
#######################################################
#                                                     #
#                        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   62 (  488),  selected   62 , name one
# Molecule2: number of CA atoms   71 (  553),  selected   62 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    62       3_B - 64_B        1.24     1.24
  LCS_AVERAGE:     87.32

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    62       3_B - 64_B        1.24     1.24
  LCS_AVERAGE:     87.32

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    52       3_B - 54_B        0.98     1.30
  LCS_AVERAGE:     69.38

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   62
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     V     3_B     V     3_B     52   62   62     20   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     S     4_B     S     4_B     52   62   62     22   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     K     5_B     K     5_B     52   62   62     18   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     W     6_B     W     6_B     52   62   62     22   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     S     7_B     S     7_B     52   62   62     22   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     T     8_B     T     8_B     52   62   62     22   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     D     9_B     D     9_B     52   62   62     19   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     E    10_B     E    10_B     52   62   62     22   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     V    11_B     V    11_B     52   62   62     22   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     S    12_B     S    12_B     52   62   62     17   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     E    13_B     E    13_B     52   62   62     18   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     F    14_B     F    14_B     52   62   62     22   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     I    15_B     I    15_B     52   62   62     22   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     Q    16_B     Q    16_B     52   62   62     22   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     S    17_B     S    17_B     52   62   62     22   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     L    18_B     L    18_B     52   62   62     18   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     P    19_B     P    19_B     52   62   62     13   40   51   56   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     G    20_B     G    20_B     52   62   62      5   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     C    21_B     C    21_B     52   62   62     18   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     E    22_B     E    22_B     52   62   62      5   12   25   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     E    23_B     E    23_B     52   62   62      5    9   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     H    24_B     H    24_B     52   62   62     10   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     G    25_B     G    25_B     52   62   62      6   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     K    26_B     K    26_B     52   62   62     13   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     V    27_B     V    27_B     52   62   62     22   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     F    28_B     F    28_B     52   62   62     22   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     K    29_B     K    29_B     52   62   62     22   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     D    30_B     D    30_B     52   62   62     22   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     E    31_B     E    31_B     52   62   62     22   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     Q    32_B     Q    32_B     52   62   62     22   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     I    33_B     I    33_B     52   62   62     22   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     D    34_B     D    34_B     52   62   62     22   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     G    35_B     G    35_B     52   62   62     22   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     E    36_B     E    36_B     52   62   62     22   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     A    37_B     A    37_B     52   62   62     22   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     F    38_B     F    38_B     52   62   62     22   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     L    39_B     L    39_B     52   62   62     22   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     L    40_B     L    40_B     52   62   62     22   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     M    41_B     M    41_B     52   62   62     18   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     T    42_B     T    42_B     52   62   62     17   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     Q    43_B     Q    43_B     52   62   62     11   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     T    44_B     T    44_B     52   62   62     11   38   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     D    45_B     D    45_B     52   62   62     18   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     I    46_B     I    46_B     52   62   62     18   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     V    47_B     V    47_B     52   62   62     16   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     K    48_B     K    48_B     52   62   62     18   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     I    49_B     I    49_B     52   62   62     14   32   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     M    50_B     M    50_B     52   62   62     17   35   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     S    51_B     S    51_B     52   62   62     14   40   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     I    52_B     I    52_B     52   62   62     14   36   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     K    53_B     K    53_B     52   62   62     14   34   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     E    54_B     E    54_B     52   62   62     14   19   45   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     G    55_B     G    55_B     36   62   62     14   16   32   53   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     P    56_B     P    56_B     36   62   62     14   20   40   53   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     A    57_B     A    57_B     36   62   62     14   35   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     E    58_B     E    58_B     36   62   62     14   26   45   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     K    59_B     K    59_B     36   62   62     14   31   45   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     I    60_B     I    60_B     36   62   62     12   36   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     F    61_B     F    61_B     36   62   62      7   38   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     N    62_B     N    62_B     36   62   62      8   38   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     S    63_B     S    63_B     33   62   62      6   12   51   57   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_GDT     I    64_B     I    64_B     29   62   62      5   17   42   56   61   62   62   62   62   62   62   62   62   62   62   62   62   62   62   62 
LCS_AVERAGE  LCS_A:  81.34  (  69.38   87.32   87.32 )

