
#######################################################
#                                                     #
#                        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   97 (  681),  selected   64 , name one
# Molecule2: number of CA atoms   64 (  433),  selected   64 , 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:    64      22_A - 85_A        4.39     4.39
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      61_A - 85_A        1.98     4.99
  LCS_AVERAGE:     30.69

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17      69_A - 85_A        0.78     5.15
  LCS_AVERAGE:     19.68

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   64
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    22_A     A    22_A      3    3   64      3    3    3    3    8   10   14   21   22   28   33   58   59   62   62   62   62   62   63   63 
LCS_GDT     D    23_A     D    23_A      3    4   64      3    3    5    7    9   21   27   35   43   56   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     G    24_A     G    24_A      3   16   64      3    3    9   20   36   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     D    25_A     D    25_A     14   16   64      4    4   19   33   37   42   46   49   52   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     G    26_A     G    26_A     14   16   64      4   28   31   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     Q    27_A     Q    27_A     14   16   64      9   28   31   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     G    28_A     G    28_A     14   16   64      7   28   31   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     L    29_A     L    29_A     14   16   64     11   28   31   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     Y    30_A     Y    30_A     14   16   64     14   28   31   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     A    31_A     A    31_A     14   16   64     13   28   31   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     A    32_A     A    32_A     14   16   64     14   28   31   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     N    33_A     N    33_A     14   16   64     14   28   31   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     C    34_A     C    34_A     14   16   64      7   28   31   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     A    35_A     A    35_A     14   16   64      4   28   31   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     A    36_A     A    36_A     14   16   64     14   28   31   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     C    37_A     C    37_A     14   16   64      4   25   31   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     H    38_A     H    38_A     14   16   64      6   28   31   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     G    39_A     G    39_A      7   16   64      5    7   20   32   37   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     A    40_A     A    40_A      7    7   64      5    7    7    9   12   17   28   43   52   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     L    41_A     L    41_A      7    7   64      5    7    7    7    7    7    8    9   19   25   28   34   43   52   57   61   62   62   63   63 
LCS_GDT     A    42_A     A    42_A      7    7   64      5    7    7    7    7    7    9    9   14   20   26   27   32   37   42   52   57   60   63   63 
LCS_GDT     T    43_A     T    43_A      7    7   64      5    7    7    7    7   10   16   21   25   29   34   49   58   62   62   62   62   62   63   63 
LCS_GDT     S    44_A     S    44_A      7    7   64      4    7    7   10   14   17   23   29   42   55   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     E    45_A     E    45_A      7   19   64      5    7   15   17   19   22   43   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     K    46_A     K    46_A      4   21   64      3    4   10   16   19   21   31   49   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     K    47_A     K    47_A      4   21   64      3    4    5    8   14   25   36   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     G    48_A     G    48_A      4   21   64      2    4    8   20   25   32   38   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     T    49_A     T    49_A     15   21   64     10   13   14   16   19   21   26   47   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     T    50_A     T    50_A     15   21   64     11   13   14   16   20   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     L    51_A     L    51_A     15   21   64     11   13   15   17   24   42   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     A    52_A     A    52_A     15   21   64     11   13   18   32   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     R    53_A     R    53_A     15   21   64     11   13   16   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     L    54_A     L    54_A     15   21   64     11   13   15   23   35   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     Q    55_A     Q    55_A     15   21   64     11   13   15   20   33   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     S    56_A     S    56_A     15   21   64     11   13   18   32   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     A    57_A     A    57_A     15   21   64     11   13   20   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     V    58_A     V    58_A     15   21   64     11   13   15   18   25   42   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     S    59_A     S    59_A     15   21   64     11   13   15   17   22   31   47   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     A    60_A     A    60_A     15   21   64     11   13   15   17   28   38   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     N    61_A     N    61_A     15   25   64      9   13   18   32   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     A    62_A     A    62_A     15   25   64      3   18   31   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     G    63_A     G    63_A     15   25   64      3   18   31   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     G    64_A     G    64_A      6   25   64      3   19   31   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     M    65_A     M    65_A      6   25   64      3   19   31   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     G    66_A     G    66_A      6   25   64      3    9   20   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     F    67_A     F    67_A      4   25   64      3    3    4    7    9   27   33   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     L    68_A     L    68_A      4   25   64      3    4    5    7    9   16   44   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     S    69_A     S    69_A     17   25   64      3   28   31   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     S    70_A     S    70_A     17   25   64      3    7   13   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     L    71_A     L    71_A     17   25   64     12   28   31   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     T    72_A     T    72_A     17   25   64     14   28   31   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     S    73_A     S    73_A     17   25   64      7   28   31   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     A    74_A     A    74_A     17   25   64     14   28   31   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     Q    75_A     Q    75_A     17   25   64     14   28   31   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     L    76_A     L    76_A     17   25   64     14   28   31   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     Q    77_A     Q    77_A     17   25   64     14   28   31   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     A    78_A     A    78_A     17   25   64     14   28   31   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     I    79_A     I    79_A     17   25   64     14   28   31   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     V    80_A     V    80_A     17   25   64     14   28   31   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     D    81_A     D    81_A     17   25   64     14   28   31   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     V    82_A     V    82_A     17   25   64     14   28   31   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     L    83_A     L    83_A     17   25   64     13   28   31   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     A    84_A     A    84_A     17   25   64     13   28   31   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_GDT     V    85_A     V    85_A     17   25   64      3   28   31   33   39   43   48   50   54   57   58   60   60   62   62   62   62   62   63   63 
LCS_AVERAGE  LCS_A:  50.12  (  19.68   30.69  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     14     28     31     33     39     43     48     50     54     57     58     60     60     62     62     62     62     62     63     63 
GDT PERCENT_AT  21.88  43.75  48.44  51.56  60.94  67.19  75.00  78.12  84.38  89.06  90.62  93.75  93.75  96.88  96.88  96.88  96.88  96.88  98.44  98.44
GDT RMS_LOCAL    0.34   0.63   0.80   0.88   1.45   1.75   2.08   2.24   2.62   2.84   3.00   3.29   3.29   3.72   3.72   3.72   3.72   3.72   4.00   4.00
GDT RMS_ALL_AT   5.04   5.15   5.13   5.13   5.14   5.01   5.00   5.01   4.80   4.70   4.63   4.52   4.52   4.44   4.44   4.44   4.44   4.44   4.41   4.41

