
#######################################################
#                                                     #
#                        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   66 (  511),  selected   66 , name one
# Molecule2: number of CA atoms   67 (  519),  selected   66 , 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:    66       2_A - 67_A        3.31     3.31
  LCS_AVERAGE:     98.51

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    54      14_A - 67_A        1.96     3.59
  LCS_AVERAGE:     70.28

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    32      36_A - 67_A        0.92     3.67
  LCS_AVERAGE:     30.51

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   66
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     S     2_A     S     2_A      5   10   66      4    5   12   15   17   18   24   28   30   30   34   47   55   60   63   65   66   66   66   66 
LCS_GDT     P     3_A     P     3_A      5   10   66      4    5    5    9   10   12   24   28   30   30   34   43   57   60   64   65   66   66   66   66 
LCS_GDT     E     4_A     E     4_A      5   10   66      4    5    5    9   10   12   15   19   23   31   48   62   63   63   64   65   66   66   66   66 
LCS_GDT     E     5_A     E     5_A      6   10   66      4   12   30   33   37   50   57   58   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     Q     6_A     Q     6_A      6   10   66      4    5    6   27   36   50   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     K     7_A     K     7_A      6   10   66      4    6   13   21   47   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     Q     8_A     Q     8_A      6   10   66      4    8   13   21   47   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     M     9_A     M     9_A      6   10   66      4    5    6    9   10   38   46   50   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     L    10_A     L    10_A      6   10   66      3    4    6    9   10   38   46   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     G    11_A     G    11_A      4   25   66      3   14   20   39   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     E    12_A     E    12_A      3   25   66      3    3    4    9   15   19   30   40   54   56   59   61   63   63   64   64   66   66   66   66 
LCS_GDT     A    13_A     A    13_A     10   52   66      6   10   17   21   24   36   53   57   60   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     I    14_A     I    14_A     10   54   66      6   10   17   22   37   48   56   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     Y    15_A     Y    15_A     10   54   66      7   14   26   40   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     P    16_A     P    16_A     10   54   66      6   13   18   37   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     K    17_A     K    17_A     10   54   66      8   14   18   39   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     V    18_A     V    18_A     10   54   66      6   16   29   40   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     A    19_A     A    19_A     10   54   66      6   11   29   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     A    20_A     A    20_A     10   54   66      7   14   29   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     S    21_A     S    21_A     10   54   66      5   11   21   39   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     Q    22_A     Q    22_A     10   54   66      5   10   18   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     P    23_A     P    23_A      4   54   66      4    4   24   34   44   53   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     E    24_A     E    24_A      7   54   66      4    4   21   27   38   46   53   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     L    25_A     L    25_A     12   54   66      8   15   29   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     A    26_A     A    26_A     12   54   66      8   16   29   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     G    27_A     G    27_A     12   54   66      7   16   29   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     K    28_A     K    28_A     12   54   66      8   14   29   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     L    29_A     L    29_A     12   54   66      8   14   29   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     T    30_A     T    30_A     12   54   66      8   14   26   40   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     G    31_A     G    31_A     12   54   66      8   14   25   40   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     M    32_A     M    32_A     12   54   66      4   14   18   39   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     I    33_A     I    33_A     12   54   66      8   14   18   39   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     L    34_A     L    34_A     23   54   66      5   14   25   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     E    35_A     E    35_A     25   54   66      4   16   29   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     L    36_A     L    36_A     32   54   66      5   25   31   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     P    37_A     P    37_A     32   54   66      5   19   31   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     V    38_A     V    38_A     32   54   66      6   25   31   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     T    39_A     T    39_A     32   54   66     10   25   31   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     E    40_A     E    40_A     32   54   66     10   25   31   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     L    41_A     L    41_A     32   54   66     10   25   31   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     L    42_A     L    42_A     32   54   66     10   25   31   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     H    43_A     H    43_A     32   54   66      8   25   31   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     L    44_A     L    44_A     32   54   66     10   25   31   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     L    45_A     L    45_A     32   54   66     10   25   31   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     E    46_A     E    46_A     32   54   66     10   25   31   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     E    47_A     E    47_A     32   54   66      9   25   31   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     S    48_A     S    48_A     32   54   66     10   25   31   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     E    49_A     E    49_A     32   54   66     10   25   31   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     A    50_A     A    50_A     32   54   66      6   16   31   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     L    51_A     L    51_A     32   54   66      6   16   31   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     D    52_A     D    52_A     32   54   66      6   25   31   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     A    53_A     A    53_A     32   54   66     10   25   31   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     K    54_A     K    54_A     32   54   66      6   17   31   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     V    55_A     V    55_A     32   54   66      6   15   29   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     N    56_A     N    56_A     32   54   66      8   25   31   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     E    57_A     E    57_A     32   54   66      5   25   31   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     A    58_A     A    58_A     32   54   66     10   25   31   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     L    59_A     L    59_A     32   54   66      5   25   31   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     E    60_A     E    60_A     32   54   66      5   25   31   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     V    61_A     V    61_A     32   54   66      9   25   31   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     L    62_A     L    62_A     32   54   66      5   25   31   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     K    63_A     K    63_A     32   54   66      9   25   31   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     E    64_A     E    64_A     32   54   66      9   25   31   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     Y    65_A     Y    65_A     32   54   66      9   25   31   35   48   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     Q    66_A     Q    66_A     32   54   66      4   25   31   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_GDT     Q    67_A     Q    67_A     32   54   66      4   21   31   41   51   54   57   59   61   62   62   62   63   63   64   65   66   66   66   66 
LCS_AVERAGE  LCS_A:  66.43  (  30.51   70.28   98.51 )

