
#######################################################
#                                                     #
#                        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        1.13     1.13
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    64      22_A - 85_A        1.13     1.13
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63      22_A - 84_A        0.94     1.14
  LCS_AVERAGE:     98.39

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     63   64   64      3    3   46   58   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    23_A     D    23_A     63   64   64      3    5   30   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    24_A     G    24_A     63   64   64      3    3    3    3   59   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    25_A     D    25_A     63   64   64      3    3    4   27   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    26_A     G    26_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    27_A     Q    27_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    28_A     G    28_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    29_A     L    29_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Y    30_A     Y    30_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    31_A     A    31_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    32_A     A    32_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     N    33_A     N    33_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     C    34_A     C    34_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    35_A     A    35_A     63   64   64     32   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    36_A     A    36_A     63   64   64     21   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     C    37_A     C    37_A     63   64   64     28   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     H    38_A     H    38_A     63   64   64     15   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    39_A     G    39_A     63   64   64     15   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    40_A     A    40_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    41_A     L    41_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    42_A     A    42_A     63   64   64     37   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    43_A     T    43_A     63   64   64     37   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    44_A     S    44_A     63   64   64     37   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     E    45_A     E    45_A     63   64   64     22   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    46_A     K    46_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    47_A     K    47_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    48_A     G    48_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    49_A     T    49_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    50_A     T    50_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    51_A     L    51_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    52_A     A    52_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     R    53_A     R    53_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    54_A     L    54_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    55_A     Q    55_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    56_A     S    56_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    57_A     A    57_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    58_A     V    58_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    59_A     S    59_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    60_A     A    60_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     N    61_A     N    61_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    62_A     A    62_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    63_A     G    63_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    64_A     G    64_A     63   64   64     17   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     M    65_A     M    65_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    66_A     G    66_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     F    67_A     F    67_A     63   64   64     15   56   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    68_A     L    68_A     63   64   64     15   56   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    69_A     S    69_A     63   64   64     40   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    70_A     S    70_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    71_A     L    71_A     63   64   64     40   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    72_A     T    72_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    73_A     S    73_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    74_A     A    74_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    75_A     Q    75_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    76_A     L    76_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    77_A     Q    77_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    78_A     A    78_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     I    79_A     I    79_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    80_A     V    80_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    81_A     D    81_A     63   64   64     41   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    82_A     V    82_A     63   64   64     37   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    83_A     L    83_A     63   64   64     35   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    84_A     A    84_A     63   64   64     27   57   59   60   61   62   63   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    85_A     V    85_A     61   64   64      3    3    4    5   17   40   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_AVERAGE  LCS_A:  99.46  (  98.39  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     41     57     59     60     61     62     63     63     64     64     64     64     64     64     64     64     64     64     64     64 
GDT PERCENT_AT  64.06  89.06  92.19  93.75  95.31  96.88  98.44  98.44 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.34   0.48   0.52   0.60   0.68   0.79   0.94   0.94   1.13   1.13   1.13   1.13   1.13   1.13   1.13   1.13   1.13   1.13   1.13   1.13
GDT RMS_ALL_AT   1.15   1.14   1.14   1.14   1.14   1.15   1.14   1.14   1.13   1.13   1.13   1.13   1.13   1.13   1.13   1.13   1.13   1.13   1.13   1.13

