
#######################################################
#                                                     #
#                        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        3.19     3.19
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      44_A - 68_A        1.88     5.89
  LONGEST_CONTINUOUS_SEGMENT:    25      45_A - 69_A        1.98     5.57
  LCS_AVERAGE:     35.30

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19      45_A - 63_A        0.94     6.15
  LCS_AVERAGE:     25.39

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      3    3   64      3    3    4    5   11   19   28   36   49   58   61   62   64   64   64   64   64   64   64   64 
LCS_GDT     D    23_A     D    23_A      3    4   64      3    3    5   15   22   31   36   41   52   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    24_A     G    24_A      3   20   64      3    3   11   31   37   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     D    25_A     D    25_A     15   20   64      3    3   11   29   39   42   46   54   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    26_A     G    26_A     16   20   64     21   27   30   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     Q    27_A     Q    27_A     16   20   64     21   27   30   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    28_A     G    28_A     16   20   64     21   27   30   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    29_A     L    29_A     16   20   64     21   27   30   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     Y    30_A     Y    30_A     16   20   64     21   27   30   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    31_A     A    31_A     16   20   64     21   27   30   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    32_A     A    32_A     16   20   64     21   27   30   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     N    33_A     N    33_A     16   20   64     21   27   30   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     C    34_A     C    34_A     16   20   64     19   27   30   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    35_A     A    35_A     16   20   64     21   27   30   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    36_A     A    36_A     16   20   64      6   25   30   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     C    37_A     C    37_A     16   20   64      6   27   30   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     H    38_A     H    38_A     16   20   64      6   27   30   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    39_A     G    39_A     16   20   64      6   25   30   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    40_A     A    40_A     16   20   64      9   22   29   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    41_A     L    41_A     16   20   64      3   12   29   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    42_A     A    42_A      4   22   64      3    5    7   12   25   33   37   44   55   58   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     T    43_A     T    43_A      4   23   64      3    4   14   32   34   44   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     S    44_A     S    44_A     17   25   64      3   11   14   19   21   31   36   55   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     E    45_A     E    45_A     19   25   64      6   14   18   21   23   32   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     K    46_A     K    46_A     19   25   64      8   13   18   21   29   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     K    47_A     K    47_A     19   25   64      8   14   18   21   23   31   49   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    48_A     G    48_A     19   25   64      8   14   18   21   25   38   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     T    49_A     T    49_A     19   25   64      8   14   18   21   32   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     T    50_A     T    50_A     19   25   64      8   14   18   21   29   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    51_A     L    51_A     19   25   64      8   14   18   21   29   43   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    52_A     A    52_A     19   25   64      8   14   18   21   36   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     R    53_A     R    53_A     19   25   64      8   14   18   26   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    54_A     L    54_A     19   25   64      8   14   18   21   29   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     Q    55_A     Q    55_A     19   25   64      7   14   18   21   29   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     S    56_A     S    56_A     19   25   64      7   14   18   26   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    57_A     A    57_A     19   25   64      8   14   18   27   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     V    58_A     V    58_A     19   25   64      7   14   18   21   25   36   52   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     S    59_A     S    59_A     19   25   64      8   14   18   21   23   33   47   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    60_A     A    60_A     19   25   64      7   14   18   21   23   34   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     N    61_A     N    61_A     19   25   64      7   14   18   21   23   36   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    62_A     A    62_A     19   25   64      8   14   18   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    63_A     G    63_A     19   25   64      5   14   18   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    64_A     G    64_A     16   25   64      4    4    8   19   31   40   49   56   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     M    65_A     M    65_A     16   25   64      4    4   17   21   33   40   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    66_A     G    66_A      5   25   64      4    4    8    8    9   18   37   44   51   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     F    67_A     F    67_A     13   25   64      5   11   16   27   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    68_A     L    68_A     18   25   64      5   11   17   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     S    69_A     S    69_A     18   25   64      5   16   30   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     S    70_A     S    70_A     18   24   64      5   16   29   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    71_A     L    71_A     18   24   64     15   27   30   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     T    72_A     T    72_A     18   24   64     21   27   30   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     S    73_A     S    73_A     18   24   64     21   27   30   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    74_A     A    74_A     18   24   64     21   27   30   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     Q    75_A     Q    75_A     18   24   64     21   27   30   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    76_A     L    76_A     18   24   64     21   27   30   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     Q    77_A     Q    77_A     18   24   64     21   27   30   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    78_A     A    78_A     18   24   64     21   27   30   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     I    79_A     I    79_A     18   24   64     21   27   30   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     V    80_A     V    80_A     18   24   64     21   27   30   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     D    81_A     D    81_A     18   24   64     21   27   30   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     V    82_A     V    82_A     18   24   64     12   27   30   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    83_A     L    83_A     18   24   64     21   27   30   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    84_A     A    84_A     18   24   64     21   27   30   33   40   45   53   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     V    85_A     V    85_A     18   24   64     12   27   30   33   40   45   52   57   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_AVERAGE  LCS_A:  53.56  (  25.39   35.30  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     21     27     30     33     40     45     53     57     59     60     62     63     64     64     64     64     64     64     64     64 
GDT PERCENT_AT  32.81  42.19  46.88  51.56  62.50  70.31  82.81  89.06  92.19  93.75  96.88  98.44 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.30   0.45   0.63   0.87   1.61   2.00   2.46   2.61   2.68   2.75   2.91   3.04   3.19   3.19   3.19   3.19   3.19   3.19   3.19   3.19
GDT RMS_ALL_AT   4.02   3.98   3.93   3.89   3.52   3.36   3.25   3.23   3.25   3.24   3.22   3.20   3.19   3.19   3.19   3.19   3.19   3.19   3.19   3.19

