
#######################################################
#                                                     #
#                        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:    63      23_A - 85_A        0.75     1.12
  LCS_AVERAGE:     96.97

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    4    4    5   48   54   62   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    23_A     D    23_A     63   64   64      3    4   42   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    24_A     G    24_A     63   64   64      3    4   32   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    25_A     D    25_A     63   64   64      3    4   34   49   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    26_A     G    26_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    27_A     Q    27_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    28_A     G    28_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    29_A     L    29_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Y    30_A     Y    30_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    31_A     A    31_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    32_A     A    32_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     N    33_A     N    33_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     C    34_A     C    34_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    35_A     A    35_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    36_A     A    36_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     C    37_A     C    37_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     H    38_A     H    38_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    39_A     G    39_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    40_A     A    40_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    41_A     L    41_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    42_A     A    42_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    43_A     T    43_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    44_A     S    44_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     E    45_A     E    45_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    46_A     K    46_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    47_A     K    47_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    48_A     G    48_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    49_A     T    49_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    50_A     T    50_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    51_A     L    51_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    52_A     A    52_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     R    53_A     R    53_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    54_A     L    54_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    55_A     Q    55_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    56_A     S    56_A     63   64   64     52   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    57_A     A    57_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    58_A     V    58_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    59_A     S    59_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    60_A     A    60_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     N    61_A     N    61_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    62_A     A    62_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    63_A     G    63_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    64_A     G    64_A     63   64   64     41   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     M    65_A     M    65_A     63   64   64     21   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    66_A     G    66_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     F    67_A     F    67_A     63   64   64     12   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    68_A     L    68_A     63   64   64     12   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    69_A     S    69_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    70_A     S    70_A     63   64   64     52   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    71_A     L    71_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    72_A     T    72_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    73_A     S    73_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    74_A     A    74_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    75_A     Q    75_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    76_A     L    76_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    77_A     Q    77_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    78_A     A    78_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     I    79_A     I    79_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    80_A     V    80_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    81_A     D    81_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    82_A     V    82_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    83_A     L    83_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    84_A     A    84_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    85_A     V    85_A     63   64   64     54   60   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_AVERAGE  LCS_A:  98.99  (  96.97  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     54     60     60     61     62     63     63     63     63     64     64     64     64     64     64     64     64     64     64     64 
GDT PERCENT_AT  84.38  93.75  93.75  95.31  96.88  98.44  98.44  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
GDT RMS_LOCAL    0.30   0.38   0.38   0.52   0.65   0.75   0.75   0.75   0.75   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   1.14   1.14   1.14   1.13   1.11   1.12   1.12   1.12   1.12   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

