
#######################################################
#                                                     #
#                        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        1.94     1.94
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.94     1.94
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    35       3_A - 37_A        1.00     2.88
  LCS_AVERAGE:     42.13

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      3    6    7   45   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     2_A     S     2_A     13   63   63      4   10   25   45   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     3_A     S     3_A     35   63   63      4   12   32   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     F     4_A     F     4_A     35   63   63      4   12   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     35   63   63      6   21   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     35   63   63      4   27   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     7_A     S     7_A     35   63   63      4   27   33   45   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     8_A     K     8_A     35   63   63     10   27   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     35   63   63     13   27   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    10_A     G    10_A     35   63   63     13   27   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    11_A     V    11_A     35   63   63     13   27   33   44   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     35   63   63     13   27   33   44   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     35   63   63      7   27   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     35   63   63      8   27   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     35   63   63      4   22   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     35   63   63      4   24   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    17_A     G    17_A     35   63   63     11   27   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    18_A     Y    18_A     35   63   63     11   27   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Q    19_A     Q    19_A     35   63   63      4   21   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    20_A     E    20_A     35   63   63     13   27   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     35   63   63     13   27   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     35   63   63     13   27   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     35   63   63     13   27   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     35   63   63     13   27   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     35   63   63     13   27   33   47   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     35   63   63     13   27   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     35   63   63     13   27   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     35   63   63     11   27   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     35   63   63     11   27   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     35   63   63     13   27   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     35   63   63     11   27   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     35   63   63     11   27   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     35   63   63     11   27   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    34_A     H    34_A     35   63   63     11   27   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     35   63   63     11   25   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     35   63   63     11   27   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     35   63   63     11   21   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    38_A     S    38_A     28   63   63      5   21   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     28   63   63      9   20   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A     28   63   63      5   17   33   44   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     13   63   63      5    9   21   31   53   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     10   63   63      3    6   12   16   31   50   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     11   63   63      3   12   33   48   56   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    44_A     K    44_A     11   63   63      3    8   31   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A     14   63   63      3    7   14   37   50   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    46_A     E    46_A     16   63   63      3   12   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     16   63   63      5   21   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     16   63   63      5   17   28   45   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     16   63   63      5   18   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     16   63   63      5   20   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    51_A     R    51_A     16   63   63      6   21   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    52_A     D    52_A     16   63   63      6   21   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     16   63   63      4   18   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     16   63   63      6   21   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     16   63   63      6   20   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     16   63   63      5   20   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     16   63   63      6   21   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     16   63   63      5   21   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    59_A     N    59_A     16   63   63      9   21   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    60_A     P    60_A     16   63   63      5   18   33   48   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     16   63   63      4   13   21   41   57   60   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     16   63   63      4   11   30   39   45   55   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     12   63   63      3    6   11   18   23   27   33   52   61   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  80.71  (  42.13  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     13     27     33     48     57     60     61     62     62     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  20.63  42.86  52.38  76.19  90.48  95.24  96.83  98.41  98.41 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.29   6.12   0.80   1.39   1.61   1.70   1.75   1.80   1.80   1.94   1.94   1.94   1.94   1.94   1.94   1.94   1.94   1.94   1.94   1.94