# Checking swapping
#   possible swapping detected:  D    23_A      D    23_A
#   possible swapping detected:  D    25_A      D    25_A
#   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     8.841     0    0.369   0.363     9.402    4.048    3.810
LGA    D    23_A      D    23_A     7.656     0    0.098   1.345    12.337   16.190    8.452
LGA    G    24_A      G    24_A     3.066     0    0.442   0.442     4.964   49.405   49.405
LGA    D    25_A      D    25_A     3.991     0    0.276   1.102     8.306   43.690   26.429
LGA    G    26_A      G    26_A     1.814     0    0.144   0.144     2.049   70.833   70.833
LGA    Q    27_A      Q    27_A     1.471     0    0.038   0.318     2.617   79.286   74.921
LGA    G    28_A      G    28_A     1.360     0    0.072   0.072     1.360   81.429   81.429
LGA    L    29_A      L    29_A     1.378     0    0.009   0.109     1.671   81.429   78.214
LGA    Y    30_A      Y    30_A     1.328     0    0.077   0.133     1.552   79.286   80.714
LGA    A    31_A      A    31_A     1.268     0    0.004   0.010     1.486   81.429   81.429
LGA    A    32_A      A    32_A     1.447     0    0.038   0.040     1.610   77.143   78.000
LGA    N    33_A      N    33_A     1.609     0    0.024   0.074     1.975   72.857   72.857
LGA    C    34_A      C    34_A     1.524     0    0.031   0.088     1.605   75.000   74.286
LGA    A    35_A      A    35_A     1.640     0    0.025   0.023     2.142   72.976   72.952
LGA    A    36_A      A    36_A     2.441     0    0.026   0.024     2.784   62.857   61.714
LGA    C    37_A      C    37_A     2.046     0    0.024   0.075     2.265   66.786   67.460
LGA    H    38_A      H    38_A     1.938     0    0.088   0.137     2.197   68.810   71.238
LGA    G    39_A      G    39_A     2.447     0    0.251   0.251     2.447   70.952   70.952
LGA    A    40_A      A    40_A     1.040     0    0.038   0.047     2.100   81.905   78.476
LGA    L    41_A      L    41_A     1.921     0    0.600   1.482     3.534   68.929   68.333
LGA    A    42_A      A    42_A     5.917     0    0.496   0.506     6.737   24.048   21.905
LGA    T    43_A      T    43_A     3.506     0    0.608   1.301     4.992   40.238   41.837
LGA    S    44_A      S    44_A     5.233     0    0.265   0.365     6.285   28.810   25.635
LGA    E    45_A      E    45_A     4.182     0    0.134   0.773     6.204   40.238   32.116
LGA    K    46_A      K    46_A     3.215     0    0.068   0.088     3.899   45.000   61.640
LGA    K    47_A      K    47_A     4.986     0    0.063   0.108     7.801   31.429   22.487
LGA    G    48_A      G    48_A     4.311     0    0.114   0.114     4.662   42.262   42.262
LGA    T    49_A      T    49_A     3.090     0    0.199   0.986     4.479   51.905   48.299
LGA    T    50_A      T    50_A     3.375     0    0.030   0.060     3.383   50.000   51.020
LGA    L    51_A      L    51_A     3.730     0    0.006   1.388     7.423   46.667   32.560
LGA    A    52_A      A    52_A     2.786     0    0.013   0.016     3.088   59.167   58.762
LGA    R    53_A      R    53_A     2.193     0    0.020   0.596     3.802   64.762   58.745
LGA    L    54_A      L    54_A     3.177     0    0.024   1.394     7.325   51.786   37.917
LGA    Q    55_A      Q    55_A     3.330     0    0.020   0.135     4.104   50.000   47.831
LGA    S    56_A      S    56_A     2.347     0    0.053   0.058     2.621   60.952   64.921
LGA    A    57_A      A    57_A     2.363     0    0.010   0.019     3.009   59.167   60.286
