
#######################################################
#                                                     #
#                        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   63 (  471),  selected   63 , name one
# Molecule2: number of CA atoms   63 (  471),  selected   63 , 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:    63       1_A - 63_A        2.69     2.69
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       4_A - 63_A        1.99     2.79
  LCS_AVERAGE:     93.15

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      14_A - 37_A        0.99     3.17
  LONGEST_CONTINUOUS_SEGMENT:    24      16_A - 39_A        0.95     3.22
  LCS_AVERAGE:     28.24

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   63
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     1_A     A     1_A      3    4   63      3    3    4    4    4    4    5    7    7   18   26   29   35   39   42   51   60   63   63   63 
LCS_GDT     H     2_A     H     2_A      3   40   63      3    3    4    4   14   32   42   54   58   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     I     3_A     I     3_A      3   53   63      3    6    8   17   20   29   42   46   58   60   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     D     4_A     D     4_A     15   60   63      7   17   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C     5_A     C     5_A     19   60   63      7   14   31   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     D     6_A     D     6_A     19   60   63      7   12   29   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     K     7_A     K     7_A     19   60   63      7   19   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     E     8_A     E     8_A     19   60   63     10   20   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C     9_A     C     9_A     19   60   63      7   20   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     N    10_A     N    10_A     19   60   63     10   20   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     R    11_A     R    11_A     19   60   63     10   20   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     R    12_A     R    12_A     19   60   63      4   20   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    13_A     C    13_A     19   60   63      6   20   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     S    14_A     S    14_A     24   60   63      6   20   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     K    15_A     K    15_A     24   60   63      3   10   19   41   48   57   57   58   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     A    16_A     A    16_A     24   60   63      5   20   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     S    17_A     S    17_A     24   60   63      6   20   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     A    18_A     A    18_A     24   60   63      4   13   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     H    19_A     H    19_A     24   60   63      4   20   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     D    20_A     D    20_A     24   60   63      5   20   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     R    21_A     R    21_A     24   60   63      6   20   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    22_A     C    22_A     24   60   63     10   20   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     L    23_A     L    23_A     24   60   63     10   20   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     K    24_A     K    24_A     24   60   63      5   20   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     24   60   63      6   20   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    26_A     C    26_A     24   60   63      5   20   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     G    27_A     G    27_A     24   60   63      4   19   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     I    28_A     I    28_A     24   60   63      6   20   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    29_A     C    29_A     24   60   63      6   20   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    30_A     C    30_A     24   60   63      5   19   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     E    31_A     E    31_A     24   60   63      4   12   33   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     K    32_A     K    32_A     24   60   63      4   18   34   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    33_A     C    33_A     24   60   63      6   20   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     N    34_A     N    34_A     24   60   63      4   20   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    35_A     C    35_A     24   60   63      6   20   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     V    36_A     V    36_A     24   60   63     10   20   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     P    37_A     P    37_A     24   60   63     10   20   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     P    38_A     P    38_A     24   60   63     10   20   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     G    39_A     G    39_A     24   60   63      6   20   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     T    40_A     T    40_A      8   60   63      3    6   13   30   42   50   55   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     Y    41_A     Y    41_A      8   60   63      3    6   17   24   39   47   55   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     G    42_A     G    42_A     13   60   63      3    5   17   24   39   47   55   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     N    43_A     N    43_A     13   60   63      5   17   36   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     E    44_A     E    44_A     13   60   63      8   19   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     D    45_A     D    45_A     13   60   63      5   19   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     S    46_A     S    46_A     13   60   63      5   18   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    47_A     C    47_A     13   60   63     10   20   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     P    48_A     P    48_A     13   60   63     10   20   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    49_A     C    49_A     13   60   63      9   20   35   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     13   60   63      4   20   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     A    51_A     A    51_A     13   60   63     10   20   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     N    52_A     N    52_A     13   60   63      8   19   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     L    53_A     L    53_A     13   60   63      8   18   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     K    54_A     K    54_A     13   60   63      4   12   33   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     N    55_A     N    55_A     13   60   63      6   13   29   48   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     S    56_A     S    56_A     13   60   63      6   10   20   31   48   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     K    57_A     K    57_A     13   60   63      6   11   27   37   48   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     G    58_A     G    58_A     13   60   63      6   12   24   37   48   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     G    59_A     G    59_A     13   60   63      6   12   28   49   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     H    60_A     H    60_A     13   60   63      6   13   38   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     K    61_A     K    61_A     13   60   63      5   16   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    62_A     C    62_A     13   60   63      5   20   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     P    63_A     P    63_A     13   60   63      6   20   39   50   53   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_AVERAGE  LCS_A:  73.80  (  28.24   93.15  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     10     20     39     50     53     57     57     59     60     61     62     62     62     62     62     62     62     63     63     63 
GDT PERCENT_AT  15.87  31.75  61.90  79.37  84.13  90.48  90.48  93.65  95.24  96.83  98.41  98.41  98.41  98.41  98.41  98.41  98.41 100.00 100.00 100.00
GDT RMS_LOCAL    0.29   0.63   1.11   1.32   1.44   1.72   1.72   1.95   1.99   2.13   2.25   2.25   2.25   2.25   2.25   2.25   2.25   2.69   2.69   2.69
GDT RMS_ALL_AT   3.16   3.33   3.01   2.87   2.82   2.82   2.82   2.80   2.79   2.75   2.72   2.72   2.72   2.72   2.72   2.72   2.72   2.69   2.69   2.69