# 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     2.853     0    0.021   0.025     4.198   71.548   64.667
LGA    D    23_A      D    23_A     2.190     0    0.113   0.854     3.724   65.238   58.571
LGA    G    24_A      G    24_A     4.036     0    0.672   0.672     4.036   54.048   54.048
LGA    D    25_A      D    25_A     3.127     0    0.473   1.076     5.018   45.833   43.095
LGA    G    26_A      G    26_A     0.260     0    0.094   0.094     0.585   97.619   97.619
LGA    Q    27_A      Q    27_A     0.219     0    0.012   1.474     5.718  100.000   77.884
LGA    G    28_A      G    28_A     0.266     0    0.008   0.008     0.277  100.000  100.000
LGA    L    29_A      L    29_A     0.199     0    0.001   1.255     2.719  100.000   90.238
LGA    Y    30_A      Y    30_A     0.216     0    0.018   0.092     0.298  100.000  100.000
LGA    A    31_A      A    31_A     0.209     0    0.024   0.030     0.512   97.619   98.095
LGA    A    32_A      A    32_A     0.244     0    0.018   0.021     0.346  100.000  100.000
LGA    N    33_A      N    33_A     0.288     0    0.025   0.066     0.335  100.000  100.000
LGA    C    34_A      C    34_A     0.335     0    0.010   0.034     0.464  100.000  100.000
LGA    A    35_A      A    35_A     0.593     0    0.045   0.050     1.030   90.595   90.571
LGA    A    36_A      A    36_A     0.706     0    0.019   0.021     0.906   90.476   90.476
LGA    C    37_A      C    37_A     0.764     0    0.022   0.052     1.015   88.214   88.968
LGA    H    38_A      H    38_A     0.804     0    0.034   0.196     1.187   90.476   89.571
LGA    G    39_A      G    39_A     0.952     0    0.085   0.085     0.952   90.476   90.476
LGA    A    40_A      A    40_A     0.416     0    0.016   0.023     0.636  100.000   98.095
LGA    L    41_A      L    41_A     0.534     0    0.018   0.080     0.951   92.857   91.667
LGA    A    42_A      A    42_A     0.811     0    0.025   0.024     0.920   90.476   90.476
LGA    T    43_A      T    43_A     0.648     0    0.107   0.092     0.735   90.476   90.476
LGA    S    44_A      S    44_A     0.681     0    0.010   0.028     0.741   95.238   93.651
LGA    E    45_A      E    45_A     0.781     0    0.037   0.680     3.674   90.476   69.259
LGA    K    46_A      K    46_A     0.422     0    0.055   0.196     1.673   95.238   89.683
LGA    K    47_A      K    47_A     0.388     0    0.023   0.051     0.610  100.000   97.884
LGA    G    48_A      G    48_A     0.487     0    0.088   0.088     0.562   97.619   97.619
LGA    T    49_A      T    49_A     0.369     0    0.049   0.096     0.600  100.000   98.639
LGA    T    50_A      T    50_A     0.504     0    0.034   0.104     1.053   97.619   93.265
LGA    L    51_A      L    51_A     0.317     0    0.010   0.093     0.651  100.000   98.810
LGA    A    52_A      A    52_A     0.482     0    0.013   0.014     0.534  100.000   98.095
LGA    R    53_A      R    53_A     0.535     0    0.014   0.607     3.303   92.857   82.164
LGA    L    54_A      L    54_A     0.323     0    0.018   0.091     0.466  100.000  100.000
LGA    Q    55_A      Q    55_A     0.355     0    0.011   0.240     0.601  100.000   98.942
LGA    S    56_A      S    56_A     0.504     0    0.039   0.685     2.327   97.619   90.952
LGA    A    57_A      A    57_A     0.397     0    0.018   0.018     0.444  100.000  100.000
LGA    V    58_A      V    58_A     0.442     0    0.026   1.340     2.856  100.000   87.483
LGA    S    59_A      S    59_A     0.474     0    0.019   0.557     2.176   97.619   90.952
LGA    A    60_A      A    60_A     0.517     0    0.016   0.025     0.593   97.619   96.190
LGA    N    61_A      N    61_A     0.263     0    0.038   0.118     0.708  100.000   97.619
LGA    A    62_A      A    62_A     0.282     0    0.045   0.056     0.593   97.619   98.095
LGA    G    63_A      G    63_A     0.377     0    0.054   0.054     0.755   95.238   95.238
LGA    G    64_A      G    64_A     0.647     0    0.054   0.054     0.938   90.476   90.476
LGA    M    65_A      M    65_A     0.559     0    0.046   0.164     0.784   90.476   91.667
LGA    G    66_A      G    66_A     0.557     0    0.012   0.012     0.751   90.476   90.476
LGA    F    67_A      F    67_A     1.262     0    0.025   0.218     2.292   81.429   76.061
LGA    L    68_A      L    68_A     1.211     0    0.077   1.254     4.026   85.952   75.000
LGA    S    69_A      S    69_A     0.609     0    0.037   0.039     0.817   92.857   92.063
LGA    S    70_A      S    70_A     0.481     0    0.019   0.035     0.659   97.619   95.238
LGA    L    71_A      L    71_A     0.528     0    0.031   1.243     2.960   92.857   84.286
LGA    T    72_A      T    72_A     0.405     0    0.015   0.030     0.505  100.000   98.639
LGA    S    73_A      S    73_A     0.201     0    0.012   0.635     2.447  100.000   94.127
LGA    A    74_A      A    74_A     0.312     0    0.018   0.021     0.459  100.000  100.000
LGA    Q    75_A      Q    75_A     0.336     0    0.031   0.116     0.808  100.000   95.767
LGA    L    76_A      L    76_A     0.194     0    0.013   1.238     2.548  100.000   90.238
LGA    Q    77_A      Q    77_A     0.128     0    0.007   0.084     0.287  100.000  100.000
LGA    A    78_A      A    78_A     0.129     0    0.007   0.009     0.212  100.000  100.000
LGA    I    79_A      I    79_A     0.174     0    0.021   0.047     0.273  100.000  100.000
LGA    V    80_A      V    80_A     0.145     0    0.022   1.339     2.660  100.000   88.844
LGA    D    81_A      D    81_A     0.238     0    0.014   0.023     0.799  100.000   95.238
LGA    V    82_A      V    82_A     0.630     0    0.077   1.258     2.948   92.857   83.401
LGA    L    83_A      L    83_A     0.746     0    0.099   1.228     2.899   83.810   79.762
LGA    A    84_A      A    84_A     1.032     0    0.541   0.489     1.748   83.810   87.048
LGA    V    85_A      V    85_A     5.236     0    0.495   0.804     8.136   21.310   17.007

# 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):     1.132          1.164                  1.478           92.416   89.139

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   97   64    4.0     63    0.94    95.312    97.444     6.043

LGA_LOCAL      RMSD:   0.942  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.141  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   1.132  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.606960 * X  +   0.643520 * Y  +   0.466349 * Z  +  22.602428
  Y_new =  -0.548899 * X  +   0.084907 * Y  +  -0.831565 * Z  + -12.509052
  Z_new =  -0.574725 * X  +  -0.760705 * Y  +   0.301693 * Z  + -15.117906 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.406384  0.612269 -1.193228   [DEG: -137.8756   35.0804  -68.3669 ]
ZXZ:  0.511104  1.264329 -2.494570   [DEG:   29.2841   72.4407 -142.9283 ]
 
# END of job
