
#######################################################
#                                                     #
#                        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   99 (  793),  selected   61 , name one
# Molecule2: number of CA atoms   61 (  480),  selected   61 , 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:    61      32_A - 98_A        3.79     3.79
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      33_A - 57_A        1.92     7.25
  LCS_AVERAGE:     35.80

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20      57_A - 76_A        0.86     6.49
  LCS_AVERAGE:     27.28

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   61
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    32_A     A    32_A      3   21   61      0    3    7   12   19   29   40   44   50   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     T    33_A     T    33_A     18   25   61      9   17   18   24   33   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     M    34_A     M    34_A     18   25   61      9   17   18   24   33   37   43   48   51   54   55   59   60   60   61   61   61   61   61   61 
LCS_GDT     A    35_A     A    35_A     18   25   61      9   17   18   21   26   36   42   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     D    36_A     D    36_A     18   25   61      9   17   18   24   33   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     L    37_A     L    37_A     18   25   61      9   17   18   24   33   37   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     K    38_A     K    38_A     18   25   61      9   17   18   24   33   37   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     M    39_A     M    39_A     18   25   61      9   17   18   24   33   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     Q    40_A     Q    40_A     18   25   61      9   17   18   24   33   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     A    41_A     A    41_A     18   25   61      9   17   18   24   33   37   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     V    42_A     V    42_A     18   25   61      8   17   18   24   33   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     K    43_A     K    43_A     18   25   61      9   17   18   24   33   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     E    44_A     E    44_A     18   25   61      8   17   18   24   33   37   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     I    45_A     I    45_A     18   25   61      6   17   18   24   33   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     C    46_A     C    46_A     18   25   61      6   17   18   24   33   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     Y    47_A     Y    47_A     18   25   61      6   17   18   24   33   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     E    48_A     E    48_A     18   25   61      5   17   18   24   33   37   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     V    49_A     V    49_A     18   25   61      5   11   18   21   32   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     A    50_A     A    50_A     18   25   61      5   11   17   21   33   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     L    51_A     L    51_A     18   25   61      5   11   18   24   33   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     A    52_A     A    52_A     18   25   61      5   12   18   24   33   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     D    53_A     D    53_A     15   25   61      5    8   15   19   25   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     F    54_A     F    54_A      3   25   61      7   17   18   24   33   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     R    55_A     R    55_A      3   25   61      4    8   17   23   33   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     H    56_A     H    56_A      3   25   61      3   13   18   24   32   37   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     G    57_A     G    57_A     20   25   61      3   11   19   21   24   27   32   37   44   52   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     R    58_A     R    58_A     20   22   61      6   16   19   21   24   27   32   41   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     A    59_A     A    59_A     20   22   61      6   16   19   21   24   27   32   41   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     E    60_A     E    60_A     20   22   61      5   16   19   21   24   34   38   45   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     I    61_A     I    61_A     20   22   61      6   16   19   23   33   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     E    62_A     E    62_A     20   22   61      6   16   19   21   33   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     A    63_A     A    63_A     20   22   61      6   16   19   23   33   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     L    64_A     L    64_A     20   22   61      6   16   19   23   33   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     A    65_A     A    65_A     20   22   61      6   16   19   21   33   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     A    66_A     A    66_A     20   22   61      5   16   19   21   28   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     L    67_A     L    67_A     20   22   61      6   16   19   21   29   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     K    68_A     K    68_A     20   22   61      6   16   19   21   25   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     M    69_A     M    69_A     20   22   61      5   14   19   21   24   36   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     R    70_A     R    70_A     20   22   61      5   13   19   21   24   30   42   45   50   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     E    71_A     E    71_A     20   22   61      6   16   19   21   24   30   40   45   50   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     L    72_A     L    72_A     20   22   61      6   16   19   21   24   28   34   42   47   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     C    73_A     C    73_A     20   22   61      4   16   19   21   24   26   32   38   47   52   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     R    74_A     R    74_A     20   22   61      5   16   19   21   24   27   34   42   47   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     T    75_A     T    75_A     20   22   61      5   16   19   21   24   27   32   38   47   51   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     Y    76_A     Y    76_A     20   22   61      3   10   19   20   24   25   28   33   40   46   53   55   60   60   61   61   61   61   61   61 
LCS_GDT     G    83_A     G    83_A      3   22   61      3    3    6   14   23   33   43   47   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     D    84_A     D    84_A     15   22   61      4    9   15   16   22   30   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     A    85_A     A    85_A     15   16   61      4   12   15   19   25   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     W    86_A     W    86_A     15   16   61      5   12   15   19   25   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     R    87_A     R    87_A     15   16   61      7   12   15   19   25   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     A    88_A     A    88_A     15   16   61      7   12   15   19   25   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     V    89_A     V    89_A     15   16   61      7   12   15   19   25   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     A    90_A     A    90_A     15   16   61      7   12   15   19   25   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     R    91_A     R    91_A     15   16   61      7   12   15   20   33   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     D    92_A     D    92_A     15   16   61      7   12   17   21   33   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     V    93_A     V    93_A     15   16   61      7   12   17   22   33   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     W    94_A     W    94_A     15   16   61      7   12   17   24   33   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     D    95_A     D    95_A     15   16   61      7   12   18   24   33   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     T    96_A     T    96_A     15   16   61      4   12   18   24   33   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     V    97_A     V    97_A     15   16   61      6   12   15   24   33   38   43   48   51   54   57   59   60   60   61   61   61   61   61   61 
LCS_GDT     G    98_A     G    98_A     15   16   61      3    3   15   24   33   38   43   48   50   54   57   59   60   60   61   61   61   61   61   61 
LCS_AVERAGE  LCS_A:  54.36  (  27.28   35.80  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      9     17     19     24     33     38     43     48     51     54     57     59     60     60     61     61     61     61     61     61 
GDT PERCENT_AT  14.75  27.87  31.15  39.34  54.10  62.30  70.49  78.69  83.61  88.52  93.44  96.72  98.36  98.36 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.34   0.63   0.80   1.34   1.80   2.29   2.42   2.64   2.95   3.22   3.41   3.58   3.64   3.64   3.79   3.79   3.79   3.79   3.79   3.79
GDT RMS_ALL_AT   8.81   8.20   6.61   6.33   5.47   4.29   4.43   4.37   4.23   3.85   3.82   3.79   3.80   3.80   3.79   3.79   3.79   3.79   3.79   3.79

