
#######################################################
#                                                     #
#                        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        1.40     1.40
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    64      22_A - 85_A        1.40     1.40
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63      23_A - 85_A        0.91     1.43
  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    3    3    4    4    7   30   37   55   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     D    23_A     D    23_A     63   64   64      3    4    5    6   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    24_A     G    24_A     63   64   64      3    4    5   18   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     D    25_A     D    25_A     63   64   64      3   15   25   36   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    26_A     G    26_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     Q    27_A     Q    27_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    28_A     G    28_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    29_A     L    29_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     Y    30_A     Y    30_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    31_A     A    31_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    32_A     A    32_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     N    33_A     N    33_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     C    34_A     C    34_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    35_A     A    35_A     63   64   64     28   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    36_A     A    36_A     63   64   64     29   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     C    37_A     C    37_A     63   64   64     31   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     H    38_A     H    38_A     63   64   64     29   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    39_A     G    39_A     63   64   64     28   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    40_A     A    40_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    41_A     L    41_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    42_A     A    42_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     T    43_A     T    43_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     S    44_A     S    44_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     E    45_A     E    45_A     63   64   64     34   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     K    46_A     K    46_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     K    47_A     K    47_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    48_A     G    48_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     T    49_A     T    49_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     T    50_A     T    50_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    51_A     L    51_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    52_A     A    52_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     R    53_A     R    53_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    54_A     L    54_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     Q    55_A     Q    55_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     S    56_A     S    56_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    57_A     A    57_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     V    58_A     V    58_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     S    59_A     S    59_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    60_A     A    60_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     N    61_A     N    61_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    62_A     A    62_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    63_A     G    63_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    64_A     G    64_A     63   64   64     14   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     M    65_A     M    65_A     63   64   64     14   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    66_A     G    66_A     63   64   64     21   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     F    67_A     F    67_A     63   64   64     14   48   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    68_A     L    68_A     63   64   64     14   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     S    69_A     S    69_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     S    70_A     S    70_A     63   64   64     34   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    71_A     L    71_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     T    72_A     T    72_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     S    73_A     S    73_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    74_A     A    74_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     Q    75_A     Q    75_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    76_A     L    76_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     Q    77_A     Q    77_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    78_A     A    78_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     I    79_A     I    79_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     V    80_A     V    80_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     D    81_A     D    81_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     V    82_A     V    82_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    83_A     L    83_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    84_A     A    84_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     V    85_A     V    85_A     63   64   64     48   59   60   60   61   63   63   63   63   63   63   63   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     48     59     60     60     61     63     63     63     63     63     63     63     64     64     64     64     64     64     64     64 
GDT PERCENT_AT  75.00  92.19  93.75  93.75  95.31  98.44  98.44  98.44  98.44  98.44  98.44  98.44 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.29   0.44   0.46   0.46   0.60   0.91   0.91   0.91   0.91   0.91   0.91   0.91   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40
GDT RMS_ALL_AT   1.46   1.45   1.45   1.45   1.47   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40