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     10     25     31     41     51     54     57     59     61     62     62     62     63     63     64     65     66     66     66     66 
GDT PERCENT_AT  14.93  37.31  46.27  61.19  76.12  80.60  85.07  88.06  91.04  92.54  92.54  92.54  94.03  94.03  95.52  97.01  98.51  98.51  98.51  98.51
GDT RMS_LOCAL    0.39   0.65   0.87   1.45   1.72   1.82   2.04   2.15   2.28   2.35   2.35   2.35   2.53   2.53   2.88   3.15   3.31   3.31   3.31   3.31
GDT RMS_ALL_AT   3.57   3.74   3.68   3.55   3.69   3.60   3.43   3.48   3.42   3.44   3.44   3.44   3.47   3.47   3.32   3.31   3.31   3.31   3.31   3.31

# Checking swapping
#   possible swapping detected:  E     4_A      E     4_A
#   possible swapping detected:  E     5_A      E     5_A
#   possible swapping detected:  E    24_A      E    24_A
#   possible swapping detected:  E    35_A      E    35_A
#   possible swapping detected:  E    40_A      E    40_A
#   possible swapping detected:  E    46_A      E    46_A
#   possible swapping detected:  E    49_A      E    49_A
#   possible swapping detected:  E    57_A      E    57_A
#   possible swapping detected:  E    64_A      E    64_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     2_A      S     2_A    13.013     0    0.052   0.084    13.029    0.000    0.000
LGA    P     3_A      P     3_A    11.904     0    0.027   0.059    15.625    0.714    0.408
LGA    E     4_A      E     4_A     9.137     0    0.163   1.440    15.386    9.048    4.021
LGA    E     5_A      E     5_A     4.828     0    0.229   1.295     6.851   31.310   23.968
LGA    Q     6_A      Q     6_A     4.151     0    0.071   0.554     6.633   41.905   31.852
LGA    K     7_A      K     7_A     2.516     0    0.141   0.651     6.568   53.690   43.439
LGA    Q     8_A      Q     8_A     2.527     0    0.181   0.321     4.160   53.810   53.492
LGA    M     9_A      M     9_A     5.097     0    0.225   0.877    10.915   29.286   18.631
LGA    L    10_A      L    10_A     4.405     0    0.188   1.331     6.052   45.714   36.131
LGA    G    11_A      G    11_A     2.631     0    0.409   0.409     5.737   47.143   47.143
LGA    E    12_A      E    12_A     7.688     0    0.203   1.319    12.532   12.976    5.820
LGA    A    13_A      A    13_A     4.909     0    0.213   0.206     5.778   31.786   31.714
LGA    I    14_A      I    14_A     3.814     0    0.155   0.146     5.238   46.905   41.488
LGA    Y    15_A      Y    15_A     2.248     0    0.017   0.171     2.962   64.881   73.135
LGA    P    16_A      P    16_A     3.073     0    0.067   0.333     4.170   55.357   49.320
LGA    K    17_A      K    17_A     2.747     0    0.007   0.730     4.010   62.976   57.672
LGA    V    18_A      V    18_A     1.537     0    0.156   1.211     2.564   75.000   70.680
LGA    A    19_A      A    19_A     1.592     0    0.076   0.085     2.291   77.143   74.667
LGA    A    20_A      A    20_A     1.511     0    0.080   0.094     1.975   75.000   74.571
LGA    S    21_A      S    21_A     2.376     0    0.258   0.597     3.655   59.524   64.286
LGA    Q    22_A      Q    22_A     2.531     0    0.504   1.403    11.380   69.048   35.503
LGA    P    23_A      P    23_A     3.273     0    0.027   0.303     5.538   49.048   55.510
LGA    E    24_A      E    24_A     4.459     0    0.246   1.093     8.681   45.119   25.820
LGA    L    25_A      L    25_A     0.761     0    0.234   1.432     5.692   81.548   63.214
LGA    A    26_A      A    26_A     1.320     0    0.014   0.015     1.494   81.429   81.429
LGA    G    27_A      G    27_A     1.034     0    0.047   0.047     1.055   81.429   81.429
LGA    K    28_A      K    28_A     1.302     0    0.089   0.770     4.561   79.286   63.862
LGA    L    29_A      L    29_A     1.486     0    0.081   1.129     3.024   75.119   73.274
LGA    T    30_A      T    30_A     2.031     0    0.034   0.966     4.075   66.786   59.864
LGA    G    31_A      G    31_A     2.124     0    0.126   0.126     2.124   66.786   66.786
LGA    M    32_A      M    32_A     2.473     0    0.011   0.704     5.283   64.762   53.869
LGA    I    33_A      I    33_A     2.561     0    0.221   1.424     5.266   67.143   60.179
