
#######################################################
#                                                     #
#                        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:    54       1_A - 54_A        4.89     7.55
  LCS_AVERAGE:     79.82

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39       1_A - 39_A        1.85     7.90
  LCS_AVERAGE:     46.89

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    28       4_A - 31_A        0.94     7.68
  LONGEST_CONTINUOUS_SEGMENT:    28       5_A - 32_A        0.93     7.58
  LCS_AVERAGE:     27.66

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      9   39   54      3    7    8   27   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     S     2_A     S     2_A     13   39   54      3   12   27   30   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     S     3_A     S     3_A     13   39   54      3   12   27   33   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     F     4_A     F     4_A     28   39   54      4   12   27   33   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     C     5_A     C     5_A     28   39   54      6   24   27   33   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     D     6_A     D     6_A     28   39   54      5   24   27   33   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     S     7_A     S     7_A     28   39   54     11   24   27   33   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     K     8_A     K     8_A     28   39   54      7   24   27   33   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     C     9_A     C     9_A     28   39   54     14   24   27   33   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     G    10_A     G    10_A     28   39   54     14   24   27   33   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     V    11_A     V    11_A     28   39   54     14   24   27   33   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     R    12_A     R    12_A     28   39   54     14   24   27   33   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     C    13_A     C    13_A     28   39   54     14   24   27   33   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     S    14_A     S    14_A     28   39   54      3   24   27   33   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     K    15_A     K    15_A     28   39   54      4   24   27   33   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     A    16_A     A    16_A     28   39   54      3   24   27   33   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     G    17_A     G    17_A     28   39   54      3   14   27   33   39   40   41   42   42   43   45   46   47   49   50   51   53   54   59   59 
LCS_GDT     Y    18_A     Y    18_A     28   39   54     14   24   27   33   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     Q    19_A     Q    19_A     28   39   54      3   21   27   33   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     E    20_A     E    20_A     28   39   54     11   24   27   33   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     R    21_A     R    21_A     28   39   54     14   24   27   33   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     C    22_A     C    22_A     28   39   54     14   24   27   33   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     L    23_A     L    23_A     28   39   54     14   24   27   33   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     K    24_A     K    24_A     28   39   54     14   24   27   33   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     Y    25_A     Y    25_A     28   39   54     14   24   27   33   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     C    26_A     C    26_A     28   39   54     14   24   27   33   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     G    27_A     G    27_A     28   39   54     14   24   27   33   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     I    28_A     I    28_A     28   39   54     14   24   27   33   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     C    29_A     C    29_A     28   39   54     12   24   27   33   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     C    30_A     C    30_A     28   39   54     14   24   27   33   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     E    31_A     E    31_A     28   39   54      7   21   27   33   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     K    32_A     K    32_A     28   39   54      4    9   25   32   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     C    