# Checking swapping
#   possible swapping detected:  D    36_A      D    36_A
#   possible swapping detected:  D    53_A      D    53_A
#   possible swapping detected:  F    54_A      F    54_A
#   possible swapping detected:  E    71_A      E    71_A
#   possible swapping detected:  Y    76_A      Y    76_A
#   possible swapping detected:  D    84_A      D    84_A
#   possible swapping detected:  D    92_A      D    92_A
#   possible swapping detected:  D    95_A      D    95_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    32_A      A    32_A     6.756     0    0.390   0.376     8.082   22.262   18.762
LGA    T    33_A      T    33_A     1.591     0    0.630   1.234     4.847   66.905   58.027
LGA    M    34_A      M    34_A     3.669     0    0.125   1.130     5.773   46.786   38.690
LGA    A    35_A      A    35_A     3.773     0    0.113   0.123     4.218   48.452   46.190
LGA    D    36_A      D    36_A     1.019     0    0.114   0.229     2.192   79.286   79.405
LGA    L    37_A      L    37_A     2.754     0    0.060   0.108     4.135   57.262   50.357
LGA    K    38_A      K    38_A     3.246     0    0.071   1.468    10.023   55.476   36.296
LGA    M    39_A      M    39_A     1.817     0    0.060   0.747     4.853   72.976   59.702
LGA    Q    40_A      Q    40_A     2.194     0    0.031   1.296     5.059   62.976   53.228
LGA    A    41_A      A    41_A     3.391     0    0.046   0.043     4.073   51.786   48.857
LGA    V    42_A      V    42_A     2.264     0    0.107   0.190     3.323   73.095   66.327
LGA    K    43_A      K    43_A     0.949     0    0.018   0.925     4.755   79.405   63.862
LGA    E    44_A      E    44_A     2.998     0    0.172   0.298     4.363   57.262   47.460
LGA    I    45_A      I    45_A     2.247     0    0.052   0.101     3.812   73.095   62.500
LGA    C    46_A      C    46_A     0.298     0    0.049   0.071     1.271   92.857   90.556
LGA    Y    47_A      Y    47_A     2.310     0    0.055   1.477    12.424   68.929   31.548
LGA    E    48_A      E    48_A     3.088     0    0.068   0.837     8.285   61.071   35.503
LGA    V    49_A      V    49_A     2.642     0    0.078   1.273     6.272   64.881   54.966
LGA    A    50_A      A    50_A     1.908     0    0.159   0.163     3.247   77.143   71.714
LGA    L    51_A      L    51_A     2.353     0    0.237   1.344     6.033   65.238   56.369
LGA    A    52_A      A    52_A     2.510     0    0.107   0.111     4.183   56.071   52.286
LGA    D    53_A      D    53_A     3.126     0    0.202   1.156     5.668   53.810   42.083
LGA    F    54_A      F    54_A     1.753     0    0.385   1.455     3.621   69.048   66.190
LGA    R    55_A      R    55_A     1.218     0    0.080   0.740     7.676   86.190   45.108
LGA    H    56_A      H    56_A     3.362     0    0.596   1.412     5.223   44.524   40.286
LGA    G    57_A      G    57_A     7.379     0    0.564   0.564     7.379   17.500   17.500
LGA    R    58_A      R    58_A     6.031     0    0.269   1.373    11.411   23.452   12.381
LGA    A    59_A      A    59_A     6.316     0    0.058   0.056     7.500   22.976   19.810
LGA    E    60_A      E    60_A     5.133     0    0.111   0.853     7.764   33.571   20.635
LGA    I    61_A      I    61_A     2.731     0    0.033   0.694     5.040   59.524   55.536
LGA    E    62_A      E    62_A     2.677     0    0.100   0.226     6.668   60.952   41.799
LGA    A    63_A      A    63_A     2.566     0    0.075   0.081     3.252   67.143   63.714
LGA    L    64_A      L    64_A     1.875     0    0.167   1.037     3.158   72.976   64.226
