
#######################################################
#                                                     #
#                        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        1.39     1.39
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    64      22_A - 85_A        1.39     1.39
  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    4    5    6    7   20   30   39   56   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    23_A     D    23_A     63   64   64      3    3    4    4   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    24_A     G    24_A     63   64   64      3    3    4    6   27   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    25_A     D    25_A     63   64   64      3    3    5   49   60   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    26_A     G    26_A     63   64   64     52   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    27_A     Q    27_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    28_A     G    28_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    29_A     L    29_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     Y    30_A     Y    30_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    31_A     A    31_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    32_A     A    32_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     N    33_A     N    33_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     C    34_A     C    34_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    35_A     A    35_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    36_A     A    36_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     C    37_A     C    37_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     H    38_A     H    38_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    39_A     G    39_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    40_A     A    40_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    41_A     L    41_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    42_A     A    42_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    43_A     T    43_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    44_A     S    44_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     E    45_A     E    45_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    46_A     K    46_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    47_A     K    47_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    48_A     G    48_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    49_A     T    49_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    50_A     T    50_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    51_A     L    51_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    52_A     A    52_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     R    53_A     R    53_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    54_A     L    54_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    55_A     Q    55_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    56_A     S    56_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    57_A     A    57_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    58_A     V    58_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    59_A     S    59_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    60_A     A    60_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     N    61_A     N    61_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    62_A     A    62_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    63_A     G    63_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    64_A     G    64_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     M    65_A     M    65_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    66_A     G    66_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     F    67_A     F    67_A     63   64   64     11   57   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    68_A     L    68_A     63   64   64     11   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    69_A     S    69_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    70_A     S    70_A     63   64   64     19   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    71_A     L    71_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    72_A     T    72_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    73_A     S    73_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    74_A     A    74_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    75_A     Q    75_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    76_A     L    76_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    77_A     Q    77_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    78_A     A    78_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     I    79_A     I    79_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    80_A     V    80_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    81_A     D    81_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    82_A     V    82_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    83_A     L    83_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    84_A     A    84_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    85_A     V    85_A     63   64   64     56   59   60   60   61   61   62   63   63   63   63   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     56     59     60     60     61     61     62     63     63     63     63     64     64     64     64     64     64     64     64     64 
GDT PERCENT_AT  87.50  92.19  93.75  93.75  95.31  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
GDT RMS_LOCAL    0.30   0.34   0.36   0.36   0.61   0.57   0.78   0.91   0.91   0.91   0.91   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39
GDT RMS_ALL_AT   1.46   1.46   1.46   1.46   1.43   1.48   1.45   1.43   1.43   1.43   1.43   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39

