
#######################################################
#                                                     #
#                        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 (  472),  selected   63 , name one
# Molecule2: number of CA atoms   63 (  472),  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        1.80     1.80
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.80     1.80
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    35       5_A - 39_A        0.98     2.54
  LCS_AVERAGE:     40.74

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     G     1_A     G     1_A      7   63   63      0    4   28   44   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     2_A     S     2_A     12   63   63      3    9   28   43   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     3_A     S     3_A     12   63   63      3   14   32   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     F     4_A     F     4_A     34   63   63      3   10   37   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     35   63   63      4   22   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     35   63   63      8   26   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     7_A     S     7_A     35   63   63      8   26   35   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     8_A     K     8_A     35   63   63     13   26   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     35   63   63      4   26   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    10_A     G    10_A     35   63   63      6   26   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    11_A     V    11_A     35   63   63     14   26   35   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     35   63   63     14   26   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     35   63   63      8   26   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     35   63   63      5   26   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     35   63   63      4   18   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     35   63   63      4   23   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    17_A     G    17_A     35   63   63      4   22   29   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    18_A     Y    18_A     35   63   63     14   26   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Q    19_A     Q    19_A     35   63   63      4   22   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    20_A     E    20_A     35   63   63     11   26   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     35   63   63     14   26   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     35   63   63      6   26   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     35   63   63     14   26   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     35   63   63     14   26   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     35   63   63     14   26   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     35   63   63     14   26   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     35   63   63     14   26   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     35   63   63     14   26   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     35   63   63     14   26   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     35   63   63     14   26   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     35   63   63     14   26   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     35   63   63     14   26   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     35   63   63     14   26   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    34_A     H    34_A     35   63   63     11   26   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     35   63   63     10   26   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     35   63   63     11   26   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     35   63   63     10   22   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    38_A     S    38_A     35   63   63      7   22   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     35   63   63     11   26   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A     27   63   63      5   21   32   43   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     24   63   63      3   19   30   43   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     14   63   63      3    9   25   42   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     14   63   63      5   22   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    44_A     K    44_A     14   63   63      5   19   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A     14   63   63      5   10   29   47   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    46_A     E    46_A     14   63   63      5   21   37   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     14   63   63      5   21   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     12   63   63      5    8   23   44   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     12   63   63      5    9   28   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     12   63   63      5   10   26   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    51_A     R    51_A     12   63   63      5    9   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    52_A     D    52_A     12   63   63      5   22   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     12   63   63      5   21   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     12   63   63      5   19   33   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     12   63   63      3   11   27   41   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     12   63   63      6   11   26   39   47   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     12   63   63      6   14   27   40   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     12   63   63      6   19   32   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    59_A     N    59_A     12   63   63      8   21   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    60_A     P    60_A     12   63   63     11   25   38   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     12   63   63      6    8   35   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     12   63   63      3   14   31   40   54   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     12   63   63      3   11   18   37   46   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  80.25  (  40.74  100.00  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     14     26     38     48     57     60     62     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  22.22  41.27  60.32  76.19  90.48  95.24  98.41 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.59   1.14   1.32   1.55   1.66   1.76   1.80   1.80   1.80   1.80   1.80   1.80   1.80   1.80   1.80   1.80   1.80   1.80   1.80
GDT RMS_ALL_AT   3.25   2.88   1.97   1.88   1.82   1.81   1.81   1.80   1.80   1.80   1.80   1.80   1.80   1.80   1.80   1.80   1.80   1.80   1.80   1.80