33_A     C    33_A     13   39   54      4    7   21   33   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     H    34_A     H    34_A      7   39   54      5    7   27   33   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     C    35_A     C    35_A      7   39   54      5    6   13   32   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     V    36_A     V    36_A      6   39   54      5   23   27   33   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     P    37_A     P    37_A      6   39   54      5    5   15   28   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     S    38_A     S    38_A      5   39   54      5    7   19   23   34   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     G    39_A     G    39_A      4   39   54      3    4    9   14   22   27   39   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     T    40_A     T    40_A      3    5   54      3    3    4    5    9   13   18   20   23   30   36   40   46   49   50   51   53   55   59   60 
LCS_GDT     Y    41_A     Y    41_A      3    7   54      3    3    4    7   11   16   18   20   23   26   29   33   37   43   47   50   53   55   59   60 
LCS_GDT     G    42_A     G    42_A      3    7   54      3    3    4    6    9   12   18   20   23   25   27   31   34   39   44   49   53   54   59   60 
LCS_GDT     N    43_A     N    43_A      5   12   54      4    5    7   10   15   17   19   21   23   26   29   37   46   49   50   51   53   55   59   60 
LCS_GDT     K    44_A     K    44_A      5   12   54      4    5    7   10   15   17   20   30   40   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     D    45_A     D    45_A      5   12   54      4    5    7   10   15   17   19   21   23   27   32   46   47   49   50   51   53   54   59   60 
LCS_GDT     E    46_A     E    46_A      5   14   54      4    5    7   10   15   17   19   21   23   26   29   33   37   46   50   51   53   54   59   60 
LCS_GDT     C    47_A     C    47_A      5   15   54      4    5    7   10   15   17   19   21   25   42   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     P    48_A     P    48_A      6   16   54      4    5    7   11   16   18   19   21   30   32   36   46   47   49   50   51   53   54   59   60 
LCS_GDT     C    49_A     C    49_A      6   16   54      4    7    8   11   16   20   29   33   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     Y    50_A     Y    50_A      6   16   54      4   10   21   33   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     R    51_A     R    51_A      7   16   54      4    6    9   15   23   33   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     D    52_A     D    52_A     12   16   54      4    6    9   33   39   40   41   42   42   43   45   46   47   49   50   51   53   55   59   60 
LCS_GDT     L    53_A     L    53_A     12   16   54      4    6   11   12   25   33   37   40   41   43   43   45   46   48   50   51   53   55   59   60 
LCS_GDT     K    54_A     K    54_A     12   16   54      5    9   11   12   17   27   31   35   38   39   42   43   44   47   48   50   53   55   59   60 
LCS_GDT     N    55_A     N    55_A     12   16   28      5    9   11   12   16   18   19   21   23   26   29   39   40   43   46   49   52   55   57   60 
LCS_GDT     S    56_A     S    56_A     12   16   28      5    9   11   12   16   18   19   21   23   25   29   33   35   36   42   44   50   54   56   58 
LCS_GDT     K    57_A     K    57_A     12   16   28      5    9   11   12   16   18   19   21   23   26   29   33   40   43   46   48   51   54   57   60 
LCS_GDT     G    58_A     G    58_A     12   16   28      5    9   11   12   20   24   31   31   32   38   40   43   44   46   47   50   53   55   59   60 
LCS_GDT     N    59_A     N    59_A     12   16   28      5    9   11   12   16   18   19   21   23   26   29   39   43   43   47   50   53   55   59   60 
LCS_GDT     P    60_A     P    60_A     12   16   28      5    9   11   12   16   18   18   21   23   26   33   43   44   46   48   50   53   55   59   60 
LCS_GDT     K    61_A     K    61_A     12   16   28      5    9   11   12   14   18   18   21   32   35   36   42   43   43   46   49   53   55   59   60 
LCS_GDT     C    62_A     C    62_A     12   16   28      5    9   11   12   14   18   18   19   23   25   29   29   35   43   46   49   52   55   59   60 
LCS_GDT     P    63_A     P    63_A     12   16   28      5    9   11   12   16   18   18   20   23   25   29   29   31   34   37   40   42   46   50   52 
LCS_AVERAGE  LCS_A:  51.46  (  27.66   46.89   79.82 )

