
#######################################################
#                                                     #
#                        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        0.92     0.92
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    64      22_A - 85_A        0.92     0.92
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    64      22_A - 85_A        0.92     0.92
  LCS_AVERAGE:    100.00

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     64   64   64      0    3    6   32   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    23_A     D    23_A     64   64   64     10   29   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    24_A     G    24_A     64   64   64      3    3    4   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    25_A     D    25_A     64   64   64      3    5   20   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    26_A     G    26_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    27_A     Q    27_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    28_A     G    28_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    29_A     L    29_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Y    30_A     Y    30_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    31_A     A    31_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    32_A     A    32_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     N    33_A     N    33_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     C    34_A     C    34_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    35_A     A    35_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    36_A     A    36_A     64   64   64     42   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     C    37_A     C    37_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     H    38_A     H    38_A     64   64   64     47   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    39_A     G    39_A     64   64   64     30   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    40_A     A    40_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    41_A     L    41_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    42_A     A    42_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    43_A     T    43_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    44_A     S    44_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     E    45_A     E    45_A     64   64   64     25   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    46_A     K    46_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    47_A     K    47_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    48_A     G    48_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    49_A     T    49_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    50_A     T    50_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    51_A     L    51_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    52_A     A    52_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     R    53_A     R    53_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    54_A     L    54_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    55_A     Q    55_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    56_A     S    56_A     64   64   64     47   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    57_A     A    57_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    58_A     V    58_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    59_A     S    59_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    60_A     A    60_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     N    61_A     N    61_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    62_A     A    62_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    63_A     G    63_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    64_A     G    64_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     M    65_A     M    65_A     64   64   64     29   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    66_A     G    66_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     F    67_A     F    67_A     64   64   64     16   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    68_A     L    68_A     64   64   64     19   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    69_A     S    69_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    70_A     S    70_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    71_A     L    71_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    72_A     T    72_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    73_A     S    73_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    74_A     A    74_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    75_A     Q    75_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    76_A     L    76_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    77_A     Q    77_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    78_A     A    78_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     I    79_A     I    79_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    80_A     V    80_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    81_A     D    81_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    82_A     V    82_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    83_A     L    83_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    84_A     A    84_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    85_A     V    85_A     64   64   64     49   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
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     49     60     61     62     63     63     64     64     64     64     64     64     64     64     64     64     64     64     64     64 
GDT PERCENT_AT  76.56  93.75  95.31  96.88  98.44  98.44 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.29   0.40   0.49   0.65   0.82   0.82   0.92   0.92   0.92   0.92   0.92   0.92   0.92   0.92   0.92   0.92   0.92   0.92   0.92   0.92
GDT RMS_ALL_AT   0.98   0.96   0.94   0.92   0.92   0.92   0.92   0.92   0.92   0.92   0.92   0.92   0.92   0.92   0.92   0.92   0.92   0.92   0.92   0.92