# Checking swapping
#   possible swapping detected:  E     8_A      E     8_A
#   possible swapping detected:  E    31_A      E    31_A
#   possible swapping detected:  Y    41_A      Y    41_A
#   possible swapping detected:  D    45_A      D    45_A
#   possible swapping detected:  Y    50_A      Y    50_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     1_A      A     1_A    13.052     0    0.074   0.089    15.535    0.000    0.000
LGA    H     2_A      H     2_A     6.474     0    0.130   1.166     8.447   11.310   20.333
LGA    I     3_A      I     3_A     6.690     0    0.595   1.568    12.638   23.810   12.560
LGA    D     4_A      D     4_A     1.028     0    0.551   1.057     5.464   75.357   56.667
LGA    C     5_A      C     5_A     2.064     0    0.124   0.360     2.832   70.833   67.540
LGA    D     6_A      D     6_A     1.547     0    0.029   0.933     5.503   77.143   60.417
LGA    K     7_A      K     7_A     0.532     0    0.073   0.868     4.366   90.476   71.905
LGA    E     8_A      E     8_A     1.093     0    0.037   1.058     5.294   83.690   67.460
LGA    C     9_A      C     9_A     1.239     0    0.023   0.055     1.713   81.429   80.000
LGA    N    10_A      N    10_A     0.535     0    0.120   0.956     3.651   88.214   83.512
LGA    R    11_A      R    11_A     1.058     0    0.023   1.363     8.455   83.690   51.299
LGA    R    12_A      R    12_A     1.383     0    0.048   1.441     6.502   79.286   63.074
LGA    C    13_A      C    13_A     1.177     0    0.289   0.267     2.913   79.286   74.524
LGA    S    14_A      S    14_A     1.331     0    0.040   0.672     3.616   73.452   69.762
LGA    K    15_A      K    15_A     3.629     0    0.307   0.851     4.972   55.595   50.529
LGA    A    16_A      A    16_A     2.194     0    0.054   0.063     2.652   62.857   64.857
LGA    S    17_A      S    17_A     2.700     0    0.068   0.681     4.554   59.048   54.127
LGA    A    18_A      A    18_A     2.444     0    0.196   0.194     2.592   62.857   63.238
LGA    H    19_A      H    19_A     2.190     0    0.155   0.758     2.902   62.857   63.238
LGA    D    20_A      D    20_A     2.077     0    0.149   0.308     3.265   68.810   63.036
LGA    R    21_A      R    21_A     2.084     0    0.094   1.002     8.729   70.952   42.511
LGA    C    22_A      C    22_A     1.408     0    0.148   0.659     1.746   79.286   78.571
LGA    L    23_A      L    23_A     1.182     0    0.101   0.215     1.975   83.690   78.274
LGA    K    24_A      K    24_A     2.269     0    0.057   0.606     5.718   64.762   51.376
LGA    Y    25_A      Y    25_A     2.238     0    0.023   0.698     3.371   64.762   64.325
LGA    C    26_A      C    26_A     1.806     0    0.053   0.145     1.978   72.857   74.286
LGA    G    27_A      G    27_A     1.902     0    0.128   0.128     2.625   66.905   66.905
LGA    I    28_A      I    28_A     1.652     0    0.052   1.525     6.469   75.000   60.774
LGA    C    29_A      C    29_A     1.632     0    0.045   0.647     1.811   77.143   78.651
LGA    C    30_A      C    30_A     1.644     0    0.061   0.662     2.376   72.857   70.159
LGA    E    31_A      E    31_A     1.788     0    0.044   0.304     3.669   70.833   62.698
LGA    K    32_A      K    32_A     1.601     0    0.056   1.001     6.367   72.976   54.974
LGA    C    33_A      C    33_A     1.023     0    0.632   0.544     3.636   69.762   68.175
LGA    N    34_A      N    34_A     1.015     0    0.226   1.045     4.512   86.071   72.321
LGA    C    35_A      C    35_A     1.190     0    0.110   0.904     1.663   83.690   80.079
