
#######################################################
#                                                     #
#                        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   63 (  472),  selected   63 , name one
# Molecule2: number of CA atoms   63 (  472),  selected   63 , 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:    63       1_A - 63_A        1.85     1.85
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.85     1.85
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    32       5_A - 36_A        0.95     3.20
  LCS_AVERAGE:     36.94

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   63
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     G     1_A     G     1_A      7   63   63      3    8   25   44   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     2_A     S     2_A     10   63   63      3   14   29   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     3_A     S     3_A     10   63   63      3    9   24   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     F     4_A     F     4_A     11   63   63      3    9   31   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     32   63   63      3   21   34   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     32   63   63      5   24   34   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     7_A     S     7_A     32   63   63      8   24   34   40   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     8_A     K     8_A     32   63   63     14   24   34   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     32   63   63      7   24   34   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    10_A     G    10_A     32   63   63     14   24   34   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    11_A     V    11_A     32   63   63     14   24   34   46   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     32   63   63     14   24   34   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     32   63   63     12   24   34   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     32   63   63      5   24   34   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     32   63   63      4   17   34   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     32   63   63      4   24   34   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    17_A     G    17_A     32   63   63      3   20   30   40   54   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    18_A     Y    18_A     32   63   63     10   24   34   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Q    19_A     Q    19_A     32   63   63      3   20   34   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    20_A     E    20_A     32   63   63      9   24   34   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     32   63   63     14   24   34   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     32   63   63     14   24   34   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     32   63   63     14   24   34   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     32   63   63     14   24   34   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     32   63   63     14   24   34   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     32   63   63     14   24   34   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     32   63   63     14   24   34   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     32   63   63     14   24   34   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     32   63   63     14   24   34   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     32   63   63     14   24   34   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     32   63   63     10   24   34   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     32   63   63     11   24   34   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     32   63   63     14   24   34   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    34_A     H    34_A     32   63   63     10   21   34   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     32   63   63     10   20   34   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     32   63   63      9   21   34   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     25   63   63     10   20   32   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    38_A     S    38_A     25   63   63     10   20   31   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     25   63   63      8   21   34   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A     24   63   63      3   17   34   40   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     16   63   63      3   13   22   38   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     13   63   63      3    8   16   34   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     12   63   63      6   20   31   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    44_A     K    44_A     12   63   63      4   20   31   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A      8   63   63      4    8   22   42   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    46_A     E    46_A     12   63   63      4   20   30   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     14   63   63      5   20   31   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     14   63   63      4   12   21   36   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     14   63   63      4   12   28   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     14   63   63      4    9   25   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    51_A     R    51_A     14   63   63      4    9   31   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    52_A     D    52_A     14   63   63      6   20   31   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     14   63   63      6   20   31   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     14   63   63      5   20   31   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     14   63   63      4   15   29   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     14   63   63      6   16   28   41   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     14   63   63      6   20   29   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     14   63   63      6   20   31   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    59_A     N    59_A     14   63   63     10   20   31   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    60_A     P    60_A     14   63   63     10   20   34   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     12   63   63      6   10   34   43   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     12   63   63      6   15   31   38   48   58   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     12   63   63      3   15   30   36   42   55   63   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  78.98  (  36.94  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     14     24     34     47     56     61     63     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  22.22  38.10  53.97  74.60  88.89  96.83 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.34   0.58   0.96   1.45   1.63   1.76   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85
GDT RMS_ALL_AT   3.44   3.48   2.79   1.87   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85

