
#######################################################
#                                                     #
#                        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        3.12     3.12
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      61_A - 85_A        1.96     3.54
  LCS_AVERAGE:     35.30

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18      68_A - 85_A        0.93     3.56
  LCS_AVERAGE:     23.34

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    3   64      3    3    5    8    8   18   29   38   45   57   61   62   64   64   64   64   64   64   64   64 
LCS_GDT     D    23_A     D    23_A      3    4   64      3    6    9   16   22   28   33   39   50   57   61   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    24_A     G    24_A      3   22   64      3    4   12   29   35   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     D    25_A     D    25_A     17   22   64      3    4   17   33   39   45   54   58   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    26_A     G    26_A     17   22   64     20   31   31   34   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     Q    27_A     Q    27_A     17   22   64     20   31   31   34   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    28_A     G    28_A     17   22   64     20   31   31   34   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    29_A     L    29_A     17   22   64     20   31   31   34   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     Y    30_A     Y    30_A     17   22   64     20   31   31   34   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    31_A     A    31_A     17   22   64     20   31   31   34   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    32_A     A    32_A     17   22   64     20   31   31   34   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     N    33_A     N    33_A     17   22   64     20   31   31   34   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     C    34_A     C    34_A     17   22   64     20   31   31   34   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    35_A     A    35_A     17   22   64     20   31   31   34   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    36_A     A    36_A     17   22   64     20   31   31   34   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     C    37_A     C    37_A     17   22   64     20   31   31   34   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     H    38_A     H    38_A     17   22   64     14   31   31   34   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    39_A     G    39_A     17   22   64     16   31   31   34   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    40_A     A    40_A     17   22   64     16   31   31   34   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    41_A     L    41_A     17   22   64      3    5   10   29   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    42_A     A    42_A      3   22   64      3    3    5   16   19   27   32   44   54   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     T    43_A     T    43_A      3   22   64      3    5   22   33   36   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     S    44_A     S    44_A      3   22   64      3    3    3    9   16   35   47   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     E    45_A     E    45_A      3   22   64      3    4   23   33   37   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     K    46_A     K    46_A     17   22   64      3    4   16   18   20   23   41   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     K    47_A     K    47_A     17   22   64      3   13   16   18   22   31   52   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    48_A     G    48_A     17   22   64      3   11   16   18   22   30   47   56   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     T    49_A     T    49_A     17   22   64      4   13   16   18   30   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     T    50_A     T    50_A     17   22   64      9   13   16   21   36   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    51_A     L    51_A     17   22   64      9   13   16   21   32   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    52_A     A    52_A     17   22   64      9   13   17   32   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     R    53_A     R    53_A     17   22   64      9   13   18   33   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    54_A     L    54_A     17   22   64      9   13   17   25   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     Q    55_A     Q    55_A     17   22   64      9   13   16   20   35   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     S    56_A     S    56_A     17   22   64      9   13   19   32   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    57_A     A    57_A     17   22   64      9   13   23   33   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     V    58_A     V    58_A     17   22   64      9   13   16   18   35   45   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     S    59_A     S    59_A     17   22   64      9   13   16   18   22   33   51   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    60_A     A    60_A     17   22   64      9   13   16   18   28   46   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     N    61_A     N    61_A     17   25   64      3   13   16   32   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    62_A     A    62_A     17   25   64      5   14   29   34   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    63_A     G    63_A     16   25   64      3    4   10   22   34   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    64_A     G    64_A      4   25   64      3    3    4   16   35   45   53   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     M    65_A     M    65_A      4   25   64      3    4   12   18   35   45   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    66_A     G    66_A      4   25   64      3    3    8   18   35   45   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     F    67_A     F    67_A      5   25   64      3    3    5    7   21   25   47   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    68_A     L    68_A     18   25   64      5    8   25   34   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     S    69_A     S    69_A     18   25   64      7   31   31   34   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     S    70_A     S    70_A     18   25   64      5   10   31   34   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    71_A     L    71_A     18   25   64     11   31   31   34   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     T    72_A     T    72_A     18   25   64     20   31   31   34   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     S    73_A     S    73_A     18   25   64     20   31   31   34   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    74_A     A    74_A     18   25   64     20   31   31   34   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     Q    75_A     Q    75_A     18   25   64     20   31   31   34   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    76_A     L    76_A     18   25   64     17   31   31   34   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     Q    77_A     Q    77_A     18   25   64     16   31   31   34   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    78_A     A    78_A     18   25   64     20   31   31   34   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     I    79_A     I    79_A     18   25   64     20   31   31   34   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     V    80_A     V    80_A     18   25   64     20   31   31   34   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     D    81_A     D    81_A     18   25   64     20   31   31   34   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     V    82_A     V    82_A     18   25   64     20   31   31   34   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    83_A     L    83_A     18   25   64     19   31   31   34   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    84_A     A    84_A     18   25   64     15   31   31   34   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     V    85_A     V    85_A     18   25   64      9   31   31   34   39   49   54   59   61   61   62   63   64   64   64   64   64   64   64   64 
LCS_AVERAGE  LCS_A:  52.88  (  23.34   35.30  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     20     31     31     34     39     49     54     59     61     61     62     63     64     64     64     64     64     64     64     64 
GDT PERCENT_AT  31.25  48.44  48.44  53.12  60.94  76.56  84.38  92.19  95.31  95.31  96.88  98.44 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.28   0.51   0.51   0.97   1.46   2.08   2.24   2.59   2.67   2.67   2.74   2.92   3.12   3.12   3.12   3.12   3.12   3.12   3.12   3.12
GDT RMS_ALL_AT   3.87   3.83   3.83   3.60   3.54   3.22   3.25   3.17   3.16   3.16   3.16   3.13   3.12   3.12   3.12   3.12   3.12   3.12   3.12   3.12