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     22     40     51     57     61     62     62     62     62     62     62     62     62     62     62     62     62     62     62     62 
GDT PERCENT_AT  30.99  56.34  71.83  80.28  85.92  87.32  87.32  87.32  87.32  87.32  87.32  87.32  87.32  87.32  87.32  87.32  87.32  87.32  87.32  87.32
GDT RMS_LOCAL    0.34   0.64   0.84   1.05   1.18   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24
GDT RMS_ALL_AT   1.61   1.37   1.32   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24   1.24

# Checking swapping
#   possible swapping detected:  D     9_B      D     9_B
#   possible swapping detected:  E    10_B      E    10_B
#   possible swapping detected:  E    54_B      E    54_B
#   possible swapping detected:  E    58_B      E    58_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    V     3_B      V     3_B     0.643     0    0.188   1.096     3.869   97.619   80.748
LGA    S     4_B      S     4_B     0.332     0    0.077   0.545     2.271  100.000   94.127
LGA    K     5_B      K     5_B     0.670     0    0.168   1.366     7.399   92.857   68.571
LGA    W     6_B      W     6_B     0.530     0    0.021   0.123     0.706   90.476   94.558
LGA    S     7_B      S     7_B     0.590     0    0.057   0.625     2.476   95.238   89.365
LGA    T     8_B      T     8_B     0.349     0    0.049   1.163     2.794   95.238   85.034
LGA    D     9_B      D     9_B     0.999     0    0.036   0.719     3.149   88.214   75.774
LGA    E    10_B      E    10_B     0.879     0    0.041   1.086     2.971   90.476   80.952
LGA    V    11_B      V    11_B     0.535     0    0.030   0.111     0.788   90.476   93.197
LGA    S    12_B      S    12_B     1.176     0    0.029   0.748     2.606   83.690   78.889
LGA    E    13_B      E    13_B     1.226     0    0.029   1.111     6.098   83.690   65.873
LGA    F    14_B      F    14_B     0.653     0    0.033   0.223     1.784   90.476   85.628
LGA    I    15_B      I    15_B     0.951     0    0.031   0.079     1.259   85.952   87.083
LGA    Q    16_B      Q    16_B     1.416     0    0.096   1.194     3.276   81.429   70.582
LGA    S    17_B      S    17_B     1.306     0    0.125   0.694     2.881   79.286   77.460
LGA    L    18_B      L    18_B     1.435     0    0.035   0.096     1.962   77.143   79.286
LGA    P    19_B      P    19_B     2.055     0    0.619   0.895     4.559   58.452   59.048
LGA    G    20_B      G    20_B     1.019     0    0.115   0.115     1.826   79.286   79.286
LGA    C    21_B      C    21_B     1.478     0    0.110   0.119     2.513   77.143   71.746
LGA    E    22_B      E    22_B     2.130     0    0.040   0.454     2.796   68.810   64.868
LGA    E    23_B      E    23_B     1.715     0    0.140   0.420     3.885   77.143   64.762
LGA    H    24_B      H    24_B     0.786     0    0.154   0.978     2.364   85.952   82.667
LGA    G    25_B      G    25_B     0.993     0    0.029   0.029     0.997   90.476   90.476
LGA    K    26_B      K    26_B     0.736     0    0.038   1.150     5.728   92.857   73.122
LGA    V    27_B      V    27_B     0.281     0    0.045   1.083     2.664  100.000   90.000
LGA    F    28_B      F    28_B     0.491     0    0.029   0.153     1.659  100.000   87.446
LGA    K    29_B      K    29_B     0.398     0    0.027   0.978     6.934  100.000   70.370
LGA    D    30_B      D    30_B     0.517     0    0.067   0.854     4.057   95.238   76.131
LGA    E    31_B      E    31_B     0.837     0    0.124   0.277     2.758   90.476   78.995
LGA    Q    32_B      Q    32_B     0.605     0    0.034   0.904     3.547   90.476   81.323
LGA    I    33_B      I    33_B     0.439     0    0.067   0.618     1.391  100.000   94.167
LGA    D    34_B      D    34_B     0.390     0    0.041   0.195     1.029   97.619   94.107