# Checking swapping
#   possible swapping detected:  E    20_A      E    20_A
#   possible swapping detected:  Y    25_A      Y    25_A
#   possible swapping detected:  E    31_A      E    31_A
#   possible swapping detected:  D    45_A      D    45_A
#   possible swapping detected:  Y    50_A      Y    50_A
#   possible swapping detected:  D    52_A      D    52_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G     1_A      G     1_A     2.198     0    0.038   0.038     3.022   67.262   67.262
LGA    S     2_A      S     2_A     2.005     0    0.172   0.790     3.471   72.976   66.508
LGA    S     3_A      S     3_A     2.059     0    0.149   0.315     3.963   68.810   62.619
LGA    F     4_A      F     4_A     1.576     0    0.079   0.268     3.492   75.000   64.416
LGA    C     5_A      C     5_A     1.746     0    0.107   0.790     2.732   75.000   71.667
LGA    D     6_A      D     6_A     2.043     0    0.102   1.067     6.055   66.786   51.488
LGA    S     7_A      S     7_A     2.599     0    0.071   0.673     3.851   60.952   57.381
LGA    K     8_A      K     8_A     1.810     0    0.139   0.805     6.613   72.857   60.899
LGA    C     9_A      C     9_A     1.601     0    0.067   0.074     1.755   72.857   75.714
LGA    G    10_A      G    10_A     1.629     0    0.075   0.075     1.670   75.000   75.000
LGA    V    11_A      V    11_A     2.133     0    0.012   0.047     2.491   64.762   64.762
LGA    R    12_A      R    12_A     1.874     0    0.025   1.092     7.229   72.857   51.602
LGA    C    13_A      C    13_A     0.996     0    0.594   0.678     2.455   81.786   81.667
LGA    S    14_A      S    14_A     1.258     0    0.146   0.581     1.894   77.143   77.143
LGA    K    15_A      K    15_A     1.264     0    0.019   0.665     4.611   81.429   67.090
LGA    A    16_A      A    16_A     1.200     0    0.650   0.589     2.578   75.357   76.571
LGA    G    17_A      G    17_A     2.868     0    0.055   0.055     2.868   59.048   59.048
LGA    Y    18_A      Y    18_A     1.985     0    0.317   1.390     7.781   72.976   51.706
LGA    Q    19_A      Q    19_A     1.312     0    0.034   0.920     2.343   83.690   78.677
LGA    E    20_A      E    20_A     1.902     0    0.016   0.750     6.077   70.833   50.476
LGA    R    21_A      R    21_A     2.213     0    0.022   1.428    10.707   68.810   39.827
LGA    C    22_A      C    22_A     1.447     0    0.090   0.121     1.705   77.143   77.143
LGA    L    23_A      L    23_A     1.157     0    0.018   0.241     2.368   81.429   78.274
LGA    K    24_A      K    24_A     1.710     0    0.068   1.171     9.961   75.000   47.143
LGA    Y    25_A      Y    25_A     1.873     0    0.155   0.496     2.668   70.833   70.992
LGA    C    26_A      C    26_A     1.127     0    0.019   0.083     1.389   85.952   85.952
LGA    G    27_A      G    27_A     0.765     0    0.011   0.011     1.047   85.952   85.952
LGA    I    28_A      I    28_A     1.443     0    0.015   0.743     4.457   81.429   68.810
LGA    C    29_A      C    29_A     1.219     0    0.091   0.090     1.950   85.952   81.587
LGA    C    30_A      C    30_A     0.819     0    0.081   0.096     1.063   88.214   88.968
LGA    E    31_A      E    31_A     0.723     0    0.014   0.922     4.165   90.476   77.831
LGA    K    32_A      K    32_A     1.052     0    0.017   0.947     1.949   83.690   79.577
LGA    C    33_A      C    33_A     1.119     0    0.173   0.199     1.971   79.286   84.603
LGA    H    34_A      H    34_A     1.580     0    0.133   1.223     2.660   75.000   71.524
LGA    C    35_A      C    35_A     1.370     0    0.026   0.196     1.655   79.286   78.571
LGA    V    36_A      V    36_A     1.326     0    0.074   0.265     2.432   81.429   76.599
LGA    P    37_A      P    37_A     0.929     0    0.014   0.282     1.104   85.952   87.959
LGA    S    38_A      S    38_A     1.510     0    0.255   0.673     5.346   77.381   65.476
LGA    G    39_A      G    39_A     1.542     0    0.078   0.078     2.595   66.905   66.905
LGA    T    40_A      T    40_A     2.605     0    0.465   0.375     4.039   56.071   57.755
LGA    Y    41_A      Y    41_A     2.864     0    0.168   1.241    10.846   62.976   34.087
LGA    G    42_A      G    42_A     2.876     0    0.639   0.639     4.774   50.714   50.714
LGA    N    43_A      N    43_A     1.558     0    0.142   0.976     4.217   75.000   63.988
LGA    K    44_A      K    44_A     1.395     0    0.055   0.911     8.256   72.976   52.646
LGA    D    45_A      D    45_A     2.614     0    0.170   1.253     7.525   62.857   44.940
LGA    E    46_A      E    46_A     1.951     0    0.140   0.224     2.932   77.381   68.730
LGA    C    47_A      C    47_A     1.260     0    0.022   0.622     2.507   72.976   71.746
LGA    P    48_A      P    48_A     2.553     0    0.209   0.404     3.181   66.905   65.034
LGA    C    49_A      C    49_A     1.851     0    0.104   0.182     2.211   72.976   73.016
LGA    Y    50_A      Y    50_A     1.894     0    0.079   0.509     4.046   72.857   59.087
LGA    R    51_A      R    51_A     1.328     0    0.016   1.485     6.752   81.429   62.814
LGA    D    52_A      D    52_A     0.481     0    0.132   0.732     2.913   92.857   83.095
LGA    L    53_A      L    53_A     1.174     0    0.078   0.863     4.374   83.690   73.869
LGA    K    54_A      K    54_A     1.431     0    0.025   1.026     3.285   75.119   69.577
LGA    N    55_A      N    55_A     2.154     0    0.052   0.220     2.334   66.786   67.798
LGA    S    56_A      S    56_A     2.733     0    0.068   0.494     4.330   57.143   53.810
LGA    K    57_A      K    57_A     2.078     0    0.032   0.740     3.954   68.810   60.212
LGA    G    58_A      G    58_A     1.440     0    0.091   0.091     1.569   77.143   77.143
LGA    N    59_A      N    59_A     0.427     0    0.015   0.224     1.855   95.238   91.845
LGA    P    60_A      P    60_A     1.419     0    0.099   0.322     2.465   79.286   75.374
LGA    K    61_A      K    61_A     2.333     0    0.029   0.955     3.177   61.190   65.185
LGA    C    62_A      C    62_A     3.339     0    0.155   0.445     4.075   46.905   45.794
LGA    P    63_A      P    63_A     3.747     0    0.473   0.424     3.935   43.333   45.238

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       63     252    252  100.00     472    472  100.00                63
SUMMARY(RMSD_GDC):     1.846          1.864                  2.832           73.653   67.284

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    1.85    78.175    88.972     3.237

LGA_LOCAL      RMSD:   1.846  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.846  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.846  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.956748 * X  +  -0.169927 * Y  +  -0.236131 * Z  +  30.829672
  Y_new =  -0.135328 * X  +  -0.458551 * Y  +   0.878303 * Z  +  -7.172283
  Z_new =  -0.257526 * X  +   0.872270 * Y  +   0.415722 * Z  +  11.269381 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -3.001079  0.260461  1.126045   [DEG: -171.9492   14.9233   64.5176 ]
ZXZ: -2.878954  1.142059 -0.287080   [DEG: -164.9519   65.4352  -16.4485 ]
 
# END of job
