
#######################################################
#                                                     #
#                        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        1.31     1.31
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        1.31     1.31
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    64       3_A - 66_A        0.98     1.33
  LONGEST_CONTINUOUS_SEGMENT:    64       4_A - 67_A        0.90     1.34
  LONGEST_CONTINUOUS_SEGMENT:    64       5_A - 68_A        0.98     1.35
  LCS_AVERAGE:     95.46

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     61   67   67      5    8   20   49   58   62   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P     3_A     P     3_A     64   67   67      5    8   26   56   58   62   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E     4_A     E     4_A     64   67   67      5    6   13   39   58   62   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E     5_A     E     5_A     64   67   67     12   51   60   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q     6_A     Q     6_A     64   67   67     35   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K     7_A     K     7_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q     8_A     Q     8_A     64   67   67     24   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     M     9_A     M     9_A     64   67   67     21   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    10_A     L    10_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    11_A     G    11_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    12_A     E    12_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    13_A     A    13_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    14_A     I    14_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Y    15_A     Y    15_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    16_A     P    16_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    17_A     K    17_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    18_A     V    18_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    19_A     A    19_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    20_A     A    20_A     64   67   67     40   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    21_A     S    21_A     64   67   67     26   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    22_A     Q    22_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    23_A     P    23_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    24_A     E    24_A     64   67   67     40   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    25_A     L    25_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    26_A     A    26_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    27_A     G    27_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    28_A     K    28_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    29_A     L    29_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     T    30_A     T    30_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    31_A     G    31_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     M    32_A     M    32_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    33_A     I    33_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    34_A     L    34_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    35_A     E    35_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    36_A     L    36_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    37_A     P    37_A     64   67   67     41   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    38_A     V    38_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     T    39_A     T    39_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    40_A     E    40_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    41_A     L    41_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    42_A     L    42_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     H    43_A     H    43_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    44_A     L    44_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    45_A     L    45_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    46_A     E    46_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    47_A     E    47_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    48_A     S    48_A     64   67   67     41   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    49_A     E    49_A     64   67   67     19   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    50_A     A    50_A     64   67   67     41   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    51_A     L    51_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     D    52_A     D    52_A     64   67   67     19   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    53_A     A    53_A     64   67   67     19   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    54_A     K    54_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    55_A     V    55_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     N    56_A     N    56_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    57_A     E    57_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    58_A     A    58_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    59_A     L    59_A     64   67   67     42   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    60_A     E    60_A     64   67   67     24   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    61_A     V    61_A     64   67   67     13   55   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    62_A     L    62_A     64   67   67     36   56   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    63_A     K    63_A     64   67   67     12   54   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    64_A     E    64_A     64   67   67     12   52   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Y    65_A     Y    65_A     64   67   67     12   50   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    66_A     Q    66_A     64   67   67      8   26   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    67_A     Q    67_A     64   67   67     11   36   62   63   63   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     N    68_A     N    68_A     64   67   67      3    4    4    4    4    5   50   64   66   67   67   67   67   67   67   67   67   67   67   67 
LCS_AVERAGE  LCS_A:  98.49  (  95.46  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     42     56     62     63     63     63     65     66     66     67     67     67     67     67     67     67     67     67     67     67 
GDT PERCENT_AT  62.69  83.58  92.54  94.03  94.03  94.03  97.01  98.51  98.51 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.48   0.70   0.75   0.75   0.75   1.01   1.14   1.14   1.31   1.31   1.31   1.31   1.31   1.31   1.31   1.31   1.31   1.31   1.31
GDT RMS_ALL_AT   1.44   1.41   1.38   1.36   1.36   1.36   1.33   1.32   1.32   1.31   1.31   1.31   1.31   1.31   1.31   1.31   1.31   1.31   1.31   1.31

