
#######################################################
#                                                     #
#                        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 (  530),  selected   62 , name one
# Molecule2: number of CA atoms  105 (  864),  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      26_A - 87_A        2.94     2.94
  LCS_AVERAGE:     59.05

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33      26_A - 58_A        1.83     3.44
  LCS_AVERAGE:     30.05

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23      61_A - 83_A        0.86     8.32
  LCS_AVERAGE:     16.67

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     I    26_A     I    26_A     18   33   62      7   21   25   31   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     I    27_A     I    27_A     18   33   62     11   21   25   31   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     K    28_A     K    28_A     18   33   62     11   21   25   31   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     C    29_A     C    29_A     18   33   62     11   21   25   31   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     H    30_A     H    30_A     18   33   62      9   21   25   31   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     F    31_A     F    31_A     18   33   62     11   21   25   31   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     D    32_A     D    32_A     18   33   62      5   21   25   31   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     K    33_A     K    33_A     18   33   62     10   21   25   31   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     C    34_A     C    34_A     18   33   62     11   21   25   31   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     N    35_A     N    35_A     18   33   62      7   21   25   31   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     K    36_A     K    36_A     18   33   62     11   21   25   31   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     S    37_A     S    37_A     18   33   62     11   21   25   31   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     Y    38_A     Y    38_A     18   33   62     10   21   25   31   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     N    39_A     N    39_A     18   33   62      5   21   25   31   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     W    40_A     W    40_A     18   33   62      5   21   25   31   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     R    41_A     R    41_A     18   33   62      5    9   25   31   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     K    42_A     K    42_A     18   33   62      5    8   23   31   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     K    43_A     K    43_A     18   33   62      5   21   25   31   37   43   50   53   55   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     Y    44_A     Y    44_A      7   33   62      5    6    9   25   31   40   46   52   55   58   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     G    45_A     G    45_A     14   33   62      4   12   18   27   33   36   45   49   55   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     K    46_A     K    46_A     14   33   62      4   12   15   22   30   35   42   48   55   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     L    47_A     L    47_A     14   33   62      7   12   18   27   33   39   45   52   55   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     R    48_A     R    48_A     14   33   62      7   12   22   29   35   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     L    49_A     L    49_A     14   33   62      7   12   19   29   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     V    50_A     V    50_A     14   33   62      7   12   23   29   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     D    51_A     D    51_A     14   33   62      7   17   23   31   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     H    52_A     H    52_A     14   33   62     11   21   25   31   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     A    53_A     A    53_A     14   33   62     11   21   25   31   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     F    54_A     F    54_A     14   33   62     11   21   25   31   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     T    55_A     T    55_A     14   33   62     11   21   25   31   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     H    56_A     H    56_A     14   33   62     11   21   25   31   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     V    57_A     V    57_A     14   33   62      4   18   23   31   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     P    58_A     P    58_A     14   33   62      3    5   14   27   34   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     H    59_A     H    59_A      4   30   62      3    7   16   23   25   28   33   42   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     L    60_A     L    60_A      4   30   62      3    3   10   11   21   35   45   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     K    61_A     K    61_A     23   30   62      4   17   22   23   25   33   38   47   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     M    62_A     M    62_A     23   30   62     12   21   22   28   34   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     K    63_A     K    63_A     23   30   62     14   21   23   31   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     C    64_A     C    64_A     23   30   62     14   21   25   31   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     N    65_A     N    65_A     23   30   62     14   21   25   31   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     F    66_A     F    66_A     23   30   62     14   21   22   28   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     C    67_A     C    67_A     23   30   62     14   21   22   28   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     D    68_A     D    68_A     23   30   62     14   21   22   29   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     Y    69_A     Y    69_A     23   30   62     14   21   22   29   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     M    70_A     M    70_A     23   30   62     14   21   23   29   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     C    71_A     C    71_A     23   30   62     12   21   23   28   35   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     K    72_A     K    72_A     23   30   62      4   21   22   28   34   42   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     G    73_A     G    73_A     23   30   62     12   21   22   23   34   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     I    74_A     I    74_A     23   30   62     10   21   22   23   25   42   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     R    75_A     R    75_A     23   30   62     14   21   22   23   25   37   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     N    76_A     N    76_A     23   30   62     14   21   22   31   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     I    77_A     I    77_A     23   30   62     14   21   22   31   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     R    78_A     R    78_A     23   30   62     14   21   22   23   26   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     L    79_A     L    79_A     23   30   62     14   21   22   24   35   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     H    80_A     H    80_A     23   30   62     14   21   25   31   37   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     H    81_A     H    81_A     23   30   62     14   21   22   23   34   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     K    82_A     K    82_A     23   30   62     12   21   22   23   25   36   48   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     K    83_A     K    83_A     23   30   62      4    5   20   23   25   34   45   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     S    84_A     S    84_A      6   30   62      4    5   10   17   25   35   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     H    85_A     H    85_A      6   30   62      4    5   10   17   34   43   50   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     P    86_A     P    86_A      6   30   62      4    5   11   23   25   32   45   53   56   59   61   62   62   62   62   62   62   62   62   62 
LCS_GDT     D    87_A     D    87_A      3   27   62      3    3    3   18   22   28   35   41   55   59   61   62   62   62   62   62   62   62   62   62 
LCS_AVERAGE  LCS_A:  35.25  (  16.67   30.05   59.05 )