LGA    V    36_A      V    36_A     0.481     0    0.168   0.196     1.643   97.619   92.041
LGA    P    37_A      P    37_A     0.376     0    0.034   0.328     1.073   95.238   93.265
LGA    P    38_A      P    38_A     1.323     0    0.056   0.098     1.517   83.690   81.497
LGA    G    39_A      G    39_A     1.962     0    0.207   0.207     2.477   68.810   68.810
LGA    T    40_A      T    40_A     4.388     0    0.609   0.525     5.452   37.619   35.918
LGA    Y    41_A      Y    41_A     4.521     0    0.101   1.351     5.000   34.286   37.897
LGA    G    42_A      G    42_A     4.317     0    0.625   0.625     5.469   34.524   34.524
LGA    N    43_A      N    43_A     1.311     0    0.276   0.455     1.904   77.143   78.214
LGA    E    44_A      E    44_A     0.594     0    0.092   0.699     2.352   90.476   82.698
LGA    D    45_A      D    45_A     1.080     0    0.106   0.534     2.124   85.952   80.536
LGA    S    46_A      S    46_A     1.149     0    0.057   0.442     1.551   85.952   83.016
LGA    C    47_A      C    47_A     0.573     0    0.067   0.460     2.788   90.476   83.413
LGA    P    48_A      P    48_A     0.710     0    0.076   0.102     1.387   88.333   90.612
LGA    C    49_A      C    49_A     1.740     0    0.033   0.267     3.149   72.976   67.778
LGA    Y    50_A      Y    50_A     1.052     0    0.089   0.257     2.483   83.690   76.587
LGA    A    51_A      A    51_A     1.002     0    0.098   0.127     1.382   81.429   81.429
LGA    N    52_A      N    52_A     1.084     0    0.053   1.002     3.035   83.690   76.548
LGA    L    53_A      L    53_A     1.020     0    0.148   0.847     3.227   83.690   79.762
LGA    K    54_A      K    54_A     1.265     0    0.086   1.185     4.481   81.429   68.042
LGA    N    55_A      N    55_A     2.038     0    0.021   0.469     3.082   65.119   61.190
LGA    S    56_A      S    56_A     4.081     0    0.038   0.345     5.046   38.929   35.556
LGA    K    57_A      K    57_A     3.624     0    0.065   0.950     7.010   43.333   38.571
LGA    G    58_A      G    58_A     3.216     0    0.092   0.092     3.216   53.571   53.571
LGA    G    59_A      G    59_A     1.777     0    0.076   0.076     2.265   77.381   77.381
LGA    H    60_A      H    60_A     1.157     0    0.125   1.377     6.386   85.952   58.095
LGA    K    61_A      K    61_A     1.475     0    0.042   0.860     2.066   77.381   76.825
LGA    C    62_A      C    62_A     2.199     0    0.100   0.176     2.564   66.786   64.841
LGA    P    63_A      P    63_A     1.905     0    0.509   0.556     2.577   66.786   64.830

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       63     252    252  100.00     471    471  100.00                63
SUMMARY(RMSD_GDC):     2.693          2.700                  3.196           70.378   64.533

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     59    1.95    75.794    85.442     2.877

LGA_LOCAL      RMSD:   1.951  Number of atoms:   59  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.802  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   2.693  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.957262 * X  +  -0.234775 * Y  +  -0.168908 * Z  +   5.723707
  Y_new =  -0.256562 * X  +   0.958898 * Y  +   0.121203 * Z  +  -1.751283
  Z_new =   0.133510 * X  +   0.159359 * Y  +  -0.978151 * Z  +  -3.954347 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.879730 -0.133910  2.980093   [DEG: -164.9964   -7.6725  170.7468 ]
ZXZ: -2.193217  2.932171  0.697366   [DEG: -125.6621  168.0010   39.9561 ]
 
# END of job
