
#######################################################
#                                                     #
#                        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 (  529),  selected   67 , name one
# Molecule2: number of CA atoms   67 (  519),  selected   67 , 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:    67       2_A - 68_A        0.69     0.69
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.69     0.69
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.69     0.69
  LCS_AVERAGE:    100.00

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   67
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     S     2_A     S     2_A     67   67   67     14   47   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P     3_A     P     3_A     67   67   67     21   57   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E     4_A     E     4_A     67   67   67     20   58   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E     5_A     E     5_A     67   67   67     16   58   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q     6_A     Q     6_A     67   67   67     24   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K     7_A     K     7_A     67   67   67     48   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q     8_A     Q     8_A     67   67   67     36   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     M     9_A     M     9_A     67   67   67     42   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    10_A     L    10_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    11_A     G    11_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    12_A     E    12_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    13_A     A    13_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    14_A     I    14_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Y    15_A     Y    15_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    16_A     P    16_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    17_A     K    17_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    18_A     V    18_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    19_A     A    19_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    20_A     A    20_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    21_A     S    21_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    22_A     Q    22_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    23_A     P    23_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    24_A     E    24_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    25_A     L    25_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    26_A     A    26_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    27_A     G    27_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    28_A     K    28_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    29_A     L    29_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     T    30_A     T    30_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    31_A     G    31_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     M    32_A     M    32_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    33_A     I    33_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    34_A     L    34_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    35_A     E    35_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    36_A     L    36_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    37_A     P    37_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    38_A     V    38_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     T    39_A     T    39_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    40_A     E    40_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    41_A     L    41_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    42_A     L    42_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     H    43_A     H    43_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    44_A     L    44_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    45_A     L    45_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    46_A     E    46_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    47_A     E    47_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    48_A     S    48_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    49_A     E    49_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    50_A     A    50_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    51_A     L    51_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     D    52_A     D    52_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    53_A     A    53_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    54_A     K    54_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    55_A     V    55_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     N    56_A     N    56_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    57_A     E    57_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    58_A     A    58_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    59_A     L    59_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    60_A     E    60_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    61_A     V    61_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    62_A     L    62_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    63_A     K    63_A     67   67   67     51   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    64_A     E    64_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Y    65_A     Y    65_A     67   67   67     55   59   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    66_A     Q    66_A     67   67   67     21   58   62   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    67_A     Q    67_A     67   67   67      3   58   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     N    68_A     N    68_A     67   67   67      3   58   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_AVERAGE  LCS_A: 100.00  ( 100.00  100.00  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     55     59     64     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67 
GDT PERCENT_AT  82.09  88.06  95.52 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.27   0.36   0.56   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69
GDT RMS_ALL_AT   0.79   0.75   0.70   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69

