
#######################################################
#                                                     #
#                        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        1.42     1.42
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    64      22_A - 85_A        1.42     1.42
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63      23_A - 85_A        0.92     1.44
  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    8   30   37   48   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    23_A     D    23_A     63   64   64      3    3    4    8   32   62   63   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   18   61   62   63   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    4   19   28   61   61   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    26_A     G    26_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    27_A     Q    27_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    28_A     G    28_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    29_A     L    29_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     Y    30_A     Y    30_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    31_A     A    31_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    32_A     A    32_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     N    33_A     N    33_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     C    34_A     C    34_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    35_A     A    35_A     63   64   64     31   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    36_A     A    36_A     63   64   64     29   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     C    37_A     C    37_A     63   64   64     29   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     H    38_A     H    38_A     63   64   64     31   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    39_A     G    39_A     63   64   64     22   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    40_A     A    40_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    41_A     L    41_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    42_A     A    42_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    43_A     T    43_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    44_A     S    44_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     E    45_A     E    45_A     63   64   64     26   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    46_A     K    46_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    47_A     K    47_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    48_A     G    48_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    49_A     T    49_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    50_A     T    50_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    51_A     L    51_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    52_A     A    52_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     R    53_A     R    53_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    54_A     L    54_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    55_A     Q    55_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    56_A     S    56_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    57_A     A    57_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    58_A     V    58_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    59_A     S    59_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    60_A     A    60_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     N    61_A     N    61_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    62_A     A    62_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    63_A     G    63_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    64_A     G    64_A     63   64   64     12   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     M    65_A     M    65_A     63   64   64     12   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    66_A     G    66_A     63   64   64     39   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     F    67_A     F    67_A     63   64   64     12   50   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    68_A     L    68_A     63   64   64     12   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    69_A     S    69_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    70_A     S    70_A     63   64   64     44   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    71_A     L    71_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    72_A     T    72_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    73_A     S    73_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    74_A     A    74_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    75_A     Q    75_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    76_A     L    76_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    77_A     Q    77_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    78_A     A    78_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     I    79_A     I    79_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    80_A     V    80_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    81_A     D    81_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    82_A     V    82_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    83_A     L    83_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    84_A     A    84_A     63   64   64     48   59   60   60   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    85_A     V    85_A     63   64   64     48   59   60   60   61   62   63   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     48     59     60     60     61     62     63     63     63     63     63     64     64     64     64     64     64     64     64     64 
GDT PERCENT_AT  75.00  92.19  93.75  93.75  95.31  96.88  98.44  98.44  98.44  98.44  98.44 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.30   0.44   0.47   0.47   0.61   0.83   0.92   0.92   0.92   0.92   0.92   1.42   1.42   1.42   1.42   1.42   1.42   1.42   1.42   1.42
GDT RMS_ALL_AT   1.48   1.47   1.47   1.47   1.49   1.43   1.44   1.44   1.44   1.44   1.44   1.42   1.42   1.42   1.42   1.42   1.42   1.42   1.42   1.42

