
#######################################################
#                                                     #
#                        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        0.83     0.83
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.83     0.83
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.83     0.83
  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      9   15   44   65   66   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     11   59   63   65   66   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     11   53   63   65   66   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     14   59   63   65   66   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     39   59   63   65   66   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     17   59   63   65   66   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     29   59   63   65   66   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     33   59   63   65   66   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     22   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     31   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     12   58   63   65   66   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     27   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     48   59   63   65   66   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     45   59   63   65   66   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     34   59   63   65   66   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     48   59   63   65   66   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      4   51   62   64   66   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    7   13   63   66   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      0    3   48   65   66   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     48     59     63     65     66     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67 
GDT PERCENT_AT  71.64  88.06  94.03  97.01  98.51 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.31   0.44   0.57   0.74   0.77   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83
GDT RMS_ALL_AT   0.97   0.90   0.86   0.84   0.84   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83

# Checking swapping
#   possible swapping detected:  E     5_A      E     5_A
#   possible swapping detected:  E    35_A      E    35_A
#   possible swapping detected:  E    46_A      E    46_A
#   possible swapping detected:  E    47_A      E    47_A
#   possible swapping detected:  E    57_A      E    57_A
#   possible swapping detected:  E    60_A      E    60_A
#   possible swapping detected:  E    64_A      E    64_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     2_A      S     2_A     2.543     0    0.049   0.071     2.963   65.000   62.381
LGA    P     3_A      P     3_A     1.099     0    0.042   0.248     1.894   81.548   80.272
LGA    E     4_A      E     4_A     1.497     0    0.043   0.255     2.959   81.548   71.481
LGA    E     5_A      E     5_A     1.131     0    0.046   0.928     6.037   85.952   57.619
LGA    Q     6_A      Q     6_A     0.467     0    0.065   1.220     3.921   95.238   74.709
LGA    K     7_A      K     7_A     0.776     0    0.038   0.984     2.731   92.857   80.106
LGA    Q     8_A      Q     8_A     0.737     0    0.022   0.873     5.982   95.238   67.090
LGA    M     9_A      M     9_A     0.607     0    0.031   1.066     2.457   95.238   85.179
LGA    L    10_A      L    10_A     0.816     0    0.058   0.083     1.440   90.476   85.952
LGA    G    11_A      G    11_A     0.664     0    0.035   0.035     0.666   90.476   90.476
LGA    E    12_A      E    12_A     0.554     0    0.042   0.918     3.841   90.476   78.677
LGA    A    13_A      A    13_A     0.522     0    0.070   0.068     0.650   92.857   92.381
LGA    I    14_A      I    14_A     0.402     0    0.017   1.304     3.407  100.000   81.905
LGA    Y    15_A      Y    15_A     0.283     0    0.038   0.153     0.417  100.000  100.000
LGA    P    16_A      P    16_A     0.536     0    0.027   0.347     1.516   92.857   89.320
LGA    K    17_A      K    17_A     0.412     0    0.030   0.473     2.159   97.619   88.889
LGA    V    18_A      V    18_A     0.423     0    0.030   0.107     0.539   97.619   95.918
LGA    A    19_A      A    19_A     0.580     0    0.060   0.059     0.749   95.238   94.286
LGA    A    20_A      A    20_A     0.460     0    0.106   0.107     0.551   97.619   98.095
LGA    S    21_A      S    21_A     0.770     0    0.186   0.592     1.207   88.214   85.952
LGA    Q    22_A      Q    22_A     0.775     0    0.160   1.100     4.744   92.857   73.862
LGA    P    23_A      P    23_A     0.484     0    0.084   0.353     1.384   95.238   93.265
LGA    E    24_A      E    24_A     0.597     0    0.020   0.442     1.937   92.857   89.577
LGA    L    25_A      L    25_A     0.634     0    0.120   0.924     3.556   97.619   81.607