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     27     33     39     40     41     42     42     43     45     46     47     49     50     51     53     55     59     60 
GDT PERCENT_AT  22.22  38.10  42.86  52.38  61.90  63.49  65.08  66.67  66.67  68.25  71.43  73.02  74.60  77.78  79.37  80.95  84.13  87.30  93.65  95.24
GDT RMS_LOCAL    0.35   0.64   0.77   1.28   1.53   1.63   1.76   1.95   1.95   2.10   2.66   2.86   3.18   3.80   4.00   4.14   4.80   5.34   5.79   6.14
GDT RMS_ALL_AT   7.65   7.60   7.61   7.88   7.98   8.06   8.05   7.94   7.94   7.85   8.16   8.33   8.43   8.20   8.32   8.10   6.83   6.67   6.74   6.54

# Checking swapping
#   possible swapping detected:  Y    18_A      Y    18_A
#   possible swapping detected:  E    31_A      E    31_A
#   possible swapping detected:  E    46_A      E    46_A
#   possible swapping detected:  Y    50_A      Y    50_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G     1_A      G     1_A     2.406     0    0.037   0.037     3.807   54.048   54.048
LGA    S     2_A      S     2_A     2.266     0    0.195   0.835     4.023   72.976   64.365
LGA    S     3_A      S     3_A     1.668     0    0.113   0.672     5.005   79.405   68.095
LGA    F     4_A      F     4_A     1.516     0    0.062   0.359     4.108   77.143   60.173
LGA    C     5_A      C     5_A     0.595     0    0.084   0.754     2.091   88.214   84.683
LGA    D     6_A      D     6_A     0.949     0    0.084   1.074     5.083   85.952   68.095
LGA    S     7_A      S     7_A     1.583     0    0.105   0.220     2.376   72.976   75.794
LGA    K     8_A      K     8_A     1.795     0    0.123   0.818     7.442   75.000   57.619
LGA    C     9_A      C     9_A     1.728     0    0.056   0.066     2.000   72.857   72.857
LGA    G    10_A      G    10_A     1.774     0    0.078   0.078     1.847   72.857   72.857
LGA    V    11_A      V    11_A     2.327     0    0.031   1.343     4.509   64.762   61.156
LGA    R    12_A      R    12_A     2.254     0    0.035   1.256     7.102   64.762   52.554
LGA    C    13_A      C    13_A     1.376     0    0.597   0.682     2.976   73.214   74.524
LGA    S    14_A      S    14_A     1.345     0    0.083   0.598     1.548   79.286   78.571
LGA    K    15_A      K    15_A     0.898     0    0.126   0.698     3.119   83.690   78.254
LGA    A    16_A      A    16_A     0.985     0    0.640   0.580     2.815   82.143   82.000
LGA    G    17_A      G    17_A     2.078     0    0.019   0.019     2.141   68.810   68.810
LGA    Y    18_A      Y    18_A     1.181     0    0.299   1.326     8.838   83.690   53.016
LGA    Q    19_A      Q    19_A     1.492     0    0.024   1.262     4.359   85.952   73.968
LGA    E    20_A      E    20_A     1.338     0    0.045   1.384     6.237   81.429   56.138
LGA    R    21_A      R    21_A     1.340     0    0.039   1.277    10.826   81.429   43.983
LGA    C    22_A      C    22_A     1.065     0    0.097   0.114     1.643   79.286   78.571
LGA    L    23_A      L    23_A     0.812     0    0.014   1.200     3.906   90.476   81.190
LGA    K    24_A      K    24_A     1.068     0    0.067   1.188     9.441   83.690   54.392
LGA    Y    25_A      Y    25_A     1.429     0    0.144   0.449     1.985   79.286   78.571
LGA    C    26_A      C    26_A     1.161     0    0.019   0.082     1.634   81.429   80.000
LGA    G    27_A      G    27_A     0.575     0    0.026   0.026     0.706   90.476   90.476
LGA    I    28_A      I    28_A     1.043     0    0.019   0.743     3.648   88.214   75.952
LGA    C    29_A      C    29_A     1.289     0    0.120   0.129     2.017   81.429   77.222
LGA    C    30_A      C    30_A     1.079     0    0.136   0.167     1.206   83.690   82.937
LGA    E    31_A      E    31_A     1.701     0    0.029   0.779     6.030   75.000   57.037
