
#######################################################
#                                                     #
#                        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        1.88     1.88
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    64      22_A - 85_A        1.88     1.88
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22      64_A - 85_A        0.93     2.11
  LCS_AVERAGE:     27.44

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     20   64   64      3   22   43   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    23_A     D    23_A     20   64   64      8   31   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    24_A     G    24_A     20   64   64      6   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    25_A     D    25_A     20   64   64      9   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    26_A     G    26_A     20   64   64      9   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    27_A     Q    27_A     20   64   64      9   27   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    28_A     G    28_A     20   64   64      9   27   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    29_A     L    29_A     20   64   64     12   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Y    30_A     Y    30_A     20   64   64     11   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    31_A     A    31_A     20   64   64      9   29   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    32_A     A    32_A     20   64   64     12   24   44   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     N    33_A     N    33_A     20   64   64      3   20   43   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     C    34_A     C    34_A     20   64   64     12   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    35_A     A    35_A     20   64   64     12   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    36_A     A    36_A     20   64   64     12   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     C    37_A     C    37_A     20   64   64     12   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     H    38_A     H    38_A     20   64   64     12   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    39_A     G    39_A     20   64   64     12   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    40_A     A    40_A     20   64   64     12   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    41_A     L    41_A     20   64   64     12   24   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    42_A     A    42_A      3   64   64      3    3    3    4    7   10   25   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    43_A     T    43_A      3   64   64      3    3    3    9   39   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    44_A     S    44_A      5   64   64      4    4    7   11   17   48   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     E    45_A     E    45_A      8   64   64      4    9   19   41   54   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    46_A     K    46_A     12   64   64     10   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    47_A     K    47_A     14   64   64     12   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    48_A     G    48_A     14   64   64     12   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    49_A     T    49_A     14   64   64     12   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    50_A     T    50_A     14   64   64     12   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    51_A     L    51_A     14   64   64     12   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    52_A     A    52_A     14   64   64     12   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     R    53_A     R    53_A     14   64   64     10   26   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    54_A     L    54_A     14   64   64     10   23   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    55_A     Q    55_A     14   64   64     10   24   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    56_A     S    56_A     14   64   64     10   27   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    57_A     A    57_A     14   64   64     10   19   42   50   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    58_A     V    58_A     14   64   64     10   12   33   41   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    59_A     S    59_A     14   64   64     10   19   33   44   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    60_A     A    60_A     14   64   64     10   19   33   50   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     N    61_A     N    61_A      3   64   64      0    4   11   28   40   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    62_A     A    62_A      5   64   64      3    4   15   50   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    63_A     G    63_A      5   64   64      3    4    5   39   55   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    64_A     G    64_A     22   64   64      7   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     M    65_A     M    65_A     22   64   64      8   25   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    66_A     G    66_A     22   64   64      4   22   42   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     F    67_A     F    67_A     22   64   64      4    9   42   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    68_A     L    68_A     22   64   64      5   21   43   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    69_A     S    69_A     22   64   64      9   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    70_A     S    70_A     22   64   64      3    6   36   49   56   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    71_A     L    71_A     22   64   64     11   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    72_A     T    72_A     22   64   64     12   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    73_A     S    73_A     22   64   64     12   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    74_A     A    74_A     22   64   64     12   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    75_A     Q    75_A     22   64   64     12   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    76_A     L    76_A     22   64   64      9   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    77_A     Q    77_A     22   64   64      8   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    78_A     A    78_A     22   64   64      9   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     I    79_A     I    79_A     22   64   64     12   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    80_A     V    80_A     22   64   64      9   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    81_A     D    81_A     22   64   64      9   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    82_A     V    82_A     22   64   64     11   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    83_A     L    83_A     22   64   64     12   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    84_A     A    84_A     22   64   64     12   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    85_A     V    85_A     22   64   64     11   36   45   52   57   61   62   63   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_AVERAGE  LCS_A:  75.81  (  27.44  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     12     36     45     52     57     61     62     63     64     64     64     64     64     64     64     64     64     64     64     64 
GDT PERCENT_AT  18.75  56.25  70.31  81.25  89.06  95.31  96.88  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    0.28   0.67   0.90   1.08   1.35   1.57   1.67   1.77   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88
GDT RMS_ALL_AT   2.48   2.11   2.04   2.05   1.94   1.91   1.89   1.89   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88