LGA    A    26_A      A    26_A     0.177     0    0.027   0.045     0.307  100.000  100.000
LGA    G    27_A      G    27_A     0.237     0    0.019   0.019     0.298  100.000  100.000
LGA    K    28_A      K    28_A     0.395     0    0.023   1.064     4.319  100.000   80.899
LGA    L    29_A      L    29_A     0.237     0    0.039   0.991     4.465  100.000   80.238
LGA    T    30_A      T    30_A     0.507     0    0.034   0.078     0.873   92.857   91.837
LGA    G    31_A      G    31_A     0.664     0    0.030   0.030     0.678   90.476   90.476
LGA    M    32_A      M    32_A     0.441     0    0.021   0.124     0.745   97.619   95.238
LGA    I    33_A      I    33_A     0.402     0    0.023   0.658     2.513   95.238   91.071
LGA    L    34_A      L    34_A     0.668     0    0.096   0.105     1.484   95.238   89.464
LGA    E    35_A      E    35_A     0.653     0    0.023   1.007     3.505   90.476   72.540
LGA    L    36_A      L    36_A     0.940     0    0.040   1.018     3.170   90.476   81.250
LGA    P    37_A      P    37_A     1.250     0    0.065   0.342     1.786   83.690   80.272
LGA    V    38_A      V    38_A     1.208     0    0.028   0.205     2.074   83.690   79.116
LGA    T    39_A      T    39_A     0.688     0    0.028   1.009     2.456   90.476   85.646
LGA    E    40_A      E    40_A     0.181     0    0.029   0.857     3.246  100.000   86.455
LGA    L    41_A      L    41_A     0.534     0    0.036   0.154     1.187   92.857   90.536
LGA    L    42_A      L    42_A     0.625     0    0.032   0.179     1.516   90.476   88.274
LGA    H    43_A      H    43_A     0.352     0    0.040   0.244     1.279  100.000   92.524
LGA    L    44_A      L    44_A     0.179     0    0.043   1.151     2.568  100.000   89.048
LGA    L    45_A      L    45_A     0.231     0    0.042   0.253     0.923  100.000   98.810
LGA    E    46_A      E    46_A     0.262     0    0.104   0.799     3.429   97.619   79.101
LGA    E    47_A      E    47_A     0.352     0    0.102   1.167     4.021  100.000   79.365
LGA    S    48_A      S    48_A     0.316     0    0.037   0.628     1.836  100.000   93.889
LGA    E    49_A      E    49_A     0.489     0    0.120   1.000     2.941  100.000   84.339
LGA    A    50_A      A    50_A     0.207     0    0.032   0.051     0.264  100.000  100.000
LGA    L    51_A      L    51_A     0.296     0    0.048   1.166     2.369  100.000   90.000
LGA    D    52_A      D    52_A     0.256     0    0.041   0.915     3.295  100.000   83.988
LGA    A    53_A      A    53_A     0.328     0    0.046   0.048     0.438  100.000  100.000
LGA    K    54_A      K    54_A     0.278     0    0.032   0.607     2.305  100.000   90.952
LGA    V    55_A      V    55_A     0.244     0    0.037   0.085     0.524  100.000   98.639
LGA    N    56_A      N    56_A     0.376     0    0.029   0.785     2.006  100.000   92.202
LGA    E    57_A      E    57_A     0.446     0    0.049   0.484     1.503  100.000   94.868
LGA    A    58_A      A    58_A     0.504     0    0.041   0.044     0.661   95.238   94.286
LGA    L    59_A      L    59_A     0.296     0    0.030   0.540     2.216  100.000   92.024
LGA    E    60_A      E    60_A     0.430     0    0.039   1.224     5.188   97.619   75.132
LGA    V    61_A      V    61_A     0.450     0    0.034   0.183     0.882  100.000   98.639
LGA    L    62_A      L    62_A     0.597     0    0.044   0.089     1.874   95.238   86.190
LGA    K    63_A      K    63_A     0.642     0    0.049   1.560     7.676   90.476   63.333
LGA    E    64_A      E    64_A     0.520     0    0.032   0.769     2.280   97.619   82.222
LGA    Y    65_A      Y    65_A     0.538     0    0.067   0.265     2.843   90.595   78.413
LGA    Q    66_A      Q    66_A     1.779     0    0.135   0.596     5.096   69.048   53.757
LGA    Q    67_A      Q    67_A     2.559     0    0.179   1.225     9.701   66.905   40.476
LGA    N    68_A      N    68_A     2.722     0    0.687   0.997     7.824   46.310   31.607

# 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):     0.831          0.855                  1.850           93.207   84.270

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   68   67    4.0     67    0.83    96.269    98.305     7.199

LGA_LOCAL      RMSD:   0.831  Number of atoms:   67  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.831  Number of assigned atoms:   67 
Std_ASGN_ATOMS RMSD:   0.831  Standard rmsd on all 67 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.520292 * X  +   0.682337 * Y  +  -0.513530 * Z  +   8.682678
  Y_new =   0.739188 * X  +   0.660967 * Y  +   0.129316 * Z  +  17.618734
  Z_new =   0.427664 * X  +  -0.312313 * Y  +  -0.848271 * Z  +   0.153887 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.184115 -0.441906 -2.788818   [DEG:  125.1406  -25.3194 -159.7875 ]
ZXZ: -1.817486  2.583509  2.201555   [DEG: -104.1343  148.0242  126.1398 ]
 
# END of job