# Checking swapping
#   possible swapping detected:  E     5_A      E     5_A
#   possible swapping detected:  E    35_A      E    35_A
#   possible swapping detected:  E    40_A      E    40_A
#   possible swapping detected:  E    46_A      E    46_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     4.317     0    0.089   0.110     4.712   45.238   42.619
LGA    P     3_A      P     3_A     3.461     0    0.084   0.088     4.881   50.119   42.925
LGA    E     4_A      E     4_A     3.671     0    0.051   0.095     6.126   50.238   38.307
LGA    E     5_A      E     5_A     1.511     0    0.047   0.607     2.767   82.024   69.894
LGA    Q     6_A      Q     6_A     0.299     0    0.028   0.706     2.505   97.619   92.063
LGA    K     7_A      K     7_A     0.583     0    0.029   1.065     2.490   97.619   82.116
LGA    Q     8_A      Q     8_A     0.740     0    0.029   0.172     1.315   90.476   86.455
LGA    M     9_A      M     9_A     0.625     0    0.029   0.881     1.933   95.238   88.452
LGA    L    10_A      L    10_A     0.476     0    0.056   0.135     1.261  100.000   92.976
LGA    G    11_A      G    11_A     0.360     0    0.029   0.029     0.450  100.000  100.000
LGA    E    12_A      E    12_A     0.320     0    0.044   0.843     3.431   97.619   87.354
LGA    A    13_A      A    13_A     0.346     0    0.064   0.062     0.630   97.619   98.095
LGA    I    14_A      I    14_A     0.319     0    0.016   1.014     2.877  100.000   84.881
LGA    Y    15_A      Y    15_A     0.328     0    0.039   0.278     1.478  100.000   92.183
LGA    P    16_A      P    16_A     0.487     0    0.027   0.150     0.764   95.238   93.197
LGA    K    17_A      K    17_A     0.669     0    0.023   0.918     3.867   90.476   78.677
LGA    V    18_A      V    18_A     0.521     0    0.036   1.213     2.704   90.476   83.401
LGA    A    19_A      A    19_A     0.809     0    0.067   0.067     1.064   88.214   88.667
LGA    A    20_A      A    20_A     1.064     0    0.122   0.123     1.732   81.548   81.524
LGA    S    21_A      S    21_A     0.876     0    0.155   0.151     1.894   92.857   86.190
LGA    Q    22_A      Q    22_A     0.619     0    0.171   1.024     3.623   92.857   80.370
LGA    P    23_A      P    23_A     0.978     0    0.035   0.348     1.155   90.476   90.544
LGA    E    24_A      E    24_A     1.004     0    0.043   0.962     4.545   85.952   65.185
LGA    L    25_A      L    25_A     0.779     0    0.104   0.958     3.226   90.476   83.214
LGA    A    26_A      A    26_A     0.739     0    0.023   0.040     0.756   90.476   90.476
LGA    G    27_A      G    27_A     0.742     0    0.024   0.024     0.804   90.476   90.476
LGA    K    28_A      K    28_A     0.678     0    0.016   0.206     1.431   90.476   87.460
LGA    L    29_A      L    29_A     0.476     0    0.038   0.953     3.914   95.238   81.726
LGA    T    30_A      T    30_A     0.592     0    0.041   0.096     0.897   92.857   91.837
LGA    G    31_A      G    31_A     0.683     0    0.031   0.031     0.693   92.857   92.857
LGA    M    32_A      M    32_A     0.421     0    0.026   0.071     0.541  100.000   98.810
LGA    I    33_A      I    33_A     0.188     0    0.014   0.194     0.884  100.000   97.619
LGA    L    34_A      L    34_A     0.344     0    0.080   0.104     0.930  100.000   95.238
LGA    E    35_A      E    35_A     0.282     0    0.027   1.339     5.432  100.000   75.291
LGA    L    36_A      L    36_A     0.481     0    0.019   0.842     2.415   97.619   89.821
LGA    P    37_A      P    37_A     0.654     0    0.025   0.386     1.447   90.476   89.184
LGA    V    38_A      V    38_A     0.593     0    0.025   0.159     1.080   92.857   90.544