LGA    V    58_A      V    58_A     4.125     0    0.043   0.118     5.485   38.929   34.966
LGA    S    59_A      S    59_A     4.314     0    0.017   0.743     6.468   35.714   32.857
LGA    A    60_A      A    60_A     3.615     0    0.028   0.033     3.687   43.333   44.667
LGA    N    61_A      N    61_A     3.842     0    0.091   0.932     6.566   50.238   36.071
LGA    A    62_A      A    62_A     1.705     0    0.018   0.024     2.479   68.810   71.333
LGA    G    63_A      G    63_A     1.879     0    0.691   0.691     2.109   70.952   70.952
LGA    G    64_A      G    64_A     4.782     0    0.192   0.192     6.333   29.524   29.524
LGA    M    65_A      M    65_A     3.878     0    0.037   0.268     4.972   37.381   53.214
LGA    G    66_A      G    66_A     6.415     0    0.621   0.621     6.415   25.238   25.238
LGA    F    67_A      F    67_A     2.378     0    0.570   1.348     6.599   59.405   49.307
LGA    L    68_A      L    68_A     1.214     0    0.061   0.114     2.152   85.952   79.464
LGA    S    69_A      S    69_A     1.505     0    0.038   0.625     2.472   72.976   71.587
LGA    S    70_A      S    70_A     2.596     0    0.041   0.088     3.073   59.167   59.762
LGA    L    71_A      L    71_A     1.995     0    0.054   0.094     2.300   68.810   70.833
LGA    T    72_A      T    72_A     2.346     0    0.027   0.041     2.374   64.762   64.762
LGA    S    73_A      S    73_A     2.615     0    0.024   0.631     4.087   60.952   56.349
LGA    A    74_A      A    74_A     2.011     0    0.036   0.041     2.213   68.810   69.619
LGA    Q    75_A      Q    75_A     1.706     0    0.016   0.070     1.954   72.857   72.857
LGA    L    76_A      L    76_A     2.045     0    0.018   0.115     2.826   66.786   65.833
LGA    Q    77_A      Q    77_A     2.137     0    0.056   0.201     2.704   66.786   64.815
LGA    A    78_A      A    78_A     1.685     0    0.025   0.035     1.823   72.857   72.857
LGA    I    79_A      I    79_A     1.853     0    0.010   0.065     1.983   72.857   72.857
LGA    V    80_A      V    80_A     2.122     0    0.017   0.070     2.410   64.762   64.762
LGA    D    81_A      D    81_A     2.065     0    0.062   0.076     2.241   64.762   66.786
LGA    V    82_A      V    82_A     2.146     0    0.087   0.862     3.499   64.762   66.327
LGA    L    83_A      L    83_A     2.189     0    0.097   0.168     2.408   66.786   65.774
LGA    A    84_A      A    84_A     2.226     0    0.084   0.094     2.362   64.762   64.762
LGA    V    85_A      V    85_A     2.628     0    0.228   0.197     2.725   59.048   58.231

# 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):     3.190          3.143                  3.450           58.276   56.820

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   97   64    4.0     57    2.61    70.703    65.226     2.102

LGA_LOCAL      RMSD:   2.612  Number of atoms:   57  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   3.231  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   3.190  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.592866 * X  +   0.434534 * Y  +  -0.678004 * Z  +  19.394129
  Y_new =   0.777008 * X  +  -0.087460 * Y  +   0.623385 * Z  + -20.693050
  Z_new =   0.211584 * X  +  -0.896399 * Y  +  -0.389488 * Z  + -17.244556 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.919019 -0.213196 -1.980689   [DEG:   52.6559  -12.2152 -113.4851 ]
ZXZ: -2.314250  1.970872  2.909797   [DEG: -132.5967  112.9227  166.7191 ]
 
# END of job