LGA    K    32_A      K    32_A     1.941     0    0.130   1.205    10.640   72.857   43.280
LGA    C    33_A      C    33_A     1.536     0    0.243   0.279     3.423   77.143   70.556
LGA    H    34_A      H    34_A     1.747     0    0.138   0.876     4.093   65.595   57.190
LGA    C    35_A      C    35_A     2.679     0    0.074   0.544     4.493   73.214   61.190
LGA    V    36_A      V    36_A     0.600     0    0.071   0.870     5.051   79.881   62.041
LGA    P    37_A      P    37_A     2.339     0    0.043   0.327     5.262   73.214   57.075
LGA    S    38_A      S    38_A     3.541     0    0.179   0.441     8.084   61.429   45.317
LGA    G    39_A      G    39_A     5.509     0    0.707   0.707     8.765   17.143   17.143
LGA    T    40_A      T    40_A    11.359     0    0.472   0.592    13.955    0.357    0.204
LGA    Y    41_A      Y    41_A    14.031     0    0.175   1.272    23.968    0.000    0.000
LGA    G    42_A      G    42_A    14.570     0    0.653   0.653    14.570    0.000    0.000
LGA    N    43_A      N    43_A    13.231     0    0.528   1.322    16.828    0.000    0.000
LGA    K    44_A      K    44_A     8.649     0    0.028   0.340    11.322    1.786    2.275
LGA    D    45_A      D    45_A    12.455     0    0.170   0.899    14.437    0.000    0.000
LGA    E    46_A      E    46_A    13.282     0    0.284   1.080    17.022    0.000    0.000
LGA    C    47_A      C    47_A     8.452     0    0.040   0.666    10.060    4.881    7.143
LGA    P    48_A      P    48_A     9.271     0    0.103   0.273    12.248    6.548    3.741
LGA    C    49_A      C    49_A     6.214     0    0.033   0.722     6.959   26.190   21.905
LGA    Y    50_A      Y    50_A     1.694     0    0.098   1.244     3.864   65.000   65.000
LGA    R    51_A      R    51_A     4.133     0    0.018   1.465    14.442   46.905   19.654
LGA    D    52_A      D    52_A     1.956     0    0.220   1.212     4.234   58.214   56.012
LGA    L    53_A      L    53_A     5.860     0    0.125   0.802     7.823   22.857   19.821
LGA    K    54_A      K    54_A    10.361     0    0.008   1.078    13.215    0.714    0.317
LGA    N    55_A      N    55_A    16.469     0    0.048   0.245    19.993    0.000    0.000
LGA    S    56_A      S    56_A    21.089     0    0.135   0.517    24.633    0.000    0.000
LGA    K    57_A      K    57_A    20.782     0    0.037   0.538    28.162    0.000    0.000
LGA    G    58_A      G    58_A    15.111     0    0.058   0.058    17.147    0.000    0.000
LGA    N    59_A      N    59_A    15.571     0    0.060   1.063    20.874    0.000    0.000
LGA    P    60_A      P    60_A    12.053     0    0.118   0.331    14.648    0.000    0.000
LGA    K    61_A      K    61_A    13.297     0    0.051   1.360    14.868    0.000    0.000
LGA    C    62_A      C    62_A    11.962     0    0.195   0.621    14.119    0.000    0.079
LGA    P    63_A      P    63_A    16.529     0    0.373   0.505    17.645    0.000    0.000

# 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):     6.519          6.431                  7.453           50.595   43.934

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     42    1.95    59.524    58.165     2.054

LGA_LOCAL      RMSD:   1.945  Number of atoms:   42  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   7.941  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   6.519  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.024931 * X  +  -0.993155 * Y  +  -0.114116 * Z  +  -4.954607
  Y_new =   0.264001 * X  +  -0.116640 * Y  +   0.957444 * Z  +   2.399014
  Z_new =  -0.964200 * X  +  -0.006256 * Y  +   0.265102 * Z  +  -6.332068 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.664954  1.302410 -0.023595   [DEG:   95.3949   74.6226   -1.3519 ]
ZXZ: -3.022964  1.302487 -1.577285   [DEG: -173.2031   74.6270  -90.3718 ]
 
# END of job