# 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     8.887     0    0.668   0.623    10.318    8.571    6.857
LGA    D    23_A      D    23_A     3.785     0    0.417   0.808     5.113   37.500   44.702
LGA    G    24_A      G    24_A     3.594     0    0.279   0.279     3.594   55.714   55.714
LGA    D    25_A      D    25_A     3.055     0    0.444   1.019     5.027   47.619   42.440
LGA    G    26_A      G    26_A     0.307     0    0.055   0.055     0.627   97.619   97.619
LGA    Q    27_A      Q    27_A     0.298     0    0.023   1.179     3.783  100.000   85.714
LGA    G    28_A      G    28_A     0.235     0    0.042   0.042     0.337  100.000  100.000
LGA    L    29_A      L    29_A     0.244     0    0.034   0.084     0.442  100.000  100.000
LGA    Y    30_A      Y    30_A     0.329     0    0.019   0.083     0.524  100.000   97.619
LGA    A    31_A      A    31_A     0.404     0    0.027   0.032     0.485  100.000  100.000
LGA    A    32_A      A    32_A     0.296     0    0.014   0.025     0.362  100.000  100.000
LGA    N    33_A      N    33_A     0.317     0    0.014   0.082     0.428  100.000  100.000
LGA    C    34_A      C    34_A     0.389     0    0.033   0.099     0.493  100.000  100.000
LGA    A    35_A      A    35_A     0.618     0    0.017   0.021     0.921   92.857   92.381
LGA    A    36_A      A    36_A     0.732     0    0.017   0.022     0.997   90.476   90.476
LGA    C    37_A      C    37_A     0.671     0    0.015   0.055     0.766   90.476   90.476
LGA    H    38_A      H    38_A     0.676     0    0.011   0.153     0.855   90.476   92.381
LGA    G    39_A      G    39_A     0.945     0    0.084   0.084     0.945   90.476   90.476
LGA    A    40_A      A    40_A     0.391     0    0.032   0.033     0.593  100.000   98.095
LGA    L    41_A      L    41_A     0.379     0    0.013   0.027     0.528   97.619   98.810
LGA    A    42_A      A    42_A     0.694     0    0.041   0.049     0.792   90.476   90.476
LGA    T    43_A      T    43_A     0.640     0    0.128   0.107     0.878   90.476   90.476
LGA    S    44_A      S    44_A     0.583     0    0.076   0.099     0.589   92.857   93.651
LGA    E    45_A      E    45_A     0.984     0    0.019   0.655     4.123   90.476   67.143
LGA    K    46_A      K    46_A     0.268     0    0.085   0.230     1.875   97.619   90.741
LGA    K    47_A      K    47_A     0.336     0    0.010   0.105     0.365  100.000  100.000
LGA    G    48_A      G    48_A     0.382     0    0.069   0.069     0.539   97.619   97.619
LGA    T    49_A      T    49_A     0.367     0    0.130   0.189     0.691   97.619   98.639
LGA    T    50_A      T    50_A     0.317     0    0.015   0.068     0.684  100.000   97.279
LGA    L    51_A      L    51_A     0.312     0    0.037   0.101     0.844  100.000   98.810
LGA    A    52_A      A    52_A     0.479     0    0.012   0.017     0.625  100.000   98.095
LGA    R    53_A      R    53_A     0.389     0    0.016   1.302     6.281  100.000   65.801
LGA    L    54_A      L    54_A     0.150     0    0.047   0.083     0.318  100.000  100.000
LGA    Q    55_A      Q    55_A     0.097     0    0.032   0.209     0.612  100.000   98.942
LGA    S    56_A      S    56_A     0.207     0    0.028   0.700     2.170  100.000   94.127
LGA    A    57_A      A    57_A     0.108     0    0.012   0.014     0.161  100.000  100.000
LGA    V    58_A      V    58_A     0.302     0    0.031   0.041     0.527  100.000   98.639
LGA    S    59_A      S    59_A     0.273     0    0.026   0.531     1.870  100.000   95.476
LGA    A    60_A      A    60_A     0.182     0    0.022   0.034     0.227  100.000  100.000
LGA    N    61_A      N    61_A     0.272     0    0.038   0.156     1.061  100.000   94.107
LGA    A    62_A      A    62_A     0.530     0    0.047   0.056     0.846   92.857   92.381
LGA    G    63_A      G    63_A     0.569     0    0.055   0.055     0.822   90.476   90.476
LGA    G    64_A      G    64_A     0.674     0    0.073   0.073     0.915   92.857   92.857
LGA    M    65_A      M    65_A     0.916     0    0.063   0.696     1.668   90.476   86.012
LGA    G    66_A      G    66_A     0.629     0    0.016   0.016     0.765   90.476   90.476
LGA    F    67_A      F    67_A     1.264     0    0.048   0.101     1.956   81.429   75.974
LGA    L    68_A      L    68_A     0.900     0    0.032   0.106     1.527   90.476   86.012
LGA    S    69_A      S    69_A     0.564     0    0.031   0.080     1.065   90.476   88.968
LGA    S    70_A      S    70_A     0.876     0    0.013   0.015     1.014   90.476   88.968
LGA    L    71_A      L    71_A     0.597     0    0.035   0.072     0.792   90.476   90.476
LGA    T    72_A      T    72_A     0.499     0    0.034   0.048     0.637   97.619   97.279
LGA    S    73_A      S    73_A     0.387     0    0.024   0.640     2.865  100.000   91.270
LGA    A    74_A      A    74_A     0.219     0    0.046   0.060     0.322  100.000  100.000
LGA    Q    75_A      Q    75_A     0.333     0    0.014   0.050     0.650  100.000   96.825
LGA    L    76_A      L    76_A     0.230     0    0.008   0.038     0.372  100.000  100.000
LGA    Q    77_A      Q    77_A     0.292     0    0.070   0.161     0.498  100.000  100.000
LGA    A    78_A      A    78_A     0.354     0    0.025   0.033     0.358  100.000  100.000
LGA    I    79_A      I    79_A     0.260     0    0.019   0.041     0.324  100.000  100.000
LGA    V    80_A      V    80_A     0.260     0    0.019   0.069     0.313  100.000  100.000
LGA    D    81_A      D    81_A     0.323     0    0.069   0.082     0.725  100.000   96.429
LGA    V    82_A      V    82_A     0.343     0    0.038   1.261     2.505  100.000   88.844
LGA    L    83_A      L    83_A     0.191     0    0.092   0.091     0.377  100.000  100.000
LGA    A    84_A      A    84_A     0.352     0    0.154   0.173     0.736   97.619   98.095
LGA    V    85_A      V    85_A     0.374     0    0.382   1.353     3.197   95.357   84.966

# 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):     1.404          1.308                  1.508           92.932   90.470

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   97   64    4.0     63    0.91    96.094    97.643     6.262

LGA_LOCAL      RMSD:   0.906  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.429  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   1.404  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.663615 * X  +  -0.652156 * Y  +   0.366481 * Z  +  22.167534
  Y_new =   0.682418 * X  +   0.327051 * Y  +  -0.653715 * Z  +  -9.773464
  Z_new =   0.306466 * X  +   0.683908 * Y  +   0.662079 * Z  +  -7.343707 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.799367 -0.311478  0.801615   [DEG:   45.8003  -17.8464   45.9292 ]
ZXZ:  0.510955  0.847207  0.421281   [DEG:   29.2756   48.5414   24.1376 ]
 
# END of job