# Checking swapping
#   possible swapping detected:  D    23_A      D    23_A
#   possible swapping detected:  Y    30_A      Y    30_A
#   possible swapping detected:  F    67_A      F    67_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    22_A      A    22_A    10.871     0    0.644   0.606    10.871    0.476    0.381
LGA    D    23_A      D    23_A     8.652     0    0.742   1.053    13.789   10.714    5.417
LGA    G    24_A      G    24_A     4.015     0    0.450   0.450     6.150   39.048   39.048
LGA    D    25_A      D    25_A     3.367     0    0.332   1.046     9.939   48.095   29.167
LGA    G    26_A      G    26_A     1.801     0    0.082   0.082     1.934   72.857   72.857
LGA    Q    27_A      Q    27_A     1.487     0    0.037   1.210     4.032   79.286   66.561
LGA    G    28_A      G    28_A     1.555     0    0.059   0.059     1.641   77.143   77.143
LGA    L    29_A      L    29_A     1.191     0    0.033   0.891     4.034   85.952   68.393
LGA    Y    30_A      Y    30_A     0.716     0    0.042   0.156     2.226   90.476   83.889
LGA    A    31_A      A    31_A     0.891     0    0.059   0.057     1.143   90.476   88.667
LGA    A    32_A      A    32_A     0.611     0    0.103   0.101     0.890   90.476   90.476
LGA    N    33_A      N    33_A     0.841     0    0.183   0.983     2.710   83.810   81.845
LGA    C    34_A      C    34_A     0.752     0    0.023   0.145     0.941   90.476   92.063
LGA    A    35_A      A    35_A     1.346     0    0.080   0.076     1.741   83.690   81.524
LGA    A    36_A      A    36_A     0.508     0    0.105   0.103     0.873   90.476   90.476
LGA    C    37_A      C    37_A     1.235     0    0.053   0.691     3.494   81.429   76.190
LGA    H    38_A      H    38_A     1.077     0    0.623   0.439     3.587   77.619   66.429
LGA    G    39_A      G    39_A     3.187     0    0.557   0.557     6.094   39.524   39.524
LGA    A    40_A      A    40_A     8.964     0    0.076   0.098    10.743    4.048    3.238
LGA    L    41_A      L    41_A    14.815     0    0.044   1.074    20.688    0.000    0.000
LGA    A    42_A      A    42_A    18.303     0    0.134   0.131    19.714    0.000    0.000
LGA    T    43_A      T    43_A    13.500     0    0.372   1.229    14.587    0.000    0.000
LGA    S    44_A      S    44_A    10.185     0    0.213   0.763    12.806    2.976    1.984
LGA    E    45_A      E    45_A     6.017     0    0.487   0.684    10.225   13.690   10.899
LGA    K    46_A      K    46_A     6.836     0    0.577   1.241     7.109   13.333   22.222
LGA    K    47_A      K    47_A     7.167     0    0.147   0.678     9.989   10.000    7.354
LGA    G    48_A      G    48_A     6.711     0    0.558   0.558     6.788   28.810   28.810
LGA    T    49_A      T    49_A     5.489     0    0.582   1.373    10.224   27.619   17.483
LGA    T    50_A      T    50_A     3.592     0    0.051   1.069     4.119   45.119   49.388
LGA    L    51_A      L    51_A     3.619     0    0.034   1.049     5.483   48.333   41.429
LGA    A    52_A      A    52_A     2.131     0    0.053   0.058     2.455   68.810   69.619
LGA    R    53_A      R    53_A     1.895     0    0.040   1.260     5.984   70.833   54.286
LGA    L    54_A      L    54_A     2.881     0    0.032   1.377     6.941   57.143   40.298
LGA    Q    55_A      Q    55_A     3.260     0    0.032   0.709     3.461   53.571   57.407
LGA    S    56_A      S    56_A     2.196     0    0.068   0.693     2.514   62.857   67.619
LGA    A    57_A      A    57_A     1.631     0    0.032   0.041     2.304   68.810   71.333