# 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     8.812     0    0.571   0.516    10.230    6.190    4.952
LGA    D    23_A      D    23_A     3.769     0    0.160   0.205     5.830   40.476   36.190
LGA    G    24_A      G    24_A     3.973     0    0.314   0.314     3.973   53.810   53.810
LGA    D    25_A      D    25_A     3.488     0    0.402   1.034     5.471   44.048   37.083
LGA    G    26_A      G    26_A     0.474     0    0.062   0.062     0.905   97.619   97.619
LGA    Q    27_A      Q    27_A     0.248     0    0.038   0.249     0.856  100.000   98.942
LGA    G    28_A      G    28_A     0.201     0    0.033   0.033     0.360  100.000  100.000
LGA    L    29_A      L    29_A     0.410     0    0.031   0.085     0.547  100.000   97.619
LGA    Y    30_A      Y    30_A     0.347     0    0.020   0.094     0.462  100.000  100.000
LGA    A    31_A      A    31_A     0.354     0    0.028   0.034     0.444  100.000  100.000
LGA    A    32_A      A    32_A     0.333     0    0.014   0.024     0.470  100.000  100.000
LGA    N    33_A      N    33_A     0.510     0    0.016   0.071     0.633   92.857   94.048
LGA    C    34_A      C    34_A     0.469     0    0.037   0.078     0.505   97.619   98.413
LGA    A    35_A      A    35_A     0.459     0    0.017   0.021     0.644   95.238   96.190
LGA    A    36_A      A    36_A     0.351     0    0.016   0.026     0.403  100.000  100.000
LGA    C    37_A      C    37_A     0.358     0    0.017   0.048     0.672  100.000   98.413
LGA    H    38_A      H    38_A     0.208     0    0.007   0.144     0.690  100.000   97.143
LGA    G    39_A      G    39_A     0.343     0    0.036   0.036     0.363  100.000  100.000
LGA    A    40_A      A    40_A     0.357     0    0.019   0.022     0.460  100.000  100.000
LGA    L    41_A      L    41_A     0.323     0    0.024   0.038     0.421  100.000  100.000
LGA    A    42_A      A    42_A     0.527     0    0.025   0.024     0.538   95.238   96.190
LGA    T    43_A      T    43_A     0.415     0    0.118   0.110     0.609   97.619   98.639
LGA    S    44_A      S    44_A     0.410     0    0.071   0.093     0.419  100.000  100.000
LGA    E    45_A      E    45_A     0.520     0    0.025   0.654     2.874   95.238   77.778
LGA    K    46_A      K    46_A     0.291     0    0.072   0.194     1.460  100.000   93.757
LGA    K    47_A      K    47_A     0.227     0    0.016   0.151     0.497  100.000  100.000
LGA    G    48_A      G    48_A     0.082     0    0.043   0.043     0.193  100.000  100.000
LGA    T    49_A      T    49_A     0.197     0    0.067   0.085     0.389  100.000  100.000
LGA    T    50_A      T    50_A     0.209     0    0.023   0.065     0.662  100.000   97.279
LGA    L    51_A      L    51_A     0.268     0    0.026   0.097     0.891  100.000   97.619
LGA    A    52_A      A    52_A     0.375     0    0.014   0.021     0.546  100.000   98.095
LGA    R    53_A      R    53_A     0.356     0    0.021   0.430     1.574  100.000   93.203
LGA    L    54_A      L    54_A     0.232     0    0.045   0.092     0.426  100.000  100.000
LGA    Q    55_A      Q    55_A     0.264     0    0.014   0.202     0.542  100.000   98.942
LGA    S    56_A      S    56_A     0.401     0    0.051   0.049     0.572  100.000   98.413
LGA    A    57_A      A    57_A     0.232     0    0.017   0.027     0.313  100.000  100.000
LGA    V    58_A      V    58_A     0.352     0    0.022   0.035     0.633  100.000   98.639
LGA    S    59_A      S    59_A     0.326     0    0.010   0.759     2.411  100.000   94.127
LGA    A    60_A      A    60_A     0.062     0    0.016   0.034     0.332  100.000  100.000
LGA    N    61_A      N    61_A     0.499     0    0.043   0.196     1.497  100.000   94.107
LGA    A    62_A      A    62_A     0.443     0    0.017   0.024     0.658  100.000   98.095
LGA    G    63_A      G    63_A     0.284     0    0.053   0.053     0.410  100.000  100.000
LGA    G    64_A      G    64_A     0.417     0    0.045   0.045     0.540   97.619   97.619
LGA    M    65_A      M    65_A     0.486     0    0.032   0.106     0.581   95.238   94.048
LGA    G    66_A      G    66_A     0.529     0    0.025   0.025     0.746   90.476   90.476
LGA    F    67_A      F    67_A     1.175     0    0.050   0.211     2.138   83.690   79.177
LGA    L    68_A      L    68_A     0.995     0    0.078   0.089     1.714   90.476   83.810
LGA    S    69_A      S    69_A     0.473     0    0.009   0.082     0.692   92.857   93.651
LGA    S    70_A      S    70_A     0.815     0    0.021   0.021     1.029   90.476   88.968
LGA    L    71_A      L    71_A     0.570     0    0.025   0.061     0.724   90.476   90.476
LGA    T    72_A      T    72_A     0.523     0    0.043   0.055     0.660   95.238   94.558
LGA    S    73_A      S    73_A     0.376     0    0.025   0.621     2.702  100.000   92.857
LGA    A    74_A      A    74_A     0.175     0    0.053   0.066     0.321  100.000  100.000
LGA    Q    75_A      Q    75_A     0.306     0    0.017   0.053     0.696  100.000   95.767
LGA    L    76_A      L    76_A     0.181     0    0.012   0.048     0.355  100.000  100.000
LGA    Q    77_A      Q    77_A     0.247     0    0.075   0.152     0.503  100.000   98.942
LGA    A    78_A      A    78_A     0.287     0    0.021   0.029     0.344  100.000  100.000
LGA    I    79_A      I    79_A     0.197     0    0.022   0.048     0.261  100.000  100.000
LGA    V    80_A      V    80_A     0.233     0    0.017   0.053     0.313  100.000  100.000
LGA    D    81_A      D    81_A     0.345     0    0.064   0.083     0.776  100.000   96.429
LGA    V    82_A      V    82_A     0.262     0    0.045   1.252     2.580  100.000   88.844
LGA    L    83_A      L    83_A     0.176     0    0.088   0.082     0.378  100.000  100.000
LGA    A    84_A      A    84_A     0.274     0    0.143   0.160     0.678   97.619   98.095
LGA    V    85_A      V    85_A     0.293     0    0.324   1.310     3.117   95.238   85.102

# 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):     1.394          1.327                  1.439           94.302   92.408

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   97   64    4.0     63    0.91    96.094    97.416     6.228

LGA_LOCAL      RMSD:   0.912  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.425  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   1.394  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.814020 * X  +   0.408985 * Y  +  -0.412435 * Z  +  21.809135
  Y_new =  -0.384516 * X  +  -0.152753 * Y  +  -0.910392 * Z  +  -9.753795
  Z_new =  -0.435338 * X  +   0.899665 * Y  +   0.032917 * Z  + -10.174047 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.441297  0.450413  1.534225   [DEG:  -25.2845   25.8068   87.9046 ]
ZXZ: -0.425370  1.537874 -0.450676   [DEG:  -24.3719   88.1137  -25.8218 ]
 
# END of job
