
#######################################################
#                                                     #
#                        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        1.10     1.10
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    64      22_A - 85_A        1.10     1.10
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    62      24_A - 85_A        0.86     1.13
  LCS_AVERAGE:     94.02

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      3   64   64      3    3   41   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    23_A     D    23_A      4   64   64      3    3    5    8   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    24_A     G    24_A     62   64   64      3    3    5   44   55   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    25_A     D    25_A     62   64   64      3    3    5   20   34   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    26_A     G    26_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    27_A     Q    27_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    28_A     G    28_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    29_A     L    29_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Y    30_A     Y    30_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    31_A     A    31_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    32_A     A    32_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     N    33_A     N    33_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     C    34_A     C    34_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    35_A     A    35_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    36_A     A    36_A     62   64   64     39   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     C    37_A     C    37_A     62   64   64     34   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     H    38_A     H    38_A     62   64   64     34   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    39_A     G    39_A     62   64   64     21   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    40_A     A    40_A     62   64   64     12   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    41_A     L    41_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    42_A     A    42_A     62   64   64      7   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    43_A     T    43_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    44_A     S    44_A     62   64   64     22   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     E    45_A     E    45_A     62   64   64     22   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    46_A     K    46_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    47_A     K    47_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    48_A     G    48_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    49_A     T    49_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    50_A     T    50_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    51_A     L    51_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    52_A     A    52_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     R    53_A     R    53_A     62   64   64     24   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    54_A     L    54_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    55_A     Q    55_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    56_A     S    56_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    57_A     A    57_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    58_A     V    58_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    59_A     S    59_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    60_A     A    60_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     N    61_A     N    61_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    62_A     A    62_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    63_A     G    63_A     62   64   64     39   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    64_A     G    64_A     62   64   64     17   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     M    65_A     M    65_A     62   64   64     17   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    66_A     G    66_A     62   64   64     17   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     F    67_A     F    67_A     62   64   64     17   32   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    68_A     L    68_A     62   64   64     17   32   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    69_A     S    69_A     62   64   64     17   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    70_A     S    70_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    71_A     L    71_A     62   64   64     38   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    72_A     T    72_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    73_A     S    73_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    74_A     A    74_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    75_A     Q    75_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    76_A     L    76_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    77_A     Q    77_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    78_A     A    78_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     I    79_A     I    79_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    80_A     V    80_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    81_A     D    81_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    82_A     V    82_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    83_A     L    83_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    84_A     A    84_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    85_A     V    85_A     62   64   64     42   58   60   61   62   62   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_AVERAGE  LCS_A:  98.01  (  94.02  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     58     60     61     62     62     64     64     64     64     64     64     64     64     64     64     64     64     64     64 
GDT PERCENT_AT  65.62  90.62  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
GDT RMS_LOCAL    0.35   0.47   0.52   0.69   0.87   0.86   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10
GDT RMS_ALL_AT   1.16   1.14   1.14   1.12   1.11   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10