# Checking swapping
#   possible swapping detected:  D    23_A      D    23_A
#   possible swapping detected:  Y    30_A      Y    30_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    22_A      A    22_A     9.976     0    0.543   0.507    10.520    1.190    1.048
LGA    D    23_A      D    23_A     8.787     0    0.196   1.044    13.805    9.762    4.881
LGA    G    24_A      G    24_A     3.580     0    0.460   0.460     5.739   45.238   45.238
LGA    D    25_A      D    25_A     3.024     0    0.301   0.871     9.358   54.167   33.036
LGA    G    26_A      G    26_A     1.166     0    0.082   0.082     1.228   81.429   81.429
LGA    Q    27_A      Q    27_A     1.098     0    0.032   1.227     3.925   81.429   70.899
LGA    G    28_A      G    28_A     1.319     0    0.020   0.020     1.379   81.429   81.429
LGA    L    29_A      L    29_A     1.102     0    0.036   1.326     3.594   81.429   74.524
LGA    Y    30_A      Y    30_A     1.149     0    0.024   0.148     1.339   81.429   81.429
LGA    A    31_A      A    31_A     1.500     0    0.012   0.016     1.747   77.143   76.286
LGA    A    32_A      A    32_A     1.529     0    0.019   0.033     1.688   72.857   72.857
LGA    N    33_A      N    33_A     1.545     0    0.039   0.238     1.875   75.000   75.000
LGA    C    34_A      C    34_A     1.484     0    0.032   0.048     1.520   79.286   80.000
LGA    A    35_A      A    35_A     1.632     0    0.044   0.055     2.079   70.833   71.238
LGA    A    36_A      A    36_A     2.059     0    0.027   0.036     2.335   66.786   66.381
LGA    C    37_A      C    37_A     2.089     0    0.052   0.065     2.456   66.786   68.810
LGA    H    38_A      H    38_A     2.067     0    0.081   0.216     2.067   70.833   72.048
LGA    G    39_A      G    39_A     2.044     0    0.033   0.033     2.044   70.952   70.952
LGA    A    40_A      A    40_A     1.626     0    0.626   0.595     3.379   67.143   68.286
LGA    L    41_A      L    41_A     2.063     0    0.345   0.876     7.740   70.833   45.595
LGA    A    42_A      A    42_A     5.752     0    0.248   0.278     7.447   26.071   22.857
LGA    T    43_A      T    43_A     3.526     0    0.341   1.297     5.302   45.000   46.871
LGA    S    44_A      S    44_A     5.037     0    0.186   0.643     6.762   36.071   30.635
LGA    E    45_A      E    45_A     2.920     0    0.689   1.176     6.985   55.357   42.011
LGA    K    46_A      K    46_A     5.193     0    0.198   1.388     7.952   23.452   17.249
LGA    K    47_A      K    47_A     4.663     0    0.670   0.728     7.648   41.190   28.095
LGA    G    48_A      G    48_A     5.292     0    0.278   0.278     5.971   29.048   29.048
LGA    T    49_A      T    49_A     3.204     0    0.053   0.129     3.887   48.333   52.177
LGA    T    50_A      T    50_A     2.881     0    0.053   0.086     2.958   57.143   59.320
LGA    L    51_A      L    51_A     3.234     0    0.023   0.407     5.544   55.357   45.833
LGA    A    52_A      A    52_A     2.327     0    0.020   0.020     2.442   64.762   64.762
LGA    R    53_A      R    53_A     1.777     0    0.029   1.107     3.963   72.857   70.390
LGA    L    54_A      L    54_A     2.587     0    0.022   1.266     6.169   59.048   47.262
LGA    Q    55_A      Q    55_A     3.104     0    0.015   0.818     5.062   53.571   48.201
LGA    S    56_A      S    56_A     2.309     0    0.023   0.036     2.498   64.762   66.111
LGA    A    57_A      A    57_A     1.788     0    0.017   0.021     2.447   68.810   69.619