LGA    V    58_A      V    58_A     3.633     0    0.029   0.059     4.939   45.238   40.952
LGA    S    59_A      S    59_A     4.415     0    0.108   0.202     5.643   37.262   34.603
LGA    A    60_A      A    60_A     3.763     0    0.315   0.318     4.674   42.024   43.619
LGA    N    61_A      N    61_A     2.061     0    0.556   0.643     3.866   59.405   64.226
LGA    A    62_A      A    62_A     0.805     0    0.057   0.079     1.396   85.952   85.048
LGA    G    63_A      G    63_A     1.462     0    0.686   0.686     3.306   75.833   75.833
LGA    G    64_A      G    64_A     1.741     0    0.264   0.264     1.741   77.143   77.143
LGA    M    65_A      M    65_A     1.598     0    0.658   0.801     3.384   67.143   71.250
LGA    G    66_A      G    66_A     1.654     0    0.567   0.567     2.083   70.833   70.833
LGA    F    67_A      F    67_A     4.676     0    0.060   1.129     6.962   38.810   30.736
LGA    L    68_A      L    68_A     4.438     0    0.266   1.062    11.015   43.452   24.048
LGA    S    69_A      S    69_A     2.735     0    0.244   0.607     3.509   57.619   55.079
LGA    S    70_A      S    70_A     2.828     0    0.097   0.088     3.496   61.190   58.651
LGA    L    71_A      L    71_A     1.208     0    0.071   0.080     2.052   75.119   85.179
LGA    T    72_A      T    72_A     1.875     0    0.074   1.106     3.506   75.000   71.088
LGA    S    73_A      S    73_A     2.336     0    0.113   0.600     2.669   64.762   66.270
LGA    A    74_A      A    74_A     1.367     0    0.037   0.040     1.602   77.143   79.810
LGA    Q    75_A      Q    75_A     0.785     0    0.054   1.120     2.282   85.952   81.693
LGA    L    76_A      L    76_A     1.428     0    0.030   0.147     1.837   77.143   77.143
LGA    Q    77_A      Q    77_A     1.743     0    0.045   1.408     6.741   72.857   53.704
LGA    A    78_A      A    78_A     1.350     0    0.023   0.031     1.467   81.429   81.429
LGA    I    79_A      I    79_A     1.271     0    0.033   1.278     3.418   79.286   70.357
LGA    V    80_A      V    80_A     1.898     0    0.027   0.104     2.306   70.833   69.388
LGA    D    81_A      D    81_A     1.993     0    0.039   0.511     2.616   68.810   67.857
LGA    V    82_A      V    82_A     1.806     0    0.087   0.934     3.384   72.857   72.109
LGA    L    83_A      L    83_A     1.883     0    0.170   0.907     3.841   75.000   69.226
LGA    A    84_A      A    84_A     2.424     0    0.093   0.090     2.499   64.762   64.762
LGA    V    85_A      V    85_A     2.465     0    0.252   1.311     4.292   64.762   62.109

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       64     256    256  100.00     433    433  100.00                64
SUMMARY(RMSD_GDC):     4.387          4.267                  4.844           57.431   54.649

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   97   64    4.0     50    2.24    67.578    61.530     2.136

LGA_LOCAL      RMSD:   2.241  Number of atoms:   50  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.009  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   4.387  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.974396 * X  +  -0.046475 * Y  +   0.219985 * Z  +  -9.335327
  Y_new =  -0.063287 * X  +   0.995537 * Y  +  -0.069999 * Z  +   3.030854
  Z_new =  -0.215750 * X  +  -0.082129 * Y  +  -0.972989 * Z  +  31.700808 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -3.076734  0.217460 -3.057383   [DEG: -176.2839   12.4595 -175.1752 ]
ZXZ:  1.262727  2.908638 -1.934527   [DEG:   72.3489  166.6527 -110.8402 ]
 
# END of job