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    22_A      A    22_A     6.728     0    0.453   0.419     7.725   20.714   18.000
LGA    D    23_A      D    23_A     3.014     0    0.311   0.304     4.135   50.119   48.452
LGA    G    24_A      G    24_A     2.584     0    0.422   0.422     4.018   54.048   54.048
LGA    D    25_A      D    25_A     3.041     0    0.313   1.020     5.051   47.738   41.726
LGA    G    26_A      G    26_A     0.317     0    0.037   0.037     0.659   97.619   97.619
LGA    Q    27_A      Q    27_A     0.257     0    0.027   0.701     1.968  100.000   94.921
LGA    G    28_A      G    28_A     0.142     0    0.045   0.045     0.255  100.000  100.000
LGA    L    29_A      L    29_A     0.225     0    0.028   0.083     0.374  100.000  100.000
LGA    Y    30_A      Y    30_A     0.250     0    0.019   0.066     0.329  100.000  100.000
LGA    A    31_A      A    31_A     0.265     0    0.027   0.032     0.330  100.000  100.000
LGA    A    32_A      A    32_A     0.229     0    0.020   0.032     0.346  100.000  100.000
LGA    N    33_A      N    33_A     0.307     0    0.020   0.079     0.426  100.000  100.000
LGA    C    34_A      C    34_A     0.257     0    0.026   0.083     0.290  100.000  100.000
LGA    A    35_A      A    35_A     0.298     0    0.019   0.021     0.527   97.619   98.095
LGA    A    36_A      A    36_A     0.294     0    0.018   0.028     0.409  100.000  100.000
LGA    C    37_A      C    37_A     0.291     0    0.026   0.048     0.506  100.000   98.413
LGA    H    38_A      H    38_A     0.263     0    0.010   0.163     0.627  100.000   98.095
LGA    G    39_A      G    39_A     0.465     0    0.052   0.052     0.465  100.000  100.000
LGA    A    40_A      A    40_A     0.368     0    0.023   0.027     0.503  100.000   98.095
LGA    L    41_A      L    41_A     0.321     0    0.012   0.050     0.427  100.000  100.000
LGA    A    42_A      A    42_A     0.623     0    0.023   0.022     0.661   90.476   90.476
LGA    T    43_A      T    43_A     0.564     0    0.115   0.096     0.754   90.476   90.476
LGA    S    44_A      S    44_A     0.533     0    0.070   0.087     0.536   95.238   96.825
LGA    E    45_A      E    45_A     0.620     0    0.023   0.740     2.866   90.476   75.661
LGA    K    46_A      K    46_A     0.309     0    0.071   0.257     1.669  100.000   93.862
LGA    K    47_A      K    47_A     0.293     0    0.013   0.122     0.462  100.000  100.000
LGA    G    48_A      G    48_A     0.195     0    0.046   0.046     0.266  100.000  100.000
LGA    T    49_A      T    49_A     0.290     0    0.076   0.097     0.423  100.000  100.000
LGA    T    50_A      T    50_A     0.280     0    0.011   0.068     0.644  100.000   97.279
LGA    L    51_A      L    51_A     0.234     0    0.029   0.097     0.805  100.000   97.619
LGA    A    52_A      A    52_A     0.281     0    0.014   0.022     0.426  100.000  100.000
LGA    R    53_A      R    53_A     0.331     0    0.012   1.028     4.382  100.000   79.913
LGA    L    54_A      L    54_A     0.255     0    0.047   0.080     0.503   97.619   98.810
LGA    Q    55_A      Q    55_A     0.336     0    0.031   0.224     0.558  100.000   98.942
LGA    S    56_A      S    56_A     0.434     0    0.017   0.703     2.427  100.000   94.127
LGA    A    57_A      A    57_A     0.257     0    0.011   0.020     0.342  100.000  100.000
LGA    V    58_A      V    58_A     0.321     0    0.023   0.036     0.609  100.000   98.639
LGA    S    59_A      S    59_A     0.337     0    0.014   0.544     2.090  100.000   94.127
LGA    A    60_A      A    60_A     0.201     0    0.016   0.036     0.330  100.000  100.000
LGA    N    61_A      N    61_A     0.349     0    0.040   0.201     1.469  100.000   94.107
LGA    A    62_A      A    62_A     0.269     0    0.018   0.025     0.513  100.000   98.095
LGA    G    63_A      G    63_A     0.063     0    0.058   0.058     0.630   97.619   97.619
LGA    G    64_A      G    64_A     0.653     0    0.033   0.033     0.795   92.857   92.857
LGA    M    65_A      M    65_A     0.629     0    0.032   0.173     0.778   90.476   90.476
LGA    G    66_A      G    66_A     0.544     0    0.020   0.020     0.728   90.476   90.476
LGA    F    67_A      F    67_A     1.261     0    0.070   0.216     2.200   81.429   76.061
LGA    L    68_A      L    68_A     1.150     0    0.095   0.096     1.810   85.952   80.476
LGA    S    69_A      S    69_A     0.517     0    0.025   0.030     0.796   92.857   93.651
LGA    S    70_A      S    70_A     0.749     0    0.028   0.037     1.009   92.857   90.556
LGA    L    71_A      L    71_A     0.603     0    0.018   0.071     0.761   90.476   90.476
LGA    T    72_A      T    72_A     0.613     0    0.034   0.050     0.820   95.238   93.197
LGA    S    73_A      S    73_A     0.351     0    0.025   0.636     2.714  100.000   92.857
LGA    A    74_A      A    74_A     0.120     0    0.053   0.067     0.313  100.000  100.000
LGA    Q    75_A      Q    75_A     0.312     0    0.017   0.045     0.770  100.000   95.767
LGA    L    76_A      L    76_A     0.190     0    0.014   0.065     0.479  100.000  100.000
LGA    Q    77_A      Q    77_A     0.212     0    0.065   0.129     0.357  100.000  100.000
LGA    A    78_A      A    78_A     0.235     0    0.024   0.031     0.294  100.000  100.000
LGA    I    79_A      I    79_A     0.194     0    0.027   0.069     0.298  100.000  100.000
LGA    V    80_A      V    80_A     0.155     0    0.016   0.049     0.227  100.000  100.000
LGA    D    81_A      D    81_A     0.220     0    0.047   0.065     0.594  100.000   97.619
LGA    V    82_A      V    82_A     0.293     0    0.044   1.261     2.643  100.000   88.844
LGA    L    83_A      L    83_A     0.288     0    0.072   0.068     0.444  100.000  100.000
LGA    A    84_A      A    84_A     0.303     0    0.137   0.154     0.754   97.619   98.095
LGA    V    85_A      V    85_A     0.247     0    0.300   1.297     3.083   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):     1.100          1.089                  1.250           94.338   92.217

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   97   64    4.0     63    0.75    96.875    98.163     7.391

LGA_LOCAL      RMSD:   0.752  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.125  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   1.100  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.014113 * X  +   0.616571 * Y  +  -0.787173 * Z  +  22.612198
  Y_new =   0.249214 * X  +   0.760239 * Y  +   0.599942 * Z  + -12.642826
  Z_new =   0.968346 * X  +  -0.204641 * Y  +  -0.142929 * Z  +  -9.537758 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.514228 -1.318516 -2.180472   [DEG:   86.7589  -75.5454 -124.9318 ]
ZXZ: -2.222026  1.714216  1.779063   [DEG: -127.3127   98.2174  101.9328 ]
 
# END of job