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     21     25     31     37     43     50     53     56     59     61     62     62     62     62     62     62     62     62     62 
GDT PERCENT_AT  13.33  20.00  23.81  29.52  35.24  40.95  47.62  50.48  53.33  56.19  58.10  59.05  59.05  59.05  59.05  59.05  59.05  59.05  59.05  59.05
GDT RMS_LOCAL    0.34   0.54   0.85   1.22   1.52   1.78   2.14   2.31   2.62   2.81   2.89   2.94   2.94   2.94   2.94   2.94   2.94   2.94   2.94   2.94
GDT RMS_ALL_AT   8.31   8.12   3.19   3.08   3.10   3.05   2.99   2.98   2.99   2.97   2.95   2.94   2.94   2.94   2.94   2.94   2.94   2.94   2.94   2.94

# Checking swapping
#   possible swapping detected:  F    31_A      F    31_A
#   possible swapping detected:  D    32_A      D    32_A
#   possible swapping detected:  Y    38_A      Y    38_A
#   possible swapping detected:  Y    44_A      Y    44_A
#   possible swapping detected:  Y    69_A      Y    69_A
#   possible swapping detected:  D    87_A      D    87_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    I    26_A      I    26_A     2.264     0    0.611   1.453     6.950   66.786   55.238
LGA    I    27_A      I    27_A     1.406     0    0.054   0.149     1.658   79.286   80.357
LGA    K    28_A      K    28_A     1.166     0    0.020   0.460     1.771   81.429   82.487
LGA    C    29_A      C    29_A     1.175     0    0.021   0.105     1.310   81.429   81.429
LGA    H    30_A      H    30_A     1.114     0    0.041   0.241     2.251   81.429   74.667
LGA    F    31_A      F    31_A     1.539     0    0.098   0.220     3.734   79.286   64.156
LGA    D    32_A      D    32_A     1.611     0    0.021   0.708     2.773   72.857   68.869
LGA    K    33_A      K    33_A     1.367     0    0.152   0.778     2.071   79.286   77.672
LGA    C    34_A      C    34_A     1.372     0    0.592   0.555     3.848   69.762   73.651
LGA    N    35_A      N    35_A     1.162     0    0.015   0.150     1.982   81.429   77.143
LGA    K    36_A      K    36_A     1.149     0    0.014   0.796     3.368   85.952   71.852
LGA    S    37_A      S    37_A     1.054     0    0.030   0.644     2.768   83.690   80.397
LGA    Y    38_A      Y    38_A     1.168     0    0.101   0.176     2.242   81.429   77.183
LGA    N    39_A      N    39_A     1.708     0    0.276   1.178     5.647   61.905   52.083
LGA    W    40_A      W    40_A     1.567     0    0.087   1.249     8.946   79.405   37.449
LGA    R    41_A      R    41_A     1.257     0    0.049   1.259     8.188   81.548   46.753
LGA    K    42_A      K    42_A     1.352     0    0.013   0.767    10.330   77.619   49.206
LGA    K    43_A      K    43_A     2.398     0    0.081   1.003     4.723   55.238   57.249
LGA    Y    44_A      Y    44_A     4.457     0    0.173   1.049    11.095   35.000   21.944
LGA    G    45_A      G    45_A     5.467     0    0.150   0.150     5.467   34.524   34.524
LGA    K    46_A      K    46_A     5.437     0    0.179   1.147     6.595   27.619   26.138
LGA    L    47_A      L    47_A     4.502     0    0.066   0.163     5.517   39.048   33.333
LGA    R    48_A      R    48_A     3.030     0    0.032   1.219     5.654   53.810   43.160
LGA    L    49_A      L    49_A     3.027     0    0.012   1.462     6.687   55.476   41.369
LGA    V    50_A      V    50_A     2.776     0    0.009   0.036     4.146   61.190   54.558
LGA    D    51_A      D    51_A     2.102     0    0.035   0.119     4.176   73.095   60.833
LGA    H    52_A      H    52_A     0.792     0    0.018   0.225     1.313   88.214   84.143
LGA    A    53_A      A    53_A     1.031     0    0.012   0.015     1.258   88.214   86.857
LGA    F    54_A      F    54_A     0.660     0    0.029   0.600     2.369   95.238   87.576
LGA    T    55_A      T    55_A     0.477     0    0.136   1.150     3.038   95.238   83.742
LGA    H    56_A      H    56_A     0.810     0    0.135   0.147     1.315   92.857   86.000