LGA    A    65_A      A    65_A     0.771     0    0.048   0.053     2.051   79.524   79.905
LGA    A    66_A      A    66_A     2.270     0    0.046   0.054     2.774   66.905   64.952
LGA    L    67_A      L    67_A     1.258     0    0.025   1.356     5.332   71.190   61.548
LGA    K    68_A      K    68_A     3.466     0    0.067   1.101     4.998   47.381   46.667
LGA    M    69_A      M    69_A     4.250     0    0.075   0.832     5.935   33.690   35.476
LGA    R    70_A      R    70_A     5.585     0    0.044   0.914     6.926   21.905   22.165
LGA    E    71_A      E    71_A     6.339     0    0.038   0.841     9.300   13.333   11.534
LGA    L    72_A      L    72_A     8.142     0    0.051   0.222     9.914    4.524    5.238
LGA    C    73_A      C    73_A     9.378     0    0.113   0.328    10.562    1.667    1.825
LGA    R    74_A      R    74_A     9.381     0    0.322   1.439    11.758    0.714   14.675
LGA    T    75_A      T    75_A    10.724     0    0.123   0.951    12.545    0.119    0.068
LGA    Y    76_A      Y    76_A    12.966     0    0.555   1.329    19.017    0.000    0.000
LGA    G    83_A      G    83_A     5.400     0    0.200   0.200     5.528   25.000   25.000
LGA    D    84_A      D    84_A     4.629     0    0.305   0.404     5.492   35.833   33.690
LGA    A    85_A      A    85_A     3.634     0    0.065   0.062     4.219   46.905   46.190
LGA    W    86_A      W    86_A     3.527     0    0.173   1.654     4.201   48.452   55.748
LGA    R    87_A      R    87_A     2.856     0    0.088   1.028     4.137   57.262   50.346
LGA    A    88_A      A    88_A     2.859     0    0.142   0.155     3.130   57.143   55.714
LGA    V    89_A      V    89_A     3.284     0    0.106   0.147     4.050   53.571   48.299
LGA    A    90_A      A    90_A     2.676     0    0.032   0.035     2.987   60.952   60.190
LGA    R    91_A      R    91_A     1.904     0    0.056   1.321     6.549   70.833   51.126
LGA    D    92_A      D    92_A     2.048     0    0.093   0.235     2.706   70.833   66.845
LGA    V    93_A      V    93_A     2.140     0    0.076   0.092     2.826   64.762   61.497
LGA    W    94_A      W    94_A     2.169     0    0.059   0.999     9.875   66.786   33.163
LGA    D    95_A      D    95_A     1.741     0    0.219   0.613     2.505   68.929   73.036
LGA    T    96_A      T    96_A     2.238     0    0.107   1.135     4.590   64.762   62.585
LGA    V    97_A      V    97_A     2.596     0    0.537   1.319     3.413   66.905   60.680
LGA    G    98_A      G    98_A     2.636     0    0.232   0.232     3.068   57.262   57.262

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       61     244    244  100.00     480    480  100.00                61
SUMMARY(RMSD_GDC):     3.786          3.687                  4.747           52.492   45.857

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   99   61    4.0     48    2.64    61.475    58.964     1.752

LGA_LOCAL      RMSD:   2.639  Number of atoms:   48  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.366  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   3.786  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.100805 * X  +   0.946051 * Y  +  -0.307938 * Z  +  -0.795632
  Y_new =  -0.347835 * X  +   0.256469 * Y  +   0.901795 * Z  +  15.915436
  Z_new =   0.932121 * X  +   0.198017 * Y  +   0.303216 * Z  +  -2.007788 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.852875 -1.200226  0.578520   [DEG: -106.1619  -68.7679   33.1467 ]
ZXZ: -2.812536  1.262731  1.361472   [DEG: -161.1464   72.3491   78.0066 ]
 
# END of job