LGA    G    35_B      G    35_B     0.186     0    0.027   0.027     0.297  100.000  100.000
LGA    E    36_B      E    36_B     0.656     0    0.041   1.089     4.014   92.857   78.783
LGA    A    37_B      A    37_B     0.830     0    0.038   0.038     0.978   90.476   90.476
LGA    F    38_B      F    38_B     0.655     0    0.034   0.317     1.130   90.476   89.654
LGA    L    39_B      L    39_B     0.643     0    0.141   0.974     4.160   88.214   78.452
LGA    L    40_B      L    40_B     0.748     0    0.167   0.157     1.387   88.214   89.345
LGA    M    41_B      M    41_B     0.771     0    0.045   0.886     2.372   90.476   85.060
LGA    T    42_B      T    42_B     0.448     0    0.040   1.096     2.489   97.619   88.571
LGA    Q    43_B      Q    43_B     0.671     0    0.044   0.878     3.639   90.476   74.921
LGA    T    44_B      T    44_B     0.900     0    0.041   0.146     1.635   90.476   85.374
LGA    D    45_B      D    45_B     0.755     0    0.031   0.246     1.765   90.476   87.143
LGA    I    46_B      I    46_B     0.569     0    0.032   1.163     2.422   95.238   83.214
LGA    V    47_B      V    47_B     0.495     0    0.019   0.999     2.886   95.238   84.762
LGA    K    48_B      K    48_B     1.369     0    0.095   1.236    10.225   79.405   49.524
LGA    I    49_B      I    49_B     2.120     0    0.015   1.241     5.597   66.786   58.452
LGA    M    50_B      M    50_B     1.875     0    0.108   0.375     4.040   72.857   66.369
LGA    S    51_B      S    51_B     1.150     0    0.062   0.066     1.734   79.286   77.143
LGA    I    52_B      I    52_B     1.093     0    0.067   0.996     4.202   88.214   71.488
LGA    K    53_B      K    53_B     1.475     0    0.054   1.395     7.503   81.429   56.614
LGA    E    54_B      E    54_B     1.951     0    0.031   0.950     3.876   68.810   62.593
LGA    G    55_B      G    55_B     3.174     0    0.051   0.051     3.174   55.357   55.357
LGA    P    56_B      P    56_B     2.631     0    0.055   0.301     3.185   62.976   58.435
LGA    A    57_B      A    57_B     1.321     0    0.046   0.045     1.850   79.286   79.714
LGA    E    58_B      E    58_B     2.074     0    0.036   0.660     3.648   70.833   60.952
LGA    K    59_B      K    59_B     2.054     0    0.031   0.131     4.433   68.810   58.624
LGA    I    60_B      I    60_B     1.092     0    0.026   1.140     2.615   85.952   76.488
LGA    F    61_B      F    61_B     0.857     0    0.047   0.179     2.737   90.476   75.714
LGA    N    62_B      N    62_B     0.841     0    0.059   1.440     4.044   90.476   74.405
LGA    S    63_B      S    63_B     1.591     0    0.038   0.654     2.290   72.976   75.873
LGA    I    64_B      I    64_B     2.307     0    0.136   1.041     4.350   62.976   56.786

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       62     248    248  100.00     488    488  100.00                71
SUMMARY(RMSD_GDC):     1.237          1.246                  2.048           74.695   67.548

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   62   71    4.0     62    1.24    77.817    83.136     4.637

LGA_LOCAL      RMSD:   1.237  Number of atoms:   62  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.237  Number of assigned atoms:   62 
Std_ASGN_ATOMS RMSD:   1.237  Standard rmsd on all 62 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.795283 * X  +  -0.416403 * Y  +  -0.440605 * Z  +  26.920349
  Y_new =  -0.605938 * X  +  -0.568860 * Y  +  -0.556091 * Z  +  85.100464
  Z_new =  -0.019084 * X  +   0.709230 * Y  +  -0.704719 * Z  +  15.450717 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.651083  0.019086  2.353005   [DEG:  -37.3043    1.0935  134.8172 ]
ZXZ: -0.670044  2.352824 -0.026902   [DEG:  -38.3907  134.8069   -1.5414 ]
 
# END of job