# Checking swapping
#   possible swapping detected:  D    25_A      D    25_A
#   possible swapping detected:  Y    30_A      Y    30_A
#   possible swapping detected:  E    45_A      E    45_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    22_A      A    22_A     3.185     0    0.026   0.024     4.825   47.381   45.333
LGA    D    23_A      D    23_A     4.086     0    0.063   0.097     6.470   38.810   32.917
LGA    G    24_A      G    24_A     3.849     0    0.238   0.238     3.849   55.833   55.833
LGA    D    25_A      D    25_A     3.711     0    0.470   1.065     5.552   42.381   37.083
LGA    G    26_A      G    26_A     0.607     0    0.094   0.094     1.034   88.214   88.214
LGA    Q    27_A      Q    27_A     0.493     0    0.019   1.408     5.977  100.000   74.392
LGA    G    28_A      G    28_A     0.436     0    0.019   0.019     0.473  100.000  100.000
LGA    L    29_A      L    29_A     0.562     0    0.008   1.253     3.127   90.476   83.214
LGA    Y    30_A      Y    30_A     0.509     0    0.015   0.066     0.518   90.476   96.032
LGA    A    31_A      A    31_A     0.464     0    0.007   0.011     0.475  100.000  100.000
LGA    A    32_A      A    32_A     0.439     0    0.040   0.047     0.460  100.000  100.000
LGA    N    33_A      N    33_A     0.561     0    0.010   0.094     0.885   92.857   91.667
LGA    C    34_A      C    34_A     0.329     0    0.022   0.108     0.535  100.000   98.413
LGA    A    35_A      A    35_A     0.434     0    0.074   0.081     0.786   97.619   98.095
LGA    A    36_A      A    36_A     0.389     0    0.013   0.012     0.598   97.619   98.095
LGA    C    37_A      C    37_A     0.612     0    0.022   0.027     0.744   92.857   92.063
LGA    H    38_A      H    38_A     0.637     0    0.011   0.125     0.950   90.476   91.429
LGA    G    39_A      G    39_A     0.811     0    0.086   0.086     0.818   90.476   90.476
LGA    A    40_A      A    40_A     0.837     0    0.030   0.049     1.128   90.476   88.667
LGA    L    41_A      L    41_A     0.606     0    0.007   0.037     0.731   90.476   90.476
LGA    A    42_A      A    42_A     1.033     0    0.017   0.019     1.212   83.690   83.238
LGA    T    43_A      T    43_A     0.824     0    0.052   0.048     0.898   90.476   90.476
LGA    S    44_A      S    44_A     0.841     0    0.016   0.020     0.885   90.476   90.476
LGA    E    45_A      E    45_A     0.959     0    0.022   0.773     4.003   90.476   70.053
LGA    K    46_A      K    46_A     0.364     0    0.038   0.553     2.611   97.619   91.005
LGA    K    47_A      K    47_A     0.437     0    0.031   0.623     1.958  100.000   91.852
LGA    G    48_A      G    48_A     0.301     0    0.011   0.011     0.530   97.619   97.619
LGA    T    49_A      T    49_A     0.518     0    0.030   0.093     0.781   97.619   95.918
LGA    T    50_A      T    50_A     0.591     0    0.021   0.081     1.096   95.238   91.905
LGA    L    51_A      L    51_A     0.437     0    0.010   0.081     1.195   97.619   92.917
LGA    A    52_A      A    52_A     0.767     0    0.009   0.010     0.966   90.476   90.476
LGA    R    53_A      R    53_A     0.824     0    0.009   1.045     5.364   90.476   73.203
LGA    L    54_A      L    54_A     0.417     0    0.007   0.146     0.655  100.000   98.810
LGA    Q    55_A      Q    55_A     0.196     0    0.032   0.232     0.963  100.000   95.767
LGA    S    56_A      S    56_A     0.384     0    0.040   0.690     2.106  100.000   94.127
LGA    A    57_A      A    57_A     0.479     0    0.022   0.023     0.537  100.000   98.095
LGA    V    58_A      V    58_A     0.487     0    0.019   1.334     3.025  100.000   86.463
LGA    S    59_A      S    59_A     0.253     0    0.039   0.538     1.948  100.000   95.476
LGA    A    60_A      A    60_A     0.307     0    0.010   0.016     0.396  100.000  100.000
LGA    N    61_A      N    61_A     0.339     0    0.060   0.172     1.104  100.000   95.298
LGA    A    62_A      A    62_A     0.157     0    0.026   0.033     0.562   97.619   98.095
LGA    G    63_A      G    63_A     0.398     0    0.020   0.020     0.800   95.238   95.238
LGA    G    64_A      G    64_A     0.746     0    0.079   0.079     1.198   88.214   88.214
LGA    M    65_A      M    65_A     0.649     0    0.066   0.683     2.266   90.476   87.262
LGA    G    66_A      G    66_A     0.654     0    0.013   0.013     0.843   90.476   90.476
LGA    F    67_A      F    67_A     1.345     0    0.030   0.248     2.150   81.429   76.883
LGA    L    68_A      L    68_A     1.225     0    0.090   1.252     3.977   83.690   74.643
LGA    S    69_A      S    69_A     0.694     0    0.037   0.038     0.893   90.476   90.476
LGA    S    70_A      S    70_A     0.565     0    0.005   0.026     0.852   92.857   92.063
LGA    L    71_A      L    71_A     0.693     0    0.046   1.237     3.024   90.476   82.202
LGA    T    72_A      T    72_A     0.690     0    0.017   0.045     0.794   92.857   91.837
LGA    S    73_A      S    73_A     0.486     0    0.020   0.629     2.146   97.619   92.540
LGA    A    74_A      A    74_A     0.351     0    0.018   0.024     0.407  100.000  100.000
LGA    Q    75_A      Q    75_A     0.466     0    0.030   0.068     0.821  100.000   94.709
LGA    L    76_A      L    76_A     0.414     0    0.013   1.239     2.661  100.000   90.238
LGA    Q    77_A      Q    77_A     0.479     0    0.009   0.122     0.628  100.000   95.767
LGA    A    78_A      A    78_A     0.549     0    0.008   0.009     0.586   90.476   90.476
LGA    I    79_A      I    79_A     0.408     0    0.014   0.037     0.467  100.000  100.000
LGA    V    80_A      V    80_A     0.379     0    0.017   1.340     2.685  100.000   88.844
LGA    D    81_A      D    81_A     0.655     0    0.036   0.032     1.227   90.476   87.083
LGA    V    82_A      V    82_A     0.567     0    0.034   1.279     2.811   95.238   84.762
LGA    L    83_A      L    83_A     0.354     0    0.067   1.245     2.881  100.000   90.238
LGA    A    84_A      A    84_A     0.407     0    0.027   0.027     0.589   97.619   98.095
LGA    V    85_A      V    85_A     0.433     0    0.126   0.224     1.945   97.619   89.524

# 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):     1.096          1.092                  1.458           91.892   88.207

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   97   64    4.0     64    1.10    96.484    98.067     5.350

LGA_LOCAL      RMSD:   1.096  Number of atoms:   64  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.096  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   1.096  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.073606 * X  +   0.773252 * Y  +   0.629812 * Z  +  21.894154
  Y_new =   0.793188 * X  +   0.428194 * Y  +  -0.433016 * Z  + -16.434374
  Z_new =  -0.604513 * X  +   0.467687 * Y  +  -0.644852 * Z  + -13.825509 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.663329  0.649154  2.514112   [DEG:   95.3017   37.1938  144.0480 ]
ZXZ:  0.968487  2.271625 -0.912325   [DEG:   55.4902  130.1545  -52.2724 ]
 
# END of job
