
#######################################################
#                                                     #
#                        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   98 (  784),  selected   61 , name one
# Molecule2: number of CA atoms   61 (  480),  selected   61 , 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:    61      32_A - 98_A        2.39     2.39
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    40      32_A - 71_A        2.00     2.52
  LONGEST_CONTINUOUS_SEGMENT:    40      33_A - 72_A        1.83     2.45
  LCS_AVERAGE:     62.43

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    21      33_A - 53_A        0.72     3.24
  LCS_AVERAGE:     25.56

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   61
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     A    32_A     A    32_A      3   40   61      3    3    3    3   16   24   28   33   50   54   59   59   61   61   61   61   61   61   61   61 
LCS_GDT     T    33_A     T    33_A     21   40   61     17   27   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     M    34_A     M    34_A     21   40   61     17   27   35   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     A    35_A     A    35_A     21   40   61     17   27   38   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     D    36_A     D    36_A     21   40   61     17   27   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     L    37_A     L    37_A     21   40   61     17   27   38   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     K    38_A     K    38_A     21   40   61     17   27   38   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     M    39_A     M    39_A     21   40   61     17   27   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     Q    40_A     Q    40_A     21   40   61     17   27   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     A    41_A     A    41_A     21   40   61     17   27   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     V    42_A     V    42_A     21   40   61     17   27   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     K    43_A     K    43_A     21   40   61     17   27   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     E    44_A     E    44_A     21   40   61     17   27   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     I    45_A     I    45_A     21   40   61     17   27   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     C    46_A     C    46_A     21   40   61     17   27   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     Y    47_A     Y    47_A     21   40   61     17   27   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     E    48_A     E    48_A     21   40   61     17   27   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     V    49_A     V    49_A     21   40   61     17   27   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     A    50_A     A    50_A     21   40   61     17   27   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     L    51_A     L    51_A     21   40   61      8   27   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     A    52_A     A    52_A     21   40   61      3   16   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     D    53_A     D    53_A     21   40   61      3   16   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     F    54_A     F    54_A      5   40   61      3    4    5    5    8   36   49   55   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     R    55_A     R    55_A      5   40   61     16   27   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     H    56_A     H    56_A      5   40   61      3    5    8   29   49   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     G    57_A     G    57_A     15   40   61      4   21   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     R    58_A     R    58_A     15   40   61      7   27   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     A    59_A     A    59_A     15   40   61      6   26   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     E    60_A     E    60_A     15   40   61      5   23   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     I    61_A     I    61_A     15   40   61      9   14   38   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     E    62_A     E    62_A     15   40   61      9   24   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     A    63_A     A    63_A     15   40   61      9   25   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     L    64_A     L    64_A     15   40   61      9   14   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     A    65_A     A    65_A     15   40   61      9   16   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     A    66_A     A    66_A     15   40   61      5   20   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     L    67_A     L    67_A     15   40   61      9   15   35   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     K    68_A     K    68_A     15   40   61      9   14   28   44   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     M    69_A     M    69_A     15   40   61      9   16   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     R    70_A     R    70_A     15   40   61      9   14   33   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     E    71_A     E    71_A     15   40   61      5   14   22   44   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     L    72_A     L    72_A     14   40   61      4    4   11   20   33   43   54   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     C    73_A     C    73_A      6   36   61      4    4    7    9   22   42   46   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     R    74_A     R    74_A      6   36   61      4    4    7   37   47   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     T    75_A     T    75_A      6   35   61      4    6   12   19   32   44   52   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     Y    76_A     Y    76_A      6   35   61      3    4    9   16   24   34   43   54   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     G    83_A     G    83_A      4   35   61      3    4   13   38   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     D    84_A     D    84_A     15   35   61      8   13   20   47   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     A    85_A     A    85_A     15   35   61      4   10   27   47   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     W    86_A     W    86_A     15   35   61      4   16   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     R    87_A     R    87_A     15   35   61      4   16   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     A    88_A     A    88_A     15   35   61      4   12   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     V    89_A     V    89_A     15   35   61     13   27   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     A    90_A     A    90_A     15   35   61      4   14   38   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     R    91_A     R    91_A     15   35   61      4   24   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     D    92_A     D    92_A     15   35   61     13   27   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     V    93_A     V    93_A     15   35   61     17   27   38   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     W    94_A     W    94_A     15   35   61     13   27   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     D    95_A     D    95_A     15   35   61      5   27   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     T    96_A     T    96_A     15   35   61     16   27   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     V    97_A     V    97_A     15   35   61     16   27   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     G    98_A     G    98_A     15   16   61     16   27   39   48   52   54   55   57   58   59   60   60   61   61   61   61   61   61   61   61 
LCS_AVERAGE  LCS_A:  62.66  (  25.56   62.43  100.00 )