# 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     8.973     0    0.631   0.592    10.238    8.095    6.476
LGA    D    23_A      D    23_A     3.883     0    0.138   0.782     5.155   39.048   46.429
LGA    G    24_A      G    24_A     3.581     0    0.134   0.134     3.581   55.833   55.833
LGA    D    25_A      D    25_A     3.095     0    0.405   1.031     4.993   48.929   43.095
LGA    G    26_A      G    26_A     0.309     0    0.100   0.100     0.641   97.619   97.619
LGA    Q    27_A      Q    27_A     0.295     0    0.007   1.177     3.747  100.000   83.757
LGA    G    28_A      G    28_A     0.259     0    0.014   0.014     0.290  100.000  100.000
LGA    L    29_A      L    29_A     0.290     0    0.000   0.080     0.526  100.000   98.810
LGA    Y    30_A      Y    30_A     0.347     0    0.039   0.128     0.793  100.000   96.032
LGA    A    31_A      A    31_A     0.355     0    0.006   0.011     0.488  100.000  100.000
LGA    A    32_A      A    32_A     0.242     0    0.016   0.015     0.260  100.000  100.000
LGA    N    33_A      N    33_A     0.375     0    0.035   0.072     0.554   97.619   98.810
LGA    C    34_A      C    34_A     0.373     0    0.047   0.074     0.478  100.000  100.000
LGA    A    35_A      A    35_A     0.589     0    0.028   0.028     0.978   92.857   92.381
LGA    A    36_A      A    36_A     0.710     0    0.012   0.012     0.939   90.476   90.476
LGA    C    37_A      C    37_A     0.735     0    0.066   0.080     1.007   88.214   88.968
LGA    H    38_A      H    38_A     0.645     0    0.040   0.091     0.869   90.476   92.381
LGA    G    39_A      G    39_A     0.854     0    0.080   0.080     0.854   90.476   90.476
LGA    A    40_A      A    40_A     0.395     0    0.011   0.016     0.618  100.000   98.095
LGA    L    41_A      L    41_A     0.350     0    0.020   0.039     0.527   97.619   98.810
LGA    A    42_A      A    42_A     0.724     0    0.028   0.028     0.839   90.476   90.476
LGA    T    43_A      T    43_A     0.635     0    0.102   0.085     0.814   90.476   90.476
LGA    S    44_A      S    44_A     0.542     0    0.033   0.044     0.571   95.238   93.651
LGA    E    45_A      E    45_A     0.999     0    0.022   0.654     4.321   90.476   66.455
LGA    K    46_A      K    46_A     0.406     0    0.033   0.114     1.349   95.238   91.640
LGA    K    47_A      K    47_A     0.407     0    0.010   0.148     0.410  100.000  100.000
LGA    G    48_A      G    48_A     0.415     0    0.085   0.085     0.615   97.619   97.619
LGA    T    49_A      T    49_A     0.354     0    0.104   0.174     0.669   97.619   98.639
LGA    T    50_A      T    50_A     0.327     0    0.012   0.055     0.612  100.000   97.279
LGA    L    51_A      L    51_A     0.368     0    0.007   0.118     0.934  100.000   97.619
LGA    A    52_A      A    52_A     0.482     0    0.013   0.014     0.550  100.000   98.095
LGA    R    53_A      R    53_A     0.445     0    0.008   1.283     6.296  100.000   65.455
LGA    L    54_A      L    54_A     0.191     0    0.009   0.063     0.276  100.000  100.000
LGA    Q    55_A      Q    55_A     0.140     0    0.003   0.199     0.660  100.000   98.942
LGA    S    56_A      S    56_A     0.179     0    0.031   0.680     2.157  100.000   94.127
LGA    A    57_A      A    57_A     0.151     0    0.006   0.010     0.198  100.000  100.000
LGA    V    58_A      V    58_A     0.349     0    0.006   0.028     0.585  100.000   98.639
LGA    S    59_A      S    59_A     0.261     0    0.020   0.550     1.889  100.000   95.476
LGA    A    60_A      A    60_A     0.169     0    0.021   0.027     0.185  100.000  100.000
LGA    N    61_A      N    61_A     0.298     0    0.065   0.105     0.888  100.000   96.429
LGA    A    62_A      A    62_A     0.550     0    0.035   0.043     0.765   92.857   92.381
LGA    G    63_A      G    63_A     0.598     0    0.077   0.077     0.873   90.476   90.476
LGA    G    64_A      G    64_A     0.760     0    0.016   0.016     1.181   88.214   88.214
LGA    M    65_A      M    65_A     0.961     0    0.079   0.752     1.607   90.476   86.012
LGA    G    66_A      G    66_A     0.632     0    0.011   0.011     0.867   90.476   90.476
LGA    F    67_A      F    67_A     1.291     0    0.026   0.143     2.136   81.429   74.502
LGA    L    68_A      L    68_A     0.862     0    0.021   0.091     1.462   90.476   87.083
LGA    S    69_A      S    69_A     0.583     0    0.040   0.040     1.045   90.476   88.968
LGA    S    70_A      S    70_A     0.877     0    0.019   0.063     0.988   90.476   90.476
LGA    L    71_A      L    71_A     0.632     0    0.006   0.038     0.738   90.476   90.476
LGA    T    72_A      T    72_A     0.477     0    0.012   0.037     0.509   97.619   98.639
LGA    S    73_A      S    73_A     0.430     0    0.010   0.634     2.692  100.000   91.270
LGA    A    74_A      A    74_A     0.195     0    0.024   0.027     0.255  100.000  100.000
LGA    Q    75_A      Q    75_A     0.306     0    0.018   0.063     0.546  100.000   98.942
LGA    L    76_A      L    76_A     0.304     0    0.005   0.044     0.378  100.000  100.000
LGA    Q    77_A      Q    77_A     0.298     0    0.023   0.139     0.476  100.000  100.000
LGA    A    78_A      A    78_A     0.306     0    0.007   0.007     0.314  100.000  100.000
LGA    I    79_A      I    79_A     0.224     0    0.018   0.049     0.302  100.000  100.000
LGA    V    80_A      V    80_A     0.325     0    0.016   0.036     0.376  100.000  100.000
LGA    D    81_A      D    81_A     0.344     0    0.028   0.044     0.755  100.000   95.238
LGA    V    82_A      V    82_A     0.280     0    0.008   1.281     2.590  100.000   88.844
LGA    L    83_A      L    83_A     0.177     0    0.088   0.086     0.376  100.000  100.000
LGA    A    84_A      A    84_A     0.263     0    0.085   0.089     0.528   97.619   98.095
LGA    V    85_A      V    85_A     0.326     0    0.290   1.319     3.227   97.619   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):     1.418          1.324                  1.522           92.861   90.385

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   97   64    4.0     63    0.92    96.094    97.601     6.194

LGA_LOCAL      RMSD:   0.917  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.444  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   1.418  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.662795 * X  +  -0.653547 * Y  +   0.365485 * Z  +  22.165648
  Y_new =   0.681933 * X  +   0.325206 * Y  +  -0.655141 * Z  +  -9.774463
  Z_new =   0.309308 * X  +   0.683460 * Y  +   0.661220 * Z  +  -7.348174 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.799629 -0.314465  0.801936   [DEG:   45.8154  -18.0175   45.9475 ]
ZXZ:  0.508867  0.848353  0.424982   [DEG:   29.1559   48.6070   24.3497 ]
 
# END of job
