E   334_A      E   334_A     1.005     0    0.053   1.124     3.982   81.429   76.402
LGA    R   335_A      R   335_A     1.290     0    0.020   0.967     5.281   77.143   61.429
LGA    V   336_A      V   336_A     1.857     0    0.010   0.032     2.341   70.833   69.388
LGA    L   337_A      L   337_A     1.653     0    0.057   0.120     2.005   72.857   73.988
LGA    E   338_A      E   338_A     1.565     0    0.065   0.162     2.008   72.976   77.672
LGA    T   339_A      T   339_A     2.215     0    0.188   1.182     3.698   59.524   55.646
LGA    L   340_A      L   340_A     2.076     0    0.179   0.377     3.792   64.881   57.560
LGA    L   341_A      L   341_A     2.116     0    0.059   0.129     2.798   64.881   65.833
LGA    K   342_A      K   342_A     2.075     0    0.195   0.974     8.326   68.810   44.656
LGA    H   343_A      H   343_A     1.818     0    0.096   1.285     9.239   77.143   43.381
LGA    V   344_A      V   344_A     1.189     0    0.049   0.068     1.885   83.690   84.150
LGA    A   345_A      A   345_A     2.661     0    0.033   0.042     4.111   64.881   59.333
LGA    E   346_A      E   346_A     1.799     0    0.356   1.509     6.210   77.381   56.984
LGA    A   347_A      A   347_A     1.336     0    0.132   0.148     1.708   86.190   83.524
LGA    D   348_A      D   348_A     1.648     0    0.195   0.182     2.491   72.857   69.821
LGA    K   349_A      K   349_A     1.679     0    0.053   0.667     1.890   72.857   80.741
LGA    A   350_A      A   350_A     2.187     0    0.026   0.040     2.632   66.786   64.857
LGA    R   351_A      R   351_A     2.308     0    0.031   1.110     4.646   64.762   62.468
LGA    V   352_A      V   352_A     1.906     0    0.087   0.108     2.038   70.833   71.701
LGA    E   353_A      E   353_A     1.935     0    0.045   0.339     3.520   68.810   63.333
LGA    A   354_A      A   354_A     2.849     0    0.027   0.027     3.354   57.262   55.810
LGA    A   355_A      A   355_A     2.837     0    0.021   0.033     3.010   57.143   55.714
LGA    L   356_A      L   356_A     1.904     0    0.043   0.123     2.728   66.786   65.833
LGA    A   357_A      A   357_A     2.851     0    0.037   0.043     3.319   55.476   54.381
LGA    R   358_A      R   358_A     3.748     0    0.048   0.651     7.304   46.667   30.563
LGA    V   359_A      V   359_A     2.910     0    0.032   0.084     3.232   57.143   56.122
LGA    E   360_A      E   360_A     2.015     0    0.067   0.356     3.499   64.762   64.921
LGA    T   361_A      T   361_A     2.972     0    0.026   0.060     3.744   53.571   51.088
LGA    T   362_A      T   362_A     3.446     0    0.068   1.027     6.450   50.000   45.374
LGA    R   363_A      R   363_A     2.615     0    0.078   1.043     3.273   60.952   62.814
LGA    A   364_A      A   364_A     2.117     0    0.016   0.018     2.316   66.786   66.381
LGA    G   365_A      G   365_A     2.025     0    0.040   0.040     2.183   68.810   68.810
LGA    L   366_A      L   366_A     2.265     0    0.045   1.428     6.037   66.786   48.631
LGA    I   367_A      I   367_A     2.001     0    0.028   0.073     2.633   68.810   65.833
LGA    D   368_A      D   368_A     0.899     0    0.138   0.160     1.307   88.214   87.083
LGA    I   369_A      I   369_A     1.279     0    0.038   0.120     2.420   73.095   70.952
LGA    F   370_A      F   370_A     3.467     0    0.079   0.510     6.476   48.571   33.766
LGA    R   371_A      R   371_A     2.309     0    0.139   0.923     3.076   59.167   71.991
LGA    E   372_A      E   372_A     3.801     0    0.027   1.315     7.004   39.524   35.291
LGA    A   373_A      A   373_A     5.508     0    0.522   0.544     6.883   22.262   22.095

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       68     272    272  100.00     513    513  100.00               401
SUMMARY(RMSD_GDC):     2.839          2.762                  3.362           10.872    9.992

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   68  401    4.0     65    2.32    12.032    13.030     2.683

LGA_LOCAL      RMSD:   2.323  Number of atoms:   65  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.914  Number of assigned atoms:   68 
Std_ASGN_ATOMS RMSD:   2.839  Standard rmsd on all 68 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.099700 * X  +  -0.438411 * Y  +  -0.893228 * Z  +  81.447578
  Y_new =   0.123607 * X  +   0.885290 * Y  +  -0.448311 * Z  + -21.295338
  Z_new =   0.987310 * X  +  -0.155106 * Y  +  -0.034072 * Z  +  -3.374175 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.249540 -1.411317 -1.787035   [DEG:  128.8892  -80.8625 -102.3895 ]
ZXZ: -1.105630  1.604875  1.726622   [DEG:  -63.3479   91.9526   98.9281 ]
 
# END of job