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     17     27     39     48     52     54     55     57     58     59     60     60     61     61     61     61     61     61     61     61 
GDT PERCENT_AT  27.87  44.26  63.93  78.69  85.25  88.52  90.16  93.44  95.08  96.72  98.36  98.36 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.29   0.59   1.07   1.24   1.37   1.48   1.54   1.83   1.94   2.03   2.18   2.18   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39
GDT RMS_ALL_AT   3.06   2.77   2.61   2.55   2.54   2.48   2.49   2.44   2.42   2.42   2.41   2.41   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39

# Checking swapping
#   possible swapping detected:  E    44_A      E    44_A
#   possible swapping detected:  E    48_A      E    48_A
#   possible swapping detected:  E    60_A      E    60_A
#   possible swapping detected:  E    62_A      E    62_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    32_A      A    32_A     8.323     0    0.411   0.409     9.700    9.167    7.429
LGA    T    33_A      T    33_A     1.932     0    0.657   0.522     3.563   67.619   64.354
LGA    M    34_A      M    34_A     2.389     0    0.040   0.797     6.320   64.762   49.762
LGA    A    35_A      A    35_A     2.037     0    0.130   0.140     2.236   70.952   69.714
LGA    D    36_A      D    36_A     1.584     0    0.077   0.184     1.864   77.143   76.071
LGA    L    37_A      L    37_A     1.698     0    0.039   1.402     4.516   72.857   62.738
LGA    K    38_A      K    38_A     2.096     0    0.088   0.687     3.088   68.810   65.873
LGA    M    39_A      M    39_A     1.469     0    0.049   0.829     3.356   81.548   73.452
LGA    Q    40_A      Q    40_A     0.873     0    0.019   0.204     1.147   88.214   91.587
LGA    A    41_A      A    41_A     1.218     0    0.075   0.130     1.614   83.690   81.524
LGA    V    42_A      V    42_A     1.124     0    0.094   0.149     1.710   83.690   80.272
LGA    K    43_A      K    43_A     0.671     0    0.010   0.896     5.391   90.476   69.630
LGA    E    44_A      E    44_A     0.386     0    0.146   0.229     1.257   90.595   89.577
LGA    I    45_A      I    45_A     0.960     0    0.022   0.106     1.721   90.476   83.810
LGA    C    46_A      C    46_A     0.703     0    0.100   0.791     2.834   90.476   84.921
LGA    Y    47_A      Y    47_A     0.342     0    0.039   0.146     0.742  100.000   99.206
LGA    E    48_A      E    48_A     0.743     0    0.032   0.931     3.943   90.595   75.873
LGA    V    49_A      V    49_A     1.266     0    0.026   0.081     1.573   83.690   81.497
LGA    A    50_A      A    50_A     0.790     0    0.102   0.106     0.975   90.476   90.476
LGA    L    51_A      L    51_A     1.415     0    0.601   0.507     3.894   72.024   66.548
LGA    A    52_A      A    52_A     1.997     0    0.369   0.356     2.122   72.857   71.238
LGA    D    53_A      D    53_A     2.206     0    0.316   0.917     4.956   64.762   55.119
LGA    F    54_A      F    54_A     5.039     0    0.254   0.255    12.716   40.714   16.104
LGA    R    55_A      R    55_A     1.257     0    0.569   1.382     4.373   69.286   64.069
LGA    H    56_A      H    56_A     3.397     0    0.570   1.092     9.736   57.381   27.571
LGA    G    57_A      G    57_A     1.188     0    0.172   0.172     1.441   85.952   85.952
LGA    R    58_A      R    58_A     0.625     0    0.031   0.829     3.335   88.214   76.537
LGA    A    59_A      A    59_A     1.087     0    0.040   0.038     1.276   83.690   85.048
LGA    E    60_A      E    60_A     1.183     0    0.052   0.678     2.794   75.119   74.021
LGA    I    61_A      I    61_A     1.821     0    0.000   0.651     4.764   72.857   63.690
LGA    E    62_A      E    62_A     1.218     0    0.030   0.858     2.210   85.952   79.683