LGA    V    58_A      V    58_A     3.469     0    0.036   0.166     4.615   46.905   42.789
LGA    S    59_A      S    59_A     4.114     0    0.034   0.678     5.176   37.262   35.397
LGA    A    60_A      A    60_A     3.505     0    0.114   0.121     3.505   48.333   48.667
LGA    N    61_A      N    61_A     2.653     0    0.612   1.124     4.164   54.048   55.774
LGA    A    62_A      A    62_A     0.638     0    0.058   0.076     2.228   79.643   81.810
LGA    G    63_A      G    63_A     3.246     0    0.495   0.495     4.460   50.476   50.476
LGA    G    64_A      G    64_A     4.151     0    0.335   0.335     4.454   42.143   42.143
LGA    M    65_A      M    65_A     3.519     0    0.596   0.608     4.681   40.357   60.357
LGA    G    66_A      G    66_A     3.535     0    0.666   0.666     5.101   42.381   42.381
LGA    F    67_A      F    67_A     4.315     0    0.692   0.543    10.782   48.571   21.905
LGA    L    68_A      L    68_A     1.410     0    0.253   0.858     2.458   77.262   75.119
LGA    S    69_A      S    69_A     1.954     0    0.123   0.186     3.487   67.262   65.159
LGA    S    70_A      S    70_A     2.378     0    0.068   0.646     3.164   63.095   62.381
LGA    L    71_A      L    71_A     1.319     0    0.066   0.109     1.664   77.143   83.810
LGA    T    72_A      T    72_A     1.923     0    0.058   0.065     1.962   72.857   72.857
LGA    S    73_A      S    73_A     2.325     0    0.047   0.642     4.051   64.762   58.889
LGA    A    74_A      A    74_A     1.812     0    0.031   0.039     1.928   72.857   72.857
LGA    Q    75_A      Q    75_A     1.239     0    0.043   0.138     1.387   81.429   81.429
LGA    L    76_A      L    76_A     1.541     0    0.022   0.121     1.972   75.000   75.000
LGA    Q    77_A      Q    77_A     1.826     0    0.031   1.216     6.511   72.857   51.905
LGA    A    78_A      A    78_A     1.478     0    0.018   0.018     1.536   79.286   79.714
LGA    I    79_A      I    79_A     1.524     0    0.027   0.270     1.681   75.000   78.214
LGA    V    80_A      V    80_A     1.974     0    0.024   1.240     4.823   70.833   63.469
LGA    D    81_A      D    81_A     1.903     0    1.002   1.154     5.405   55.476   62.202
LGA    V    82_A      V    82_A     1.880     0    0.145   0.987     3.980   72.857   71.361
LGA    L    83_A      L    83_A     2.030     0    0.157   0.221     2.107   70.833   68.810
LGA    A    84_A      A    84_A     2.412     0    0.046   0.042     2.479   64.762   64.762
LGA    V    85_A      V    85_A     2.331     0    0.193   1.281     4.296   64.762   64.490

# 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):     3.116          3.104                  3.616           60.551   58.061

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   97   64    4.0     59    2.59    73.438    66.700     2.191

LGA_LOCAL      RMSD:   2.593  Number of atoms:   59  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   3.171  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   3.116  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.627107 * X  +  -0.364229 * Y  +  -0.688531 * Z  +  39.873768
  Y_new =   0.716063 * X  +  -0.617476 * Y  +  -0.325541 * Z  + -28.317600
  Z_new =  -0.306580 * X  +  -0.697181 * Y  +   0.648034 * Z  +   2.117320 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.290063  0.311598 -0.821916   [DEG:  131.2109   17.8532  -47.0923 ]
ZXZ: -1.129140  0.865796 -2.727302   [DEG:  -64.6949   49.6065 -156.2629 ]
 
# END of job