# Checking swapping
#   possible swapping detected:  F     4_A      F     4_A
#   possible swapping detected:  Y    18_A      Y    18_A
#   possible swapping detected:  E    31_A      E    31_A
#   possible swapping detected:  E    46_A      E    46_A
#   possible swapping detected:  D    52_A      D    52_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G     1_A      G     1_A     2.221     0    0.160   0.160     3.418   67.262   67.262
LGA    S     2_A      S     2_A     2.460     0    0.284   0.405     3.504   66.786   60.079
LGA    S     3_A      S     3_A     2.075     0    0.129   0.307     3.845   68.810   62.619
LGA    F     4_A      F     4_A     1.797     0    0.057   0.250     3.817   70.833   59.004
LGA    C     5_A      C     5_A     1.851     0    0.128   0.818     2.715   72.857   70.238
LGA    D     6_A      D     6_A     1.687     0    0.134   0.674     4.474   72.857   59.226
LGA    S     7_A      S     7_A     1.991     0    0.102   0.545     4.032   70.833   64.206
LGA    K     8_A      K     8_A     1.348     0    0.113   0.656     5.228   81.429   69.312
LGA    C     9_A      C     9_A     1.435     0    0.045   0.061     1.672   77.143   78.571
LGA    G    10_A      G    10_A     1.450     0    0.109   0.109     1.488   81.429   81.429
LGA    V    11_A      V    11_A     1.750     0    0.046   0.072     2.039   72.857   71.701
LGA    R    12_A      R    12_A     1.515     0    0.049   1.387     8.308   75.000   53.939
LGA    C    13_A      C    13_A     0.872     0    0.634   0.715     2.582   79.881   81.905
LGA    S    14_A      S    14_A     1.146     0    0.031   0.526     1.620   83.690   81.508
LGA    K    15_A      K    15_A     1.231     0    0.120   0.620     3.910   81.429   70.000
LGA    A    16_A      A    16_A     1.262     0    0.632   0.568     2.764   75.357   76.571
LGA    G    17_A      G    17_A     2.430     0    0.024   0.024     2.550   62.857   62.857
LGA    Y    18_A      Y    18_A     1.748     0    0.300   1.376     7.785   75.000   52.897
LGA    Q    19_A      Q    19_A     1.215     0    0.123   0.984     2.371   88.214   78.836
LGA    E    20_A      E    20_A     1.597     0    0.028   0.548     4.378   72.976   62.063
LGA    R    21_A      R    21_A     2.101     0    0.035   1.178    10.095   68.810   37.056
LGA    C    22_A      C    22_A     1.413     0    0.064   0.078     1.671   77.143   77.143
LGA    L    23_A      L    23_A     1.034     0    0.052   0.292     2.081   81.429   79.345
LGA    K    24_A      K    24_A     1.793     0    0.067   1.086     9.303   72.976   47.778
LGA    Y    25_A      Y    25_A     2.041     0    0.124   0.667     3.543   68.810   65.873
LGA    C    26_A      C    26_A     1.054     0    0.035   0.097     1.243   85.952   85.952
LGA    G    27_A      G    27_A     0.856     0    0.054   0.054     1.391   85.952   85.952
LGA    I    28_A      I    28_A     1.708     0    0.038   0.750     4.753   77.143   64.940
LGA    C    29_A      C    29_A     1.299     0    0.095   0.107     1.807   85.952   83.016
LGA    C    30_A      C    30_A     0.762     0    0.116   0.116     1.104   88.214   92.143
LGA    E    31_A      E    31_A     0.689     0    0.017   0.413     2.019   90.476   82.698
LGA    K    32_A      K    32_A     1.057     0    0.052   0.935     2.536   88.214   77.989
LGA    C    33_A      C    33_A     0.997     0    0.226   0.237     1.824   83.810   84.524
LGA    H    34_A      H    34_A     1.068     0    0.089   1.038     2.975   83.690   75.048
LGA    C    35_A      C    35_A     1.082     0    0.078   0.611     2.113   88.214   83.175
LGA    V    36_A      V    36_A     0.979     0    0.067   0.276     2.084   90.476   84.218
LGA    P    37_A      P    37_A     0.722     0    0.012   0.111     1.167   90.476   89.184
LGA    S    38_A      S    38_A     1.082     0    0.241   0.662     4.619   83.810   73.254
LGA    G    39_A      G    39_A     1.532     0    0.033   0.033     2.023   70.833   70.833
LGA    T    40_A      T    40_A     2.754     0    0.497   0.395     3.954   55.595   56.327
LGA    Y    41_A      Y    41_A     3.022     0    0.111   0.208     4.260   61.190   50.476
LGA    G    42_A      G    42_A     2.381     0    0.637   0.637     4.562   54.524   54.524
LGA    N    43_A      N    43_A     1.136     0    0.189   0.821     4.271   83.690   67.560
LGA    K    44_A      K    44_A     1.181     0    0.046   1.012     8.207   77.143   56.614
LGA    D    45_A      D    45_A     2.022     0    0.084   1.000     4.169   70.833   60.595
LGA    E    46_A      E    46_A     1.365     0    0.130   0.655     3.168   83.810   77.090
LGA    C    47_A      C    47_A     0.829     0    0.095   0.207     2.235   81.548   78.730
LGA    P    48_A      P    48_A     2.198     0    0.258   0.417     2.786   72.976   71.905
LGA    C    49_A      C    49_A     1.794     0    0.072   0.223     2.151   72.976   73.016
LGA    Y    50_A      Y    50_A     1.849     0    0.064   0.813     5.419   72.857   53.016
LGA    R    51_A      R    51_A     1.185     0    0.046   1.198     5.457   83.690   64.805
LGA    D    52_A      D    52_A     0.171     0    0.118   0.660     2.914   92.857   80.119
LGA    L    53_A      L    53_A     1.048     0    0.035   0.177     2.489   81.548   76.190
LGA    K    54_A      K    54_A     1.348     0    0.028   0.979     3.118   77.381   69.788
LGA    N    55_A      N    55_A     2.600     0    0.109   0.245     2.893   59.048   60.000
LGA    S    56_A      S    56_A     3.668     0    0.164   0.765     6.861   43.452   37.381
LGA    K    57_A      K    57_A     3.260     0    0.043   0.765     5.902   53.571   40.529
LGA    G    58_A      G    58_A     1.948     0    0.045   0.045     2.243   72.976   72.976
LGA    N    59_A      N    59_A     0.456     0    0.036   0.162     1.088   97.619   94.107
LGA    P    60_A      P    60_A     1.645     0    0.062   0.292     2.688   75.000   70.680
LGA    K    61_A      K    61_A     2.386     0    0.026   0.955     3.088   59.167   62.434
LGA    C    62_A      C    62_A     3.277     0    0.121   0.535     4.274   48.452   46.825
LGA    P    63_A      P    63_A     3.692     0    0.314   0.296     4.141   43.452   44.354

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       63     252    252  100.00     472    472  100.00                63
SUMMARY(RMSD_GDC):     1.805          1.829                  2.663           75.162   68.641

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    1.80    79.365    89.724     3.308

LGA_LOCAL      RMSD:   1.805  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.805  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.805  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.411619 * X  +  -0.905081 * Y  +  -0.106759 * Z  +  -8.203436
  Y_new =   0.910843 * X  +  -0.404626 * Y  +  -0.081498 * Z  +   2.195063
  Z_new =   0.030565 * X  +  -0.130787 * Y  +   0.990939 * Z  +  -5.565752 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.995237 -0.030570 -0.131225   [DEG:  114.3187   -1.7515   -7.5186 ]
ZXZ: -0.918784  0.134718  2.912012   [DEG:  -52.6424    7.7188  166.8460 ]
 
# END of job