# Checking swapping
#   possible swapping detected:  Y    30_A      Y    30_A
#   possible swapping detected:  E    45_A      E    45_A
#   possible swapping detected:  F    67_A      F    67_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    22_A      A    22_A     2.282     0    0.583   0.582     2.827   73.095   69.905
LGA    D    23_A      D    23_A     0.893     0    0.665   0.854     5.228   75.833   57.202
LGA    G    24_A      G    24_A     1.103     0    0.182   0.182     1.103   90.595   90.595
LGA    D    25_A      D    25_A     1.056     0    0.035   0.175     1.514   81.429   81.488
LGA    G    26_A      G    26_A     1.147     0    0.059   0.059     1.320   81.429   81.429
LGA    Q    27_A      Q    27_A     1.804     0    0.020   1.505     6.427   72.857   51.852
LGA    G    28_A      G    28_A     1.924     0    0.030   0.030     1.955   72.857   72.857
LGA    L    29_A      L    29_A     0.798     0    0.043   0.114     1.266   88.214   90.536
LGA    Y    30_A      Y    30_A     1.069     0    0.065   0.499     3.059   83.690   72.698
LGA    A    31_A      A    31_A     1.673     0    0.020   0.021     2.171   72.976   72.952
LGA    A    32_A      A    32_A     1.924     0    0.043   0.043     2.636   66.905   68.095
LGA    N    33_A      N    33_A     2.161     0    0.095   0.102     3.140   63.095   63.988
LGA    C    34_A      C    34_A     1.548     0    0.055   0.211     1.647   72.857   77.222
LGA    A    35_A      A    35_A     1.621     0    0.008   0.023     1.684   72.857   72.857
LGA    A    36_A      A    36_A     1.532     0    0.041   0.050     1.637   75.000   74.571
LGA    C    37_A      C    37_A     1.442     0    0.008   0.052     1.633   81.429   78.571
LGA    H    38_A      H    38_A     1.341     0    0.042   0.145     1.679   81.429   79.714
LGA    G    39_A      G    39_A     1.313     0    0.027   0.027     1.352   81.429   81.429
LGA    A    40_A      A    40_A     1.118     0    0.086   0.128     1.808   79.286   79.714
LGA    L    41_A      L    41_A     1.268     0    0.296   1.367     6.411   83.690   61.905
LGA    A    42_A      A    42_A     5.412     0    0.656   0.600     7.345   36.190   30.952
LGA    T    43_A      T    43_A     4.574     0    0.557   0.567     8.179   37.738   25.714
LGA    S    44_A      S    44_A     4.978     0    0.621   0.780     8.296   37.262   27.302
LGA    E    45_A      E    45_A     3.247     0    0.183   0.771     5.025   55.714   43.704
LGA    K    46_A      K    46_A     0.524     0    0.259   0.867     5.920   88.214   68.466
LGA    K    47_A      K    47_A     0.687     0    0.158   0.167     1.234   88.214   86.455
LGA    G    48_A      G    48_A     0.601     0    0.035   0.035     0.824   90.476   90.476
LGA    T    49_A      T    49_A     1.074     0    0.067   0.070     1.283   83.690   82.721
LGA    T    50_A      T    50_A     1.127     0    0.053   0.133     1.727   81.429   80.204
LGA    L    51_A      L    51_A     0.868     0    0.038   1.066     2.427   88.214   82.917
LGA    A    52_A      A    52_A     0.552     0    0.031   0.029     0.943   92.857   92.381
LGA    R    53_A      R    53_A     1.284     0    0.051   1.235     3.300   81.429   67.532
LGA    L    54_A      L    54_A     1.401     0    0.023   1.423     2.807   79.286   76.369
LGA    Q    55_A      Q    55_A     1.136     0    0.019   1.277     3.990   81.548   67.566
LGA    S    56_A      S    56_A     0.859     0    0.020   0.622     2.288   85.952   83.175