LGA    L    34_A      L    34_A     1.787     0    0.085   1.372     5.390   77.381   62.619
LGA    E    35_A      E    35_A     1.246     0    0.259   1.045     1.942   81.548   77.672
LGA    L    36_A      L    36_A     0.483     0    0.023   0.103     1.759   97.619   88.452
LGA    P    37_A      P    37_A     1.583     0    0.023   0.298     2.566   79.286   73.129
LGA    V    38_A      V    38_A     0.651     0    0.055   0.145     1.131   88.214   90.544
LGA    T    39_A      T    39_A     1.038     0    0.050   1.081     2.666   83.690   78.027
LGA    E    40_A      E    40_A     1.580     0    0.062   0.603     2.761   79.286   68.730
LGA    L    41_A      L    41_A     1.367     0    0.033   0.077     1.583   81.429   80.357
LGA    L    42_A      L    42_A     1.540     0    0.019   0.101     1.930   75.000   75.000
LGA    H    43_A      H    43_A     1.548     0    0.073   1.096     6.573   77.143   52.095
LGA    L    44_A      L    44_A     1.202     0    0.077   0.225     1.518   79.286   81.488
LGA    L    45_A      L    45_A     1.606     0    0.049   0.153     2.144   75.000   72.917
LGA    E    46_A      E    46_A     1.424     0    0.113   0.797     2.546   79.286   74.921
LGA    E    47_A      E    47_A     0.878     0    0.089   0.930     4.621   85.952   75.820
LGA    S    48_A      S    48_A     1.510     0    0.022   0.048     1.818   75.000   74.286
LGA    E    49_A      E    49_A     1.762     0    0.116   0.788     3.314   75.000   64.444
LGA    A    50_A      A    50_A     2.086     0    0.055   0.060     2.323   66.786   66.381
LGA    L    51_A      L    51_A     2.108     0    0.059   1.126     3.994   68.810   64.107
LGA    D    52_A      D    52_A     0.938     0    0.062   0.073     1.274   88.214   88.214
LGA    A    53_A      A    53_A     1.231     0    0.042   0.050     1.359   81.429   81.429
LGA    K    54_A      K    54_A     1.646     0    0.101   0.752     1.881   75.000   75.714
LGA    V    55_A      V    55_A     1.542     0    0.109   1.224     4.724   79.286   70.612
LGA    N    56_A      N    56_A     1.461     0    0.054   0.883     2.416   79.286   78.274
LGA    E    57_A      E    57_A     1.040     0    0.079   0.704     3.762   83.690   68.519
LGA    A    58_A      A    58_A     1.410     0    0.046   0.047     1.783   77.143   76.286
LGA    L    59_A      L    59_A     2.022     0    0.039   0.379     3.858   66.786   61.190
LGA    E    60_A      E    60_A     2.043     0    0.006   1.051     3.665   66.786   64.233
LGA    V    61_A      V    61_A     2.258     0    0.073   0.115     2.481   64.762   64.762
LGA    L    62_A      L    62_A     2.471     0    0.040   1.249     4.768   64.762   60.774
LGA    K    63_A      K    63_A     2.230     0    0.040   0.882     3.740   64.762   64.603
LGA    E    64_A      E    64_A     2.450     0    0.070   0.899     4.305   60.952   53.598
LGA    Y    65_A      Y    65_A     3.034     0    0.053   0.209     4.935   55.357   43.889
LGA    Q    66_A      Q    66_A     2.455     0    0.025   0.475     3.518   66.905   58.413
LGA    Q    67_A      Q    67_A     1.700     0    0.130   1.466     5.113   70.833   62.487

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       66     264    264  100.00     511    511  100.00                67
SUMMARY(RMSD_GDC):     3.309          3.174                  3.937           63.781   58.465

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   66   67    4.0     59    2.15    70.896    74.805     2.627

LGA_LOCAL      RMSD:   2.146  Number of atoms:   59  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   3.479  Number of assigned atoms:   66 
Std_ASGN_ATOMS RMSD:   3.309  Standard rmsd on all 66 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.685338 * X  +  -0.717284 * Y  +   0.125758 * Z  +  13.191784
  Y_new =   0.296539 * X  +   0.117157 * Y  +  -0.947807 * Z  +   0.900332
  Z_new =   0.665114 * X  +   0.686861 * Y  +   0.292995 * Z  +   6.156932 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.408366 -0.727647  1.167596   [DEG:   23.3976  -41.6911   66.8983 ]
ZXZ:  0.131913  1.273439  0.769315   [DEG:    7.5580   72.9627   44.0785 ]
 
# END of job
