
#######################################################
#                                                     #
#                        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 (  534),  selected   62 , name one
# Molecule2: number of CA atoms  104 (  843),  selected   62 , 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:    62      25_A - 86_A        3.17     3.17
  LCS_AVERAGE:     59.62

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33      25_A - 57_A        1.93     3.99
  LCS_AVERAGE:     30.83

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      58_A - 82_A        0.95     8.26
  LCS_AVERAGE:     15.96

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     N    25_A     N    25_A      9   33   62      3   12   20   29   35   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     I    26_A     I    26_A     13   33   62      8   14   20   29   35   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     K    27_A     K    27_A     13   33   62      9   14   20   29   35   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     C    28_A     C    28_A     13   33   62      9   14   20   29   35   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     H    29_A     H    29_A     13   33   62      4   14   20   29   35   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     F    30_A     F    30_A     13   33   62      9   14   20   29   35   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     D    31_A     D    31_A     13   33   62      9   14   20   29   35   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     N    32_A     N    32_A     13   33   62      9   14   20   29   35   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     C    33_A     C    33_A     13   33   62      9   14   20   29   35   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     N    34_A     N    34_A     13   33   62      3    8   20   29   35   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     R    35_A     R    35_A     13   33   62      8   14   20   29   35   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     K    36_A     K    36_A     13   33   62      9   14   20   29   35   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     I    37_A     I    37_A     13   33   62      3   14   20   29   35   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     H    38_A     H    38_A     13   33   62      3   14   20   29   35   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     W    39_A     W    39_A      9   33   62      4    7   19   29   35   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     K    40_A     K    40_A      7   33   62      8   14   20   29   34   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     I    41_A     I    41_A      6   33   62      4    6   19   29   35   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     R    42_A     R    42_A      6   33   62      4   11   18   23   33   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     Y    43_A     Y    43_A      6   33   62      3    6   12   23   24   37   44   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     G    44_A     G    44_A     11   33   62      3    9   13   18   31   39   43   49   54   57   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     K    45_A     K    45_A     12   33   62      8   11   15   18   26   37   43   49   54   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     L    46_A     L    46_A     12   33   62      8   11   15   27   35   39   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     R    47_A     R    47_A     12   33   62      8   11   15   29   35   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     L    48_A     L    48_A     12   33   62      8   11   15   27   35   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     V    49_A     V    49_A     12   33   62      8   11   17   29   35   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     D    50_A     D    50_A     12   33   62      8   11   20   29   35   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     H    51_A     H    51_A     12   33   62      8   14   20   29   35   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     A    52_A     A    52_A     12   33   62      8   12   20   29   35   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     L    53_A     L    53_A     12   33   62      4   14   20   29   35   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     S    54_A     S    54_A     12   33   62      9   14   20   29   35   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     H    55_A     H    55_A     12   33   62      9   14   20   29   35   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     Q    56_A     Q    56_A     12   33   62      3   12   20   29   35   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     E    57_A     E    57_A      7   33   62      3    7   16   27   35   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     E    58_A     E    58_A     25   31   62      6   20   23   26   28   34   43   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     K    59_A     K    59_A     25   31   62     10   20   23   27   35   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     S    60_A     S    60_A     25   31   62     10   20   23   27   35   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     I    61_A     I    61_A     25   31   62     10   20   23   29   35   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     D    62_A     D    62_A     25   31   62     10   20   23   29   35   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     C    63_A     C    63_A     25   31   62     10   20   23   27   34   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     Q    64_A     Q    64_A     25   31   62      6   20   23   26   29   37   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     K    65_A     K    65_A     25   31   62     10   20   23   26   28   33   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     C    66_A     C    66_A     25   31   62      7   20   23   26   29   37   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     E    67_A     E    67_A     25   31   62      3   12   22   28   34   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     Y    68_A     Y    68_A     25   31   62     10   20   23   27   34   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     S    69_A     S    69_A     25   31   62     10   20   23   29   35   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     C    70_A     C    70_A     25   31   62      7   20   23   29   35   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     Q    71_A     Q    71_A     25   31   62     10   20   23   29   35   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     T    72_A     T    72_A     25   31   62     10   20   23   26   28   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     T    73_A     T    73_A     25   31   62      9   20   23   26   28   37   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     R    74_A     R    74_A     25   31   62      9   20   23   26   28   32   37   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     Q    75_A     Q    75_A     25   31   62      9   20   23   26   28   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     M    76_A     M    76_A     25   31   62      9   20   23   26   34   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     R    77_A     R    77_A     25   31   62      9   20   23   26   28   33   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     Y    78_A     Y    78_A     25   31   62      9   18   23   26   28   33   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     H    79_A     H    79_A     25   31   62      9   20   23   27   34   40   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     Y    80_A     Y    80_A     25   31   62      9   20   23   26   28   37   45   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     K    81_A     K    81_A     25   31   62      3   18   23   26   28   33   41   49   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     K    82_A     K    82_A     25   31   62      4    7   23   26   28   33   44   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     I    83_A     I    83_A     17   31   62      4    5   16   26   28   33   44   50   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     H    84_A     H    84_A      5   31   62      4    5    5   14   28   30   41   49   55   58   60   62   62   62   62   62   62   62   62   62 
LCS_GDT     A    85_A     A    85_A      5   31   62      4    5    5   11   27   29   35   44   52   55   58   62   62   62   62   62   62   62   62   62 
LCS_GDT     N    86_A     N    86_A      3   31   62      3    3   11   17   26   33   42   45   54   57   60   62   62   62   62   62   62   62   62   62 
LCS_AVERAGE  LCS_A:  35.47  (  15.96   30.83   59.62 )

