
#######################################################
#                                                     #
#                        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        1.06     1.06
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        1.06     1.06
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    66       2_A - 67_A        0.96     1.07
  LONGEST_CONTINUOUS_SEGMENT:    66       3_A - 68_A        0.99     1.07
  LCS_AVERAGE:     98.51

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     66   67   67     10   33   53   58   63   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P     3_A     P     3_A     66   67   67     20   45   58   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E     4_A     E     4_A     66   67   67     11   41   57   61   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E     5_A     E     5_A     66   67   67     13   45   57   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q     6_A     Q     6_A     66   67   67     20   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K     7_A     K     7_A     66   67   67     21   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q     8_A     Q     8_A     66   67   67     11   49   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     M     9_A     M     9_A     66   67   67     20   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    10_A     L    10_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    11_A     G    11_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    12_A     E    12_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    13_A     A    13_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    14_A     I    14_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Y    15_A     Y    15_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    16_A     P    16_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    17_A     K    17_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    18_A     V    18_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    19_A     A    19_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    20_A     A    20_A     66   67   67     29   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    21_A     S    21_A     66   67   67     16   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    22_A     Q    22_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    23_A     P    23_A     66   67   67     28   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    24_A     E    24_A     66   67   67     29   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    25_A     L    25_A     66   67   67     38   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    26_A     A    26_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    27_A     G    27_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    28_A     K    28_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    29_A     L    29_A     66   67   67     38   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     T    30_A     T    30_A     66   67   67     38   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    31_A     G    31_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     M    32_A     M    32_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    33_A     I    33_A     66   67   67     29   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    34_A     L    34_A     66   67   67     29   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    35_A     E    35_A     66   67   67     18   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    36_A     L    36_A     66   67   67     34   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    37_A     P    37_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    38_A     V    38_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     T    39_A     T    39_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    40_A     E    40_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    41_A     L    41_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    42_A     L    42_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     H    43_A     H    43_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    44_A     L    44_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    45_A     L    45_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    46_A     E    46_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    47_A     E    47_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    48_A     S    48_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    49_A     E    49_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    50_A     A    50_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    51_A     L    51_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     D    52_A     D    52_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    53_A     A    53_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    54_A     K    54_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    55_A     V    55_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     N    56_A     N    56_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    57_A     E    57_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    58_A     A    58_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    59_A     L    59_A     66   67   67     39   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    60_A     E    60_A     66   67   67     35   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    61_A     V    61_A     66   67   67     34   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    62_A     L    62_A     66   67   67     34   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    63_A     K    63_A     66   67   67     18   53   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    64_A     E    64_A     66   67   67     21   53   59   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Y    65_A     Y    65_A     66   67   67     21   40   59   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    66_A     Q    66_A     66   67   67      3   51   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    67_A     Q    67_A     66   67   67     14   37   60   64   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     N    68_A     N    68_A     66   67   67      3    3    3   10   11   59   66   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_AVERAGE  LCS_A:  99.50  (  98.51  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     39     53     60     64     65     66     66     67     67     67     67     67     67     67     67     67     67     67     67     67 
GDT PERCENT_AT  58.21  79.10  89.55  95.52  97.01  98.51  98.51 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.34   0.46   0.69   0.83   0.88   0.96   0.96   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06
GDT RMS_ALL_AT   1.16   1.18   1.10   1.08   1.08   1.07   1.07   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06

