
#######################################################
#                                                     #
#                        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        0.81     0.81
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    64      22_A - 85_A        0.81     0.81
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    64      22_A - 85_A        0.81     0.81
  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      3   47   61   62   62   64   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      3    4   31   62   62   64   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   18   31   59   64   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    4   29   48   62   64   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     45   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     42   60   61   62   62   64   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   62   64   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     39   60   61   62   62   64   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     46   60   61   62   62   64   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     48   60   61   62   62   64   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     47   60   61   62   62   64   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     48   60   61   62   62   64   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     19   60   61   62   62   64   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     30   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     19   60   61   62   62   64   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   62   64   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     48   60   61   62   62   64   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     36   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     41   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48   60   61   62   62   64   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     48     60     61     62     62     64     64     64     64     64     64     64     64     64     64     64     64     64     64     64 
GDT PERCENT_AT  75.00  93.75  95.31  96.88  96.88 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.33   0.42   0.46   0.57   0.57   0.81   0.81   0.81   0.81   0.81   0.81   0.81   0.81   0.81   0.81   0.81   0.81   0.81   0.81   0.81
GDT RMS_ALL_AT   0.85   0.84   0.83   0.82   0.82   0.81   0.81   0.81   0.81   0.81   0.81   0.81   0.81   0.81   0.81   0.81   0.81   0.81   0.81   0.81