# Checking swapping
#   possible swapping detected:  D    25_A      D    25_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    22_A      A    22_A     4.071     0    0.449   0.413     4.777   46.905   43.810
LGA    D    23_A      D    23_A     1.812     0    0.161   0.152     2.381   66.786   69.881
LGA    G    24_A      G    24_A     3.133     0    0.696   0.696     3.133   69.524   69.524
LGA    D    25_A      D    25_A     3.221     0    0.284   1.037     5.350   47.738   37.619
LGA    G    26_A      G    26_A     0.523     0    0.038   0.038     0.848   95.238   95.238
LGA    Q    27_A      Q    27_A     0.364     0    0.032   0.693     1.916  100.000   94.921
LGA    G    28_A      G    28_A     0.350     0    0.044   0.044     0.429  100.000  100.000
LGA    L    29_A      L    29_A     0.451     0    0.029   0.080     0.648  100.000   96.429
LGA    Y    30_A      Y    30_A     0.363     0    0.022   0.059     0.388  100.000  100.000
LGA    A    31_A      A    31_A     0.352     0    0.025   0.030     0.396  100.000  100.000
LGA    A    32_A      A    32_A     0.373     0    0.024   0.036     0.461  100.000  100.000
LGA    N    33_A      N    33_A     0.399     0    0.023   0.088     0.606  100.000   98.810
LGA    C    34_A      C    34_A     0.200     0    0.030   0.086     0.299  100.000  100.000
LGA    A    35_A      A    35_A     0.345     0    0.020   0.023     0.592   97.619   98.095
LGA    A    36_A      A    36_A     0.425     0    0.022   0.034     0.537   97.619   98.095
LGA    C    37_A      C    37_A     0.390     0    0.015   0.047     0.442  100.000  100.000
LGA    H    38_A      H    38_A     0.399     0    0.019   0.112     0.551   95.238   97.143
LGA    G    39_A      G    39_A     0.691     0    0.082   0.082     0.691   90.476   90.476
LGA    A    40_A      A    40_A     0.372     0    0.027   0.030     0.488  100.000  100.000
LGA    L    41_A      L    41_A     0.339     0    0.018   0.033     0.398  100.000  100.000
LGA    A    42_A      A    42_A     0.578     0    0.032   0.036     0.633   92.857   92.381
LGA    T    43_A      T    43_A     0.610     0    0.180   0.162     0.970   90.476   90.476
LGA    S    44_A      S    44_A     0.594     0    0.090   0.135     0.646   95.238   96.825
LGA    E    45_A      E    45_A     1.034     0    0.020   0.722     4.250   88.214   66.825
LGA    K    46_A      K    46_A     0.207     0    0.075   0.239     1.649  100.000   92.804
LGA    K    47_A      K    47_A     0.194     0    0.012   0.127     0.349  100.000  100.000
LGA    G    48_A      G    48_A     0.281     0    0.037   0.037     0.477  100.000  100.000
LGA    T    49_A      T    49_A     0.234     0    0.069   0.088     0.402  100.000  100.000
LGA    T    50_A      T    50_A     0.430     0    0.016   0.057     0.969  100.000   95.918
LGA    L    51_A      L    51_A     0.447     0    0.032   0.106     1.158  100.000   94.107
LGA    A    52_A      A    52_A     0.611     0    0.014   0.019     0.832   90.476   90.476
LGA    R    53_A      R    53_A     0.530     0    0.023   0.525     2.820   95.238   85.152
LGA    L    54_A      L    54_A     0.224     0    0.045   0.079     0.462  100.000  100.000
LGA    Q    55_A      Q    55_A     0.180     0    0.019   0.222     0.644  100.000   97.884
LGA    S    56_A      S    56_A     0.425     0    0.046   0.051     0.573  100.000   98.413
LGA    A    57_A      A    57_A     0.360     0    0.015   0.022     0.409  100.000  100.000
LGA    V    58_A      V    58_A     0.347     0    0.024   0.040     0.498  100.000  100.000
LGA    S    59_A      S    59_A     0.387     0    0.015   0.759     2.199  100.000   92.540
LGA    A    60_A      A    60_A     0.286     0    0.015   0.036     0.372  100.000  100.000
LGA    N    61_A      N    61_A     0.184     0    0.040   0.192     1.107  100.000   95.298
LGA    A    62_A      A    62_A     0.137     0    0.019   0.026     0.443  100.000  100.000
LGA    G    63_A      G    63_A     0.149     0    0.054   0.054     0.513   97.619   97.619
LGA    G    64_A      G    64_A     0.429     0    0.041   0.041     0.551   97.619   97.619
LGA    M    65_A      M    65_A     0.550     0    0.033   0.163     0.771   90.476   90.476
LGA    G    66_A      G    66_A     0.367     0    0.017   0.017     0.498  100.000  100.000
LGA    F    67_A      F    67_A     0.943     0    0.053   0.210     1.900   90.476   83.203
LGA    L    68_A      L    68_A     0.860     0    0.081   0.081     1.561   90.476   84.940
LGA    S    69_A      S    69_A     0.303     0    0.021   0.034     0.661   95.238   95.238
LGA    S    70_A      S    70_A     0.847     0    0.022   0.022     1.116   90.595   87.540
LGA    L    71_A      L    71_A     0.667     0    0.013   0.065     0.732   90.476   91.667
LGA    T    72_A      T    72_A     0.837     0    0.045   0.059     1.006   90.476   89.184
LGA    S    73_A      S    73_A     0.672     0    0.027   0.620     2.608   95.238   88.095
LGA    A    74_A      A    74_A     0.352     0    0.058   0.071     0.475  100.000  100.000
LGA    Q    75_A      Q    75_A     0.515     0    0.012   0.129     0.886   95.238   92.593
LGA    L    76_A      L    76_A     0.412     0    0.012   0.064     0.626  100.000   97.619
LGA    Q    77_A      Q    77_A     0.529     0    0.071   0.152     0.721   97.619   93.651
LGA    A    78_A      A    78_A     0.518     0    0.023   0.035     0.518   90.476   90.476
LGA    I    79_A      I    79_A     0.405     0    0.028   0.056     0.486  100.000  100.000
LGA    V    80_A      V    80_A     0.388     0    0.017   0.045     0.416  100.000  100.000
LGA    D    81_A      D    81_A     0.532     0    0.050   0.068     1.053   97.619   92.917
LGA    V    82_A      V    82_A     0.353     0    0.041   1.256     2.689  100.000   88.844
LGA    L    83_A      L    83_A     0.243     0    0.074   0.073     0.452  100.000  100.000
LGA    A    84_A      A    84_A     0.296     0    0.155   0.173     0.709   97.619   98.095
LGA    V    85_A      V    85_A     0.256     0    0.293   1.294     3.149   97.619   86.463

# 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):     0.915          0.867                  1.083           94.758   92.584

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   97   64    4.0     64    0.92    97.656    98.739     6.304

LGA_LOCAL      RMSD:   0.915  Number of atoms:   64  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.915  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   0.915  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.683197 * X  +  -0.476552 * Y  +  -0.553299 * Z  +  22.571857
  Y_new =  -0.698480 * X  +  -0.647475 * Y  +  -0.304797 * Z  + -11.873250
  Z_new =  -0.212996 * X  +   0.594705 * Y  +  -0.775216 * Z  +  -9.957311 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.796458  0.214640  2.487207   [DEG:  -45.6337   12.2980  142.5065 ]
ZXZ: -1.067283  2.457853 -0.343920   [DEG:  -61.1508  140.8246  -19.7052 ]
 
# END of job