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     20     23     29     35     40     45     50     55     58     60     62     62     62     62     62     62     62     62     62 
GDT PERCENT_AT   9.62  19.23  22.12  27.88  33.65  38.46  43.27  48.08  52.88  55.77  57.69  59.62  59.62  59.62  59.62  59.62  59.62  59.62  59.62  59.62
GDT RMS_LOCAL    0.32   0.67   0.78   1.40   1.64   1.88   2.09   2.43   2.67   2.86   2.98   3.17   3.17   3.17   3.17   3.17   3.17   3.17   3.17   3.17
GDT RMS_ALL_AT   8.10   8.20   8.40   3.71   3.96   3.39   3.49   3.23   3.25   3.20   3.21   3.17   3.17   3.17   3.17   3.17   3.17   3.17   3.17   3.17

# Checking swapping
#   possible swapping detected:  Y    43_A      Y    43_A
#   possible swapping detected:  D    62_A      D    62_A
#   possible swapping detected:  Y    68_A      Y    68_A
#   possible swapping detected:  Y    80_A      Y    80_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    N    25_A      N    25_A     2.561     0    0.620   0.533     6.293   66.905   47.560
LGA    I    26_A      I    26_A     0.758     0    0.064   0.152     1.283   90.595   92.917
LGA    K    27_A      K    27_A     0.753     0    0.066   0.873     4.175   90.476   76.349
LGA    C    28_A      C    28_A     0.728     0    0.046   0.164     1.314   88.214   88.968
LGA    H    29_A      H    29_A     1.481     0    0.026   1.158     4.505   81.429   69.238
LGA    F    30_A      F    30_A     0.818     0    0.017   0.784     3.490   85.952   73.030
LGA    D    31_A      D    31_A     1.319     0    0.027   0.143     1.902   79.286   76.071
LGA    N    32_A      N    32_A     1.589     0    0.017   0.293     2.278   75.000   72.917
LGA    C    33_A      C    33_A     1.262     0    0.516   0.536     3.071   73.571   76.190
LGA    N    34_A      N    34_A     1.665     0    0.036   1.233     6.418   81.667   57.679
LGA    R    35_A      R    35_A     0.602     0    0.124   1.071     2.909   90.476   83.377
LGA    K    36_A      K    36_A     0.898     0    0.124   0.881     2.266   90.476   84.709
LGA    I    37_A      I    37_A     0.940     0    0.159   1.628     4.695   85.952   73.452
LGA    H    38_A      H    38_A     1.574     0    0.167   1.173     8.690   72.976   44.571
LGA    W    39_A      W    39_A     2.450     0    0.104   0.211     5.480   70.952   44.218
LGA    K    40_A      K    40_A     1.004     0    0.019   0.109     8.465   75.357   49.577
LGA    I    41_A      I    41_A     2.058     0    0.033   0.111     4.837   65.833   56.607
LGA    R    42_A      R    42_A     3.547     0    0.044   0.593     7.634   41.667   28.874
LGA    Y    43_A      Y    43_A     4.143     0    0.125   1.024    11.156   37.262   23.254
LGA    G    44_A      G    44_A     5.067     0    0.204   0.204     5.067   36.071   36.071
LGA    K    45_A      K    45_A     4.962     0    0.207   1.087     9.978   34.524   22.434
LGA    L    46_A      L    46_A     3.924     0    0.035   0.108     4.869   46.905   41.310
LGA    R    47_A      R    47_A     2.906     0    0.045   1.020     4.838   57.262   50.000
LGA    L    48_A      L    48_A     3.087     0    0.026   1.502     6.946   55.476   42.679
LGA    V    49_A      V    49_A     2.477     0    0.048   0.057     3.388   66.905   61.701
LGA    D    50_A      D    50_A     1.759     0    0.020   0.254     3.356   75.119   66.310
LGA    H    51_A      H    51_A     1.614     0    0.025   0.320     1.898   72.857   74.571
LGA    A    52_A      A    52_A     1.922     0    0.137   0.149     2.245   75.000   72.952
LGA    L    53_A      L    53_A     1.577     0    0.034   0.061     2.389   77.143   71.964
LGA    S    54_A      S    54_A     1.658     0    0.060   0.081     2.175   77.143   73.016
LGA    H    55_A      H    55_A     0.859     0    0.219   0.212     1.467   90.595   86.000