# Checking swapping
#   possible swapping detected:  E     5_A      E     5_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     3.139     0    0.058   0.060     3.443   55.476   53.651
LGA    P     3_A      P     3_A     1.945     0    0.067   0.073     2.804   72.976   67.279
LGA    E     4_A      E     4_A     2.286     0    0.048   0.794     6.165   68.810   51.270
LGA    E     5_A      E     5_A     1.930     0    0.033   0.858     5.983   75.119   53.492
LGA    Q     6_A      Q     6_A     1.276     0    0.079   0.626     2.322   85.952   80.635
LGA    K     7_A      K     7_A     1.105     0    0.031   1.410     8.941   83.690   54.656
LGA    Q     8_A      Q     8_A     1.388     0    0.035   0.873     5.867   81.429   61.958
LGA    M     9_A      M     9_A     1.075     0    0.039   0.793     2.015   85.952   81.607
LGA    L    10_A      L    10_A     0.237     0    0.067   0.187     0.994  100.000   96.429
LGA    G    11_A      G    11_A     0.358     0    0.028   0.028     0.465  100.000  100.000
LGA    E    12_A      E    12_A     0.330     0    0.064   0.205     0.719   97.619   97.884
LGA    A    13_A      A    13_A     0.476     0    0.066   0.064     0.776   95.238   94.286
LGA    I    14_A      I    14_A     0.393     0    0.015   1.366     4.379   97.619   82.143
LGA    Y    15_A      Y    15_A     0.439     0    0.039   0.307     2.019   97.619   86.270
LGA    P    16_A      P    16_A     0.582     0    0.026   0.150     0.943   90.476   90.476
LGA    K    17_A      K    17_A     0.595     0    0.025   0.695     2.427   90.476   83.757
LGA    V    18_A      V    18_A     0.489     0    0.046   1.041     2.250   92.857   85.850
LGA    A    19_A      A    19_A     0.665     0    0.077   0.076     1.066   88.214   90.571
LGA    A    20_A      A    20_A     0.997     0    0.122   0.123     1.707   83.810   85.143
LGA    S    21_A      S    21_A     1.177     0    0.184   0.176     1.892   90.595   84.683
LGA    Q    22_A      Q    22_A     0.763     0    0.142   0.241     0.993   90.476   90.476
LGA    P    23_A      P    23_A     1.175     0    0.071   0.365     1.297   81.429   84.014
LGA    E    24_A      E    24_A     1.150     0    0.033   0.964     4.013   81.429   69.365
LGA    L    25_A      L    25_A     0.995     0    0.085   0.112     1.270   88.214   85.952
LGA    A    26_A      A    26_A     0.801     0    0.025   0.048     0.875   90.476   90.476
LGA    G    27_A      G    27_A     0.727     0    0.025   0.025     0.816   90.476   90.476
LGA    K    28_A      K    28_A     0.733     0    0.021   0.083     0.953   90.476   90.476
LGA    L    29_A      L    29_A     0.650     0    0.036   0.986     4.346   90.476   75.476
LGA    T    30_A      T    30_A     0.678     0    0.053   0.119     0.896   90.476   90.476
LGA    G    31_A      G    31_A     0.673     0    0.033   0.033     0.702   90.476   90.476
LGA    M    32_A      M    32_A     0.527     0    0.026   0.108     0.866   95.238   92.857
LGA    I    33_A      I    33_A     0.586     0    0.011   1.132     3.604   90.476   77.202
LGA    L    34_A      L    34_A     0.535     0    0.098   0.949     4.088   95.238   77.857
LGA    E    35_A      E    35_A     0.727     0    0.029   0.323     2.349   90.476   82.698
LGA    L    36_A      L    36_A     0.648     0    0.033   0.200     1.407   90.476   89.345
LGA    P    37_A      P    37_A     0.492     0    0.035   0.364     1.475   95.238   91.905
LGA    V    38_A      V    38_A     0.623     0    0.027   0.932     2.793   90.476   83.197
LGA    T    39_A      T    39_A     0.526     0    0.032   1.083     2.679   92.857   83.673
LGA    E    40_A      E    40_A     0.375     0    0.025   0.649     1.891  100.000   91.852
LGA    L    41_A      L    41_A     0.520     0    0.028   0.140     0.709   92.857   94.048
LGA    L    42_A      L    42_A     0.652     0    0.035   1.405     2.910   90.476   79.940
LGA    H    43_A      H    43_A     0.435     0    0.034   0.201     1.113  100.000   93.429
LGA    L    44_A      L    44_A     0.396     0    0.055   0.081     0.451  100.000  100.000
LGA    L    45_A      L    45_A     0.601     0    0.067   0.252     1.555   90.476   88.274
LGA    E    46_A      E    46_A     0.630     0    0.059   0.781     3.238   90.476   78.413
LGA    E    47_A      E    47_A     0.534     0    0.064   0.144     1.143   92.857   92.646
LGA    S    48_A      S    48_A     0.195     0    0.038   0.629     2.146  100.000   94.127
LGA    E    49_A      E    49_A     0.524     0    0.109   0.878     4.007   97.619   81.005
LGA    A    50_A      A    50_A     0.237     0    0.029   0.040     0.304  100.000  100.000
LGA    L    51_A      L    51_A     0.140     0    0.048   0.166     0.550  100.000   98.810
LGA    D    52_A      D    52_A     0.211     0    0.040   0.823     3.067  100.000   83.988
LGA    A    53_A      A    53_A     0.392     0    0.052   0.052     0.481  100.000  100.000
LGA    K    54_A      K    54_A     0.350     0    0.022   0.814     2.398  100.000   87.989
LGA    V    55_A      V    55_A     0.247     0    0.038   0.076     0.393  100.000  100.000
LGA    N    56_A      N    56_A     0.287     0    0.029   1.000     3.725  100.000   86.131
LGA    E    57_A      E    57_A     0.474     0    0.040   0.388     1.366   97.619   94.762
LGA    A    58_A      A    58_A     0.454     0    0.045   0.048     0.605   97.619   98.095
LGA    L    59_A      L    59_A     0.150     0    0.039   0.751     2.908   97.619   89.940
LGA    E    60_A      E    60_A     0.867     0    0.066   0.440     2.964   88.214   79.947
LGA    V    61_A      V    61_A     0.988     0    0.022   0.859     2.155   85.952   81.701
LGA    L    62_A      L    62_A     0.945     0    0.029   1.393     3.152   85.952   76.786
LGA    K    63_A      K    63_A     1.211     0    0.033   1.340     5.417   79.286   65.079
LGA    E    64_A      E    64_A     1.664     0    0.069   0.143     2.439   72.976   71.164
LGA    Y    65_A      Y    65_A     1.853     0    0.056   1.333     8.218   70.833   46.230
LGA    Q    66_A      Q    66_A     1.440     0    0.175   0.284     3.459   83.690   71.587
LGA    Q    67_A      Q    67_A     1.558     0    0.491   1.208     5.525   70.833   58.783
LGA    N    68_A      N    68_A     3.789     0    0.374   0.861     7.142   32.381   39.881

# 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):     1.064          1.126                  1.863           89.202   82.732

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   68   67    4.0     67    1.06    93.657    96.884     5.755

LGA_LOCAL      RMSD:   1.064  Number of atoms:   67  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.064  Number of assigned atoms:   67 
Std_ASGN_ATOMS RMSD:   1.064  Standard rmsd on all 67 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.206724 * X  +  -0.309516 * Y  +  -0.928151 * Z  +  16.858404
  Y_new =  -0.884430 * X  +  -0.464780 * Y  +  -0.041993 * Z  +  15.048268
  Z_new =  -0.418389 * X  +   0.829566 * Y  +  -0.369827 * Z  +   2.270128 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.341181  0.431671  1.990158   [DEG:  -76.8440   24.7329  114.0277 ]
ZXZ: -1.525583  1.949619 -0.467119   [DEG:  -87.4095  111.7049  -26.7640 ]
 
# END of job