# Checking swapping
#   possible swapping detected:  E     4_A      E     4_A
#   possible swapping detected:  E     5_A      E     5_A
#   possible swapping detected:  E    12_A      E    12_A
#   possible swapping detected:  Y    15_A      Y    15_A
#   possible swapping detected:  E    24_A      E    24_A
#   possible swapping detected:  E    40_A      E    40_A
#   possible swapping detected:  E    47_A      E    47_A
#   possible swapping detected:  E    49_A      E    49_A
#   possible swapping detected:  E    57_A      E    57_A
#   possible swapping detected:  E    60_A      E    60_A
#   possible swapping detected:  Y    65_A      Y    65_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     2_A      S     2_A     2.174     0    0.030   0.074     2.285   68.810   67.460
LGA    P     3_A      P     3_A     1.459     0    0.009   0.038     1.718   79.286   77.755
LGA    E     4_A      E     4_A     1.416     0    0.025   0.707     4.815   81.429   63.704
LGA    E     5_A      E     5_A     1.423     0    0.048   0.488     4.016   83.690   67.725
LGA    Q     6_A      Q     6_A     1.047     0    0.016   0.287     1.381   85.952   83.439
LGA    K     7_A      K     7_A     0.422     0    0.024   0.630     2.078   97.619   86.878
LGA    Q     8_A      Q     8_A     0.757     0    0.054   0.792     4.357   92.857   76.402
LGA    M     9_A      M     9_A     0.605     0    0.030   0.821     1.741   95.238   88.393
LGA    L    10_A      L    10_A     0.336     0    0.024   0.093     0.591  100.000   98.810
LGA    G    11_A      G    11_A     0.481     0    0.046   0.046     0.570   95.238   95.238
LGA    E    12_A      E    12_A     0.504     0    0.012   0.800     3.050   95.238   86.085
LGA    A    13_A      A    13_A     0.364     0    0.024   0.038     0.523  100.000   98.095
LGA    I    14_A      I    14_A     0.279     0    0.010   0.045     0.341  100.000  100.000
LGA    Y    15_A      Y    15_A     0.314     0    0.009   0.217     0.539  100.000   98.413
LGA    P    16_A      P    16_A     0.324     0    0.012   0.309     1.240  100.000   97.347
LGA    K    17_A      K    17_A     0.254     0    0.013   0.798     3.079  100.000   90.370
LGA    V    18_A      V    18_A     0.393     0    0.011   0.083     0.510   97.619   98.639
LGA    A    19_A      A    19_A     0.457     0    0.016   0.020     0.706   95.238   96.190
LGA    A    20_A      A    20_A     0.427     0    0.058   0.078     0.619   97.619   98.095
LGA    S    21_A      S    21_A     0.258     0    0.064   0.084     0.564  100.000   98.413
LGA    Q    22_A      Q    22_A     0.179     0    0.053   0.086     0.507  100.000   98.942
LGA    P    23_A      P    23_A     0.244     0    0.067   0.068     0.526   97.619   98.639
LGA    E    24_A      E    24_A     0.347     0    0.062   0.607     1.664   95.238   90.794
LGA    L    25_A      L    25_A     0.289     0    0.041   0.071     0.548  100.000   97.619
LGA    A    26_A      A    26_A     0.313     0    0.010   0.015     0.499  100.000  100.000
LGA    G    27_A      G    27_A     0.298     0    0.015   0.015     0.339  100.000  100.000
LGA    K    28_A      K    28_A     0.264     0    0.017   0.737     4.275  100.000   85.185
LGA    L    29_A      L    29_A     0.079     0    0.029   0.073     0.517  100.000   98.810
LGA    T    30_A      T    30_A     0.369     0    0.020   0.080     0.531   97.619   98.639
LGA    G    31_A      G    31_A     0.488     0    0.025   0.025     0.488  100.000  100.000
LGA    M    32_A      M    32_A     0.141     0    0.030   0.080     0.294  100.000  100.000
LGA    I    33_A      I    33_A     0.283     0    0.037   0.078     0.444  100.000  100.000
LGA    L    34_A      L    34_A     0.337     0    0.030   0.097     0.470  100.000  100.000
LGA    E    35_A      E    35_A     0.529     0    0.033   0.746     3.412   92.857   73.545
LGA    L    36_A      L    36_A     0.481     0    0.033   0.061     0.563   95.238   97.619
LGA    P    37_A      P    37_A     0.569     0    0.070   0.315     1.457   90.476   90.544
LGA    V    38_A      V    38_A     0.682     0    0.024   0.036     0.892   90.476   90.476
LGA    T    39_A      T    39_A     0.725     0    0.031   0.983     2.921   90.476   80.952
LGA    E    40_A      E    40_A     0.460     0    0.049   0.828     3.658   97.619   83.968
LGA    L    41_A      L    41_A     0.434     0    0.031   0.061     0.563   97.619   98.810
LGA    L    42_A      L    42_A     0.521     0    0.041   0.052     0.821   95.238   92.857
LGA    H    43_A      H    43_A     0.366     0    0.018   1.153     2.500  100.000   87.619
LGA    L    44_A      L    44_A     0.305     0    0.037   0.074     0.470  100.000  100.000
LGA    L    45_A      L    45_A     0.412     0    0.030   0.058     0.493  100.000  100.000
LGA    E    46_A      E    46_A     0.404     0    0.049   0.830     3.002  100.000   80.159
LGA    E    47_A      E    47_A     0.424     0    0.043   0.729     3.283  100.000   85.767
LGA    S    48_A      S    48_A     0.296     0    0.021   0.072     0.619  100.000   98.413
LGA    E    49_A      E    49_A     0.389     0    0.078   0.200     0.926  100.000   94.709
LGA    A    50_A      A    50_A     0.241     0    0.010   0.022     0.263  100.000  100.000
LGA    L    51_A      L    51_A     0.050     0    0.026   0.090     0.406  100.000  100.000
LGA    D    52_A      D    52_A     0.116     0    0.009   0.134     0.446  100.000  100.000
LGA    A    53_A      A    53_A     0.308     0    0.047   0.063     0.478  100.000  100.000
LGA    K    54_A      K    54_A     0.072     0    0.017   0.550     1.860  100.000   93.968
LGA    V    55_A      V    55_A     0.089     0    0.017   0.051     0.274  100.000  100.000
LGA    N    56_A      N    56_A     0.237     0    0.035   0.058     0.282  100.000  100.000
LGA    E    57_A      E    57_A     0.255     0    0.015   0.220     0.555  100.000   97.884
LGA    A    58_A      A    58_A     0.209     0    0.027   0.027     0.223  100.000  100.000
LGA    L    59_A      L    59_A     0.350     0    0.025   0.228     0.830   97.619   95.238
LGA    E    60_A      E    60_A     0.481     0    0.111   1.073     4.922  100.000   78.783
LGA    V    61_A      V    61_A     0.390     0    0.028   0.060     0.506   95.238   97.279
LGA    L    62_A      L    62_A     0.811     0    0.049   0.731     2.306   88.214   82.917
LGA    K    63_A      K    63_A     1.025     0    0.013   0.203     1.560   85.952   82.487
LGA    E    64_A      E    64_A     0.612     0    0.027   0.907     2.830   90.476   78.413
LGA    Y    65_A      Y    65_A     0.920     0    0.065   0.310     2.143   85.952   80.238
LGA    Q    66_A      Q    66_A     1.620     0    0.013   0.086     3.537   75.000   63.651
LGA    Q    67_A      Q    67_A     1.481     0    0.336   0.573     3.767   77.262   65.556
LGA    N    68_A      N    68_A     2.008     0    0.085   1.003     5.521   49.762   44.405

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       67     268    268  100.00     519    519  100.00                67
SUMMARY(RMSD_GDC):     0.692          0.782                  1.296           94.803   90.333

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   68   67    4.0     67    0.69    97.015    98.723     8.464

LGA_LOCAL      RMSD:   0.692  Number of atoms:   67  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.692  Number of assigned atoms:   67 
Std_ASGN_ATOMS RMSD:   0.692  Standard rmsd on all 67 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.583417 * X  +   0.374017 * Y  +   0.720927 * Z  +   8.987410
  Y_new =  -0.086362 * X  +  -0.911189 * Y  +   0.402835 * Z  +   1.825186
  Z_new =   0.807568 * X  +   0.172760 * Y  +   0.563904 * Z  +   6.654330 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.994632 -0.940017  0.297286   [DEG: -171.5798  -53.8590   17.0332 ]
ZXZ:  2.080351  0.971691  1.360047   [DEG:  119.1953   55.6738   77.9249 ]
 
# END of job