LGA    V    57_A      V    57_A     1.126     0    0.491   1.003     4.265   75.476   71.769
LGA    P    58_A      P    58_A     3.177     0    0.600   0.653     4.106   48.810   52.653
LGA    H    59_A      H    59_A     6.158     0    0.562   1.088    13.704   19.524    8.286
LGA    L    60_A      L    60_A     4.246     0    0.226   1.394     6.250   32.976   30.476
LGA    K    61_A      K    61_A     5.707     0    0.673   1.076    16.132   28.929   13.439
LGA    M    62_A      M    62_A     3.446     0    0.143   0.896     6.650   50.357   43.155
LGA    K    63_A      K    63_A     1.648     0    0.053   0.656     2.494   75.119   71.164
LGA    C    64_A      C    64_A     0.393     0    0.050   0.066     1.411   95.238   92.143
LGA    N    65_A      N    65_A     1.614     0    0.145   1.200     4.489   75.000   62.917
LGA    F    66_A      F    66_A     2.912     0    0.367   0.305     5.361   52.262   41.818
LGA    C    67_A      C    67_A     2.891     0    0.109   0.917     3.251   59.048   57.222
LGA    D    68_A      D    68_A     2.951     0    0.035   0.806     5.877   55.357   42.381
LGA    Y    69_A      Y    69_A     2.348     0    0.046   1.095     5.923   69.048   56.389
LGA    M    70_A      M    70_A     2.526     0    0.026   0.162     3.577   57.262   53.690
LGA    C    71_A      C    71_A     3.309     0    0.104   0.811     3.769   48.452   55.714
LGA    K    72_A      K    72_A     3.804     0    0.653   0.698     6.490   37.857   30.000
LGA    G    73_A      G    73_A     3.185     0    0.030   0.030     3.185   57.262   57.262
LGA    I    74_A      I    74_A     3.276     0    0.082   0.127     4.802   50.000   44.405
LGA    R    75_A      R    75_A     3.298     0    0.020   0.945     8.359   53.571   34.069
LGA    N    76_A      N    76_A     1.855     0    0.019   0.107     2.429   72.976   69.881
LGA    I    77_A      I    77_A     1.591     0    0.093   0.127     2.508   72.857   74.167
LGA    R    78_A      R    78_A     2.917     0    0.035   0.097     6.096   57.143   39.351
LGA    L    79_A      L    79_A     2.119     0    0.034   0.039     2.487   68.810   67.798
LGA    H    80_A      H    80_A     1.484     0    0.008   0.146     2.296   70.952   75.524
LGA    H    81_A      H    81_A     2.705     0    0.144   0.510     3.496   55.476   57.286
LGA    K    82_A      K    82_A     4.216     0    0.082   0.984     4.677   37.262   42.328
LGA    K    83_A      K    83_A     4.905     0    0.035   0.208     7.799   32.857   22.804
LGA    S    84_A      S    84_A     3.737     0    0.063   0.613     5.173   46.667   41.667
LGA    H    85_A      H    85_A     2.718     0    0.126   0.279     5.320   47.262   41.524
LGA    P    86_A      P    86_A     5.582     0    0.237   0.254     7.356   22.500   25.102
LGA    D    87_A      D    87_A     6.561     0    0.671   1.128    10.951   10.238   15.536

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       62     248    248  100.00     530    530  100.00               105
SUMMARY(RMSD_GDC):     2.944          3.004                  3.959           36.722   32.799

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   62  105    4.0     53    2.31    39.762    39.796     2.202

LGA_LOCAL      RMSD:   2.306  Number of atoms:   53  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.979  Number of assigned atoms:   62 
Std_ASGN_ATOMS RMSD:   2.944  Standard rmsd on all 62 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.822350 * X  +  -0.557781 * Y  +   0.112341 * Z  + -35.815472
  Y_new =  -0.550792 * X  +   0.730865 * Y  +  -0.403069 * Z  + -42.017574
  Z_new =   0.142719 * X  +  -0.393340 * Y  +  -0.908248 * Z  +  42.018124 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.551439 -0.143208 -2.732902   [DEG: -146.1867   -8.2052 -156.5837 ]
ZXZ:  0.271815  2.709875  2.793527   [DEG:   15.5738  155.2644  160.0573 ]
 
# END of job