LGA    T    39_A      T    39_A     0.378     0    0.044   1.062     2.677  100.000   88.844
LGA    E    40_A      E    40_A     0.183     0    0.024   0.587     1.800  100.000   92.804
LGA    L    41_A      L    41_A     0.345     0    0.025   0.095     0.847  100.000   96.429
LGA    L    42_A      L    42_A     0.501     0    0.037   1.408     3.227   95.238   82.619
LGA    H    43_A      H    43_A     0.520     0    0.036   0.292     1.237   95.238   88.762
LGA    L    44_A      L    44_A     0.345     0    0.053   0.072     0.624  100.000   97.619
LGA    L    45_A      L    45_A     0.501     0    0.061   0.236     1.446   92.857   92.917
LGA    E    46_A      E    46_A     0.600     0    0.086   0.926     4.090   90.476   71.852
LGA    E    47_A      E    47_A     0.434     0    0.076   1.006     3.905  100.000   85.714
LGA    S    48_A      S    48_A     0.329     0    0.032   0.058     0.771   97.619   95.238
LGA    E    49_A      E    49_A     0.833     0    0.115   0.814     3.943   92.857   75.926
LGA    A    50_A      A    50_A     0.556     0    0.028   0.038     0.589   95.238   94.286
LGA    L    51_A      L    51_A     0.340     0    0.037   0.197     0.597  100.000   97.619
LGA    D    52_A      D    52_A     0.663     0    0.035   1.208     5.183   90.476   74.107
LGA    A    53_A      A    53_A     0.801     0    0.045   0.046     0.999   90.476   90.476
LGA    K    54_A      K    54_A     0.574     0    0.043   0.680     2.547   90.476   83.862
LGA    V    55_A      V    55_A     0.550     0    0.031   0.095     0.734   90.476   90.476
LGA    N    56_A      N    56_A     0.511     0    0.023   0.068     1.086   95.238   91.726
LGA    E    57_A      E    57_A     0.410     0    0.037   1.059     4.353  100.000   79.048
LGA    A    58_A      A    58_A     0.470     0    0.037   0.042     0.564   97.619   98.095
LGA    L    59_A      L    59_A     0.241     0    0.025   0.886     2.842   95.238   88.750
LGA    E    60_A      E    60_A     0.980     0    0.064   1.132     4.924   85.952   70.476
LGA    V    61_A      V    61_A     1.327     0    0.018   0.907     2.456   81.429   76.667
LGA    L    62_A      L    62_A     0.727     0    0.029   0.993     2.529   90.476   85.298
LGA    K    63_A      K    63_A     1.252     0    0.050   0.823     2.995   79.405   73.280
LGA    E    64_A      E    64_A     1.782     0    0.074   1.181     5.673   69.048   53.333
LGA    Y    65_A      Y    65_A     2.072     0    0.048   1.350     7.302   64.881   48.135
LGA    Q    66_A      Q    66_A     2.161     0    0.148   0.150     3.745   68.810   60.053
LGA    Q    67_A      Q    67_A     2.266     0    0.495   1.036     4.012   62.857   57.725
LGA    N    68_A      N    68_A     5.545     0    0.678   0.756     8.225   16.905   26.905

# 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):     1.307          1.317                  1.919           89.030   82.234

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   68   67    4.0     66    1.14    94.030    96.648     5.302

LGA_LOCAL      RMSD:   1.145  Number of atoms:   66  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.323  Number of assigned atoms:   67 
Std_ASGN_ATOMS RMSD:   1.307  Standard rmsd on all 67 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.224031 * X  +  -0.340172 * Y  +  -0.913287 * Z  +  17.070736
  Y_new =  -0.928079 * X  +  -0.360483 * Y  +  -0.093390 * Z  +  14.513391
  Z_new =  -0.297456 * X  +   0.868525 * Y  +  -0.396465 * Z  +   1.091286 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.333936  0.302027  1.999027   [DEG:  -76.4289   17.3049  114.5358 ]
ZXZ: -1.468894  1.978460 -0.329964   [DEG:  -84.1614  113.3574  -18.9055 ]
 
# END of job