# Checking swapping
#   possible swapping detected:  D    23_A      D    23_A
#   possible swapping detected:  Y    30_A      Y    30_A
#   possible swapping detected:  F    67_A      F    67_A
#   possible swapping detected:  D    81_A      D    81_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    22_A      A    22_A     1.407     0    0.633   0.601     3.496   67.143   63.714
LGA    D    23_A      D    23_A     2.465     0    0.104   0.108     3.899   57.738   58.452
LGA    G    24_A      G    24_A     3.517     0    0.666   0.666     3.517   65.833   65.833
LGA    D    25_A      D    25_A     3.032     0    0.301   1.012     5.250   49.524   39.167
LGA    G    26_A      G    26_A     0.411     0    0.104   0.104     0.708   97.619   97.619
LGA    Q    27_A      Q    27_A     0.313     0    0.007   1.182     3.822  100.000   83.757
LGA    G    28_A      G    28_A     0.105     0    0.018   0.018     0.208  100.000  100.000
LGA    L    29_A      L    29_A     0.312     0    0.006   0.086     0.571  100.000   97.619
LGA    Y    30_A      Y    30_A     0.303     0    0.039   0.133     0.579  100.000   99.206
LGA    A    31_A      A    31_A     0.273     0    0.013   0.013     0.349  100.000  100.000
LGA    A    32_A      A    32_A     0.212     0    0.018   0.018     0.286  100.000  100.000
LGA    N    33_A      N    33_A     0.552     0    0.045   0.095     0.846   92.857   91.667
LGA    C    34_A      C    34_A     0.426     0    0.045   0.070     0.491  100.000  100.000
LGA    A    35_A      A    35_A     0.543     0    0.012   0.012     0.716   92.857   94.286
LGA    A    36_A      A    36_A     0.538     0    0.015   0.016     0.628   92.857   92.381
LGA    C    37_A      C    37_A     0.651     0    0.073   0.095     0.953   90.476   90.476
LGA    H    38_A      H    38_A     0.434     0    0.043   0.052     0.839   97.619   93.333
LGA    G    39_A      G    39_A     0.330     0    0.071   0.071     0.373  100.000  100.000
LGA    A    40_A      A    40_A     0.588     0    0.016   0.024     0.870   95.238   94.286
LGA    L    41_A      L    41_A     0.265     0    0.018   0.072     0.495  100.000  100.000
LGA    A    42_A      A    42_A     0.839     0    0.012   0.011     1.035   88.214   88.667
LGA    T    43_A      T    43_A     0.691     0    0.057   0.047     0.768   90.476   90.476
LGA    S    44_A      S    44_A     0.409     0    0.007   0.036     0.464  100.000  100.000
LGA    E    45_A      E    45_A     0.437     0    0.048   0.750     2.720  100.000   80.741
LGA    K    46_A      K    46_A     0.314     0    0.026   0.077     1.211  100.000   93.757
LGA    K    47_A      K    47_A     0.360     0    0.011   0.076     0.399  100.000  100.000
LGA    G    48_A      G    48_A     0.345     0    0.085   0.085     0.646   97.619   97.619
LGA    T    49_A      T    49_A     0.298     0    0.076   0.131     0.688   97.619   98.639
LGA    T    50_A      T    50_A     0.322     0    0.021   0.072     0.863  100.000   95.918
LGA    L    51_A      L    51_A     0.426     0    0.005   0.120     1.170  100.000   94.107
LGA    A    52_A      A    52_A     0.624     0    0.019   0.020     0.760   90.476   90.476
LGA    R    53_A      R    53_A     0.568     0    0.006   1.080     4.268   95.238   80.346
LGA    L    54_A      L    54_A     0.203     0    0.010   0.072     0.415  100.000  100.000
LGA    Q    55_A      Q    55_A     0.155     0    0.004   0.164     0.581  100.000   95.767
LGA    S    56_A      S    56_A     0.295     0    0.039   0.672     2.005  100.000   94.127
LGA    A    57_A      A    57_A     0.318     0    0.003   0.007     0.330  100.000  100.000
LGA    V    58_A      V    58_A     0.343     0    0.006   0.049     0.516  100.000   98.639
LGA    S    59_A      S    59_A     0.246     0    0.023   0.113     0.398  100.000  100.000
LGA    A    60_A      A    60_A     0.180     0    0.023   0.027     0.198  100.000  100.000
LGA    N    61_A      N    61_A     0.324     0    0.076   0.123     0.992   97.619   95.238
LGA    A    62_A      A    62_A     0.553     0    0.048   0.058     0.795   95.238   94.286
LGA    G    63_A      G    63_A     0.413     0    0.063   0.063     0.637   97.619   97.619
LGA    G    64_A      G    64_A     0.482     0    0.042   0.042     0.780   95.238   95.238
LGA    M    65_A      M    65_A     0.537     0    0.035   0.272     0.849   97.619   94.048
LGA    G    66_A      G    66_A     0.302     0    0.027   0.027     0.537   95.238   95.238
LGA    F    67_A      F    67_A     0.771     0    0.028   0.160     1.693   90.476   84.762
LGA    L    68_A      L    68_A     0.778     0    0.045   0.043     1.364   90.476   87.083
LGA    S    69_A      S    69_A     0.427     0    0.026   0.027     0.696   92.857   93.651
LGA    S    70_A      S    70_A     0.888     0    0.027   0.039     1.158   88.214   85.952
LGA    L    71_A      L    71_A     0.659     0    0.011   0.071     0.792   90.476   90.476
LGA    T    72_A      T    72_A     0.551     0    0.014   0.030     0.593   90.476   91.837
LGA    S    73_A      S    73_A     0.615     0    0.005   0.677     3.064   92.857   85.317
LGA    A    74_A      A    74_A     0.284     0    0.027   0.030     0.377  100.000  100.000
LGA    Q    75_A      Q    75_A     0.290     0    0.017   0.047     0.575  100.000   96.825
LGA    L    76_A      L    76_A     0.406     0    0.007   0.083     0.471  100.000  100.000
LGA    Q    77_A      Q    77_A     0.401     0    0.020   0.124     0.585  100.000   97.884
LGA    A    78_A      A    78_A     0.392     0    0.009   0.010     0.394  100.000  100.000
LGA    I    79_A      I    79_A     0.323     0    0.014   0.038     0.409  100.000  100.000
LGA    V    80_A      V    80_A     0.479     0    0.021   0.043     0.527  100.000   98.639
LGA    D    81_A      D    81_A     0.518     0    0.024   0.042     0.768   97.619   94.048
LGA    V    82_A      V    82_A     0.412     0    0.009   1.277     2.651  100.000   88.844
LGA    L    83_A      L    83_A     0.491     0    0.091   0.090     0.777   95.238   97.619
LGA    A    84_A      A    84_A     0.460     0    0.068   0.072     0.859   95.238   96.190
LGA    V    85_A      V    85_A     0.434     0    0.268   1.282     2.689   97.619   86.395

# 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):     0.814          0.843                  1.078           94.680   92.317

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   97   64    4.0     64    0.81    97.656    98.732     7.004

LGA_LOCAL      RMSD:   0.814  Number of atoms:   64  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.814  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   0.814  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.988177 * X  +  -0.140642 * Y  +  -0.061042 * Z  +  23.481293
  Y_new =   0.145881 * X  +  -0.985004 * Y  +  -0.092121 * Z  + -10.119296
  Z_new =  -0.047171 * X  +  -0.099937 * Y  +   0.993875 * Z  +  -9.823707 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.995025  0.047188 -0.100216   [DEG:  171.6023    2.7037   -5.7420 ]
ZXZ: -0.585202  0.110737 -2.700592   [DEG:  -33.5296    6.3447 -154.7325 ]
 
# END of job