LGA    A    57_A      A    57_A     2.166     0    0.021   0.028     2.884   64.881   63.333
LGA    V    58_A      V    58_A     2.854     0    0.032   0.116     3.770   55.595   54.286
LGA    S    59_A      S    59_A     2.505     0    0.125   0.499     3.143   57.262   59.762
LGA    A    60_A      A    60_A     2.496     0    0.404   0.566     4.700   61.071   55.143
LGA    N    61_A      N    61_A     3.583     0    0.220   1.016     6.074   52.143   38.690
LGA    A    62_A      A    62_A     2.364     0    0.185   0.271     5.190   49.524   51.048
LGA    G    63_A      G    63_A     3.124     0    0.256   0.256     3.529   55.714   55.714
LGA    G    64_A      G    64_A     0.920     0    0.203   0.203     1.213   88.214   88.214
LGA    M    65_A      M    65_A     1.366     0    0.162   0.774     1.887   77.143   76.071
LGA    G    66_A      G    66_A     1.973     0    0.052   0.052     1.973   72.857   72.857
LGA    F    67_A      F    67_A     2.033     0    0.019   1.081     9.302   70.833   40.736
LGA    L    68_A      L    68_A     1.803     0    0.108   0.262     2.659   70.833   68.869
LGA    S    69_A      S    69_A     1.330     0    0.235   0.229     1.814   77.143   78.571
LGA    S    70_A      S    70_A     2.624     0    0.097   0.086     3.695   60.952   55.079
LGA    L    71_A      L    71_A     0.645     0    0.051   0.107     1.289   90.476   87.083
LGA    T    72_A      T    72_A     0.729     0    0.012   0.083     0.837   90.476   90.476
LGA    S    73_A      S    73_A     0.799     0    0.018   0.614     3.102   90.476   83.730
LGA    A    74_A      A    74_A     0.757     0    0.044   0.050     0.816   90.476   90.476
LGA    Q    75_A      Q    75_A     0.581     0    0.029   1.151     3.861   90.476   81.270
LGA    L    76_A      L    76_A     1.007     0    0.041   1.275     3.264   88.214   77.738
LGA    Q    77_A      Q    77_A     0.923     0    0.069   1.368     5.135   90.476   71.640
LGA    A    78_A      A    78_A     0.667     0    0.087   0.093     0.800   90.476   90.476
LGA    I    79_A      I    79_A     0.625     0    0.018   0.090     0.678   90.476   92.857
LGA    V    80_A      V    80_A     0.907     0    0.043   0.118     1.267   90.476   86.599
LGA    D    81_A      D    81_A     1.092     0    0.073   0.079     1.753   85.952   80.476
LGA    V    82_A      V    82_A     0.771     0    0.058   1.055     2.525   88.214   81.905
LGA    L    83_A      L    83_A     0.790     0    0.102   0.961     2.611   88.214   82.976
LGA    A    84_A      A    84_A     0.856     0    0.115   0.124     1.513   83.810   85.143
LGA    V    85_A      V    85_A     1.002     0    0.325   0.387     1.320   85.952   87.891

# 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):     1.882          1.837                  2.446           76.687   72.104

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   97   64    4.0     63    1.77    83.984    91.749     3.362

LGA_LOCAL      RMSD:   1.774  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.885  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   1.882  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.041875 * X  +  -0.955408 * Y  +   0.292304 * Z  +  98.677116
  Y_new =   0.377137 * X  +  -0.286032 * Y  +  -0.880882 * Z  +  29.500143
  Z_new =   0.925210 * X  +   0.073352 * Y  +   0.372297 * Z  + -56.204655 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.681376 -1.181589  0.194534   [DEG:   96.3357  -67.7001   11.1460 ]
ZXZ:  0.320397  1.189313  1.491680   [DEG:   18.3574   68.1426   85.4670 ]
 
# END of job