LGA    A    63_A      A    63_A     0.482     0    0.031   0.041     1.028   90.595   90.571
LGA    L    64_A      L    64_A     1.520     0    0.211   0.385     2.503   72.976   74.226
LGA    A    65_A      A    65_A     1.577     0    0.021   0.027     1.792   77.143   76.286
LGA    A    66_A      A    66_A     0.893     0    0.056   0.079     1.447   83.690   85.048
LGA    L    67_A      L    67_A     1.446     0    0.019   0.864     5.097   75.119   65.179
LGA    K    68_A      K    68_A     2.211     0    0.000   1.301     3.490   68.810   68.677
LGA    M    69_A      M    69_A     1.239     0    0.000   0.906     4.358   81.429   73.869
LGA    R    70_A      R    70_A     1.540     0    0.077   0.893     3.479   69.048   63.939
LGA    E    71_A      E    71_A     2.551     0    0.218   0.944     5.034   57.262   47.778
LGA    L    72_A      L    72_A     4.915     0    0.116   1.205     9.096   30.595   20.298
LGA    C    73_A      C    73_A     5.684     0    0.031   0.140     7.777   26.310   21.587
LGA    R    74_A      R    74_A     2.938     0    0.261   1.256     9.836   45.238   34.892
LGA    T    75_A      T    75_A     5.258     0    0.061   0.175     6.912   24.524   23.401
LGA    Y    76_A      Y    76_A     7.096     0    0.688   0.656     8.669   11.786    8.810
LGA    G    83_A      G    83_A     2.333     0    0.207   0.207     2.404   66.786   66.786
LGA    D    84_A      D    84_A     2.446     0    0.328   0.491     6.285   64.762   48.512
LGA    A    85_A      A    85_A     2.599     0    0.076   0.090     2.711   60.952   60.190
LGA    W    86_A      W    86_A     1.622     0    0.122   0.334     2.171   72.857   72.925
LGA    R    87_A      R    87_A     1.703     0    0.030   1.346     5.614   72.857   58.139
LGA    A    88_A      A    88_A     1.558     0    0.113   0.126     1.735   77.143   76.286
LGA    V    89_A      V    89_A     0.687     0    0.097   0.125     2.274   88.333   82.993
LGA    A    90_A      A    90_A     1.704     0    0.016   0.020     2.224   77.143   74.667
LGA    R    91_A      R    91_A     1.139     0    0.051   1.359     6.470   90.714   59.740
LGA    D    92_A      D    92_A     0.318     0    0.072   0.201     1.400   92.976   92.976
LGA    V    93_A      V    93_A     1.429     0    0.139   0.275     2.904   85.952   75.782
LGA    W    94_A      W    94_A     0.402     0    0.023   1.650     5.651   95.238   67.551
LGA    D    95_A      D    95_A     1.097     0    0.173   0.488     2.195   79.524   80.536
LGA    T    96_A      T    96_A     0.762     0    0.000   1.000     2.655   88.214   81.905
LGA    V    97_A      V    97_A     0.847     0    0.550   1.323     2.994   79.881   75.986
LGA    G    98_A      G    98_A     0.885     0    0.672   0.672     3.456   73.929   73.929

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       61     244    244  100.00     480    480  100.00                61
SUMMARY(RMSD_GDC):     2.392          2.339                  3.271           72.883   66.669

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   98   61    4.0     57    1.83    79.098    78.938     2.947

LGA_LOCAL      RMSD:   1.834  Number of atoms:   57  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.444  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   2.392  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.978042 * X  +   0.164790 * Y  +  -0.127585 * Z  + -145.798141
  Y_new =   0.085652 * X  +   0.240266 * Y  +   0.966921 * Z  + -146.404999
  Z_new =   0.189993 * X  +  -0.956617 * Y  +   0.220875 * Z  +  67.026642 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.087352 -0.191155 -1.343881   [DEG:    5.0049  -10.9524  -76.9987 ]
ZXZ: -3.010401  1.348085  2.945535   [DEG: -172.4833   77.2396  168.7667 ]
 
# END of job