LGA    Q    56_A      Q    56_A     1.419     0    0.699   0.742     4.637   71.429   55.714
LGA    E    57_A      E    57_A     2.857     4    0.124   0.140     3.384   53.571   30.159
LGA    E    58_A      E    58_A     4.249     4    0.073   0.074     4.828   41.786   22.063
LGA    K    59_A      K    59_A     3.485     0    0.105   0.515     3.893   48.333   52.487
LGA    S    60_A      S    60_A     3.654     0    0.022   0.149     4.641   46.667   41.587
LGA    I    61_A      I    61_A     2.412     0    0.039   0.119     4.505   69.048   58.155
LGA    D    62_A      D    62_A     0.946     0    0.029   0.406     2.007   79.524   83.988
LGA    C    63_A      C    63_A     2.167     0    0.101   0.152     3.101   63.333   61.349
LGA    Q    64_A      Q    64_A     3.818     0    0.039   0.768     8.538   40.476   28.201
LGA    K    65_A      K    65_A     4.520     0    0.074   1.043    12.111   34.286   19.841
LGA    C    66_A      C    66_A     3.943     0    0.702   0.625     5.081   40.714   41.667
LGA    E    67_A      E    67_A     2.171     4    0.083   0.090     3.349   64.762   34.339
LGA    Y    68_A      Y    68_A     2.308     0    0.020   0.097     4.407   75.357   54.683
LGA    S    69_A      S    69_A     1.083     0    0.059   0.073     2.247   81.548   77.302
LGA    C    70_A      C    70_A     1.805     0    0.109   0.734     2.590   69.048   67.619
LGA    Q    71_A      Q    71_A     2.628     0    0.064   0.553     3.154   57.262   58.889
LGA    T    72_A      T    72_A     3.088     0    0.079   1.111     6.004   55.357   51.633
LGA    T    73_A      T    73_A     3.176     0    0.098   1.161     5.558   46.667   42.177
LGA    R    74_A      R    74_A     4.596     0    0.028   1.415     6.052   35.714   30.260
LGA    Q    75_A      Q    75_A     3.093     0    0.016   0.229     4.632   53.810   48.201
LGA    M    76_A      M    76_A     2.351     0    0.030   0.126     3.037   59.167   62.976
LGA    R    77_A      R    77_A     4.162     0    0.053   1.139     8.180   37.262   25.584
LGA    Y    78_A      Y    78_A     4.006     0    0.057   1.358     9.278   43.571   27.817
LGA    H    79_A      H    79_A     2.273     0    0.027   0.117     3.228   57.262   63.429
LGA    Y    80_A      Y    80_A     4.279     0    0.067   0.771     7.172   33.214   25.317
LGA    K    81_A      K    81_A     6.022     0    0.082   1.047     6.340   20.476   23.439
LGA    K    82_A      K    82_A     5.705     0    0.072   0.888     6.060   20.357   34.497
LGA    I    83_A      I    83_A     5.179     0    0.065   0.081     6.112   26.190   25.060
LGA    H    84_A      H    84_A     5.605     0    0.351   1.243    10.186   15.119   11.905
LGA    A    85_A      A    85_A     8.048     0    0.256   0.265     9.926    5.833    5.238
LGA    N    86_A      N    86_A     7.167     3    0.654   0.641    10.762    6.190    6.369

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       62     248    248  100.00     519    519  100.00               104
SUMMARY(RMSD_GDC):     3.175          3.228                  3.946           35.215   30.678

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   62  104    4.0     50    2.42    38.702    39.093     1.983

LGA_LOCAL      RMSD:   2.421  Number of atoms:   50  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   3.271  Number of assigned atoms:   62 
Std_ASGN_ATOMS RMSD:   3.175  Standard rmsd on all 62 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.320593 * X  +  -0.065573 * Y  +   0.944945 * Z  +  -4.528028
  Y_new =  -0.516099 * X  +  -0.824424 * Y  +  -0.232307 * Z  +  -6.034255
  Z_new =   0.794268 * X  +  -0.562161 * Y  +   0.230462 * Z  +  22.417349 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.126647 -0.917803 -1.181735   [DEG: -121.8479  -52.5862  -67.7085 ]
ZXZ:  1.329735  1.338244  2.186719   [DEG:   76.1882   76.6757  125.2898 ]
 
# END of job