GDT RMS_ALL_AT   4.06   3.36   3.23   1.97   1.94   1.94   1.95   1.94   1.94   1.94   1.94   1.94   1.94   1.94   1.94   1.94   1.94   1.94   1.94   1.94

# Checking swapping
#   possible swapping detected:  E    20_A      E    20_A
#   possible swapping detected:  Y    25_A      Y    25_A
#   possible swapping detected:  E    31_A      E    31_A
#   possible swapping detected:  Y    41_A      Y    41_A
#   possible swapping detected:  E    46_A      E    46_A
#   possible swapping detected:  Y    50_A      Y    50_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     2.187     0    0.143   0.143     2.194   68.810   68.810
LGA    S     2_A      S     2_A     2.229     0    0.213   0.835     3.767   70.833   63.968
LGA    S     3_A      S     3_A     1.759     0    0.093   0.671     4.687   75.000   66.032
LGA    F     4_A      F     4_A     1.399     0    0.099   0.207     3.691   79.286   64.156
LGA    C     5_A      C     5_A     1.567     0    0.111   0.804     2.401   75.000   72.937
LGA    D     6_A      D     6_A     1.710     0    0.071   1.031     5.673   72.857   56.488
LGA    S     7_A      S     7_A     2.297     0    0.093   0.549     4.450   64.881   60.238
LGA    K     8_A      K     8_A     1.830     0    0.129   0.789     6.890   72.857   58.307
LGA    C     9_A      C     9_A     1.533     0    0.043   0.059     1.863   72.857   75.714
LGA    G    10_A      G    10_A     1.862     0    0.060   0.060     2.100   68.810   68.810
LGA    V    11_A      V    11_A     2.675     0    0.056   0.062     3.151   59.048   57.211
LGA    R    12_A      R    12_A     2.550     0    0.067   1.317     8.052   60.952   45.238
LGA    C    13_A      C    13_A     1.189     0    0.644   0.722     2.944   73.214   75.952
LGA    S    14_A      S    14_A     1.273     0    0.064   0.606     1.768   83.810   83.095
LGA    K    15_A      K    15_A     1.026     0    0.111   0.666     4.770   81.429   67.937
LGA    A    16_A      A    16_A     1.045     0    0.078   0.099     1.183   83.690   85.048
LGA    G    17_A      G    17_A     0.912     0    0.201   0.201     1.014   88.214   88.214
LGA    Y    18_A      Y    18_A     1.325     0    0.246   1.274     8.187   81.548   54.206
LGA    Q    19_A      Q    19_A     1.334     0    0.056   0.936     2.674   88.214   76.138
LGA    E    20_A      E    20_A     1.572     0    0.017   0.749     6.226   72.976   52.698
LGA    R    21_A      R    21_A     2.068     0    0.066   1.213     8.691   68.810   42.987
LGA    C    22_A      C    22_A     1.483     0    0.081   0.130     1.819   77.143   77.143
LGA    L    23_A      L    23_A     1.165     0    0.020   0.273     1.805   81.429   80.357
LGA    K    24_A      K    24_A     1.859     0    0.093   0.953     6.882   70.833   54.974
LGA    Y    25_A      Y    25_A     2.197     0    0.119   0.632     3.771   64.881   62.738
LGA    C    26_A      C    26_A     1.352     0    0.019   0.094     1.438   81.429   81.429
LGA    G    27_A      G    27_A     0.968     0    0.050   0.050     1.303   83.690   83.690
LGA    I    28_A      I    28_A     1.373     0    0.017   0.742     4.064   81.429   70.714
LGA    C    29_A      C    29_A     1.276     0    0.135   0.706     3.971   83.690   76.587
LGA    C    30_A      C    30_A     1.160     0    0.122   0.115     1.350   81.429   84.444
LGA    E    31_A      E    31_A     1.200     0    0.030   0.827     4.505   81.429   69.524
LGA    K    32_A      K    32_A     1.087     0    0.033   1.180     5.484   83.690   68.677
LGA    C    33_A      C    33_A     1.049     0    0.169   0.201     1.749   79.286   84.603
LGA    H    34_A      H    34_A     1.183     0    0.144   1.223     3.563   79.286   69.619
LGA    C    35_A      C    35_A     1.077     0    0.099   0.563     2.469   81.429   78.651
LGA    V    36_A      V    36_A     1.297     0    0.082   0.292     2.661   83.690   76.803
LGA    P    37_A      P    37_A     0.577     0    0.015   0.277     1.248   88.214   91.905
LGA    S    38_A      S    38_A     1.782     0    0.283   0.678     5.537   77.143   64.524
LGA    G    39_A      G    39_A     1.569     0    0.083   0.083     2.810   66.905   66.905
LGA    T    40_A      T    40_A     2.565     0    0.518   0.421     4.561   52.857   57.143
LGA    Y    41_A      Y    41_A     3.009     0    0.095   0.311     4.485   59.286   48.254
LGA    G    42_A      G    42_A     3.678     0    0.648   0.648     5.114   42.381   42.381
LGA    N    43_A      N    43_A     2.185     0    0.192   0.893     4.076   68.810   58.810
LGA    K    44_A      K    44_A     2.105     0    0.068   0.684     5.071   60.952   57.090
LGA    D    45_A      D    45_A     3.179     0    0.151   0.999     7.319   57.262   39.345
LGA    E    46_A      E    46_A     2.091     0    0.079   0.797     3.115   73.095   69.524
LGA    C    47_A      C    47_A     0.979     0    0.119   0.291     2.269   77.381   78.810
LGA    P    48_A      P    48_A     2.325     0    0.167   0.388     2.972   70.833   69.456
LGA    C    49_A      C    49_A     1.583     0    0.066   0.210     1.930   77.143   78.651
LGA    Y    50_A      Y    50_A     1.251     0    0.132   1.189     8.400   81.429   50.278
LGA    R    51_A      R    51_A     1.140     0    0.030   1.294     6.662   85.952   58.874
LGA    D    52_A      D    52_A     0.974     0    0.164   0.779     1.918   83.810   82.679
LGA    L    53_A      L    53_A     1.398     0    0.157   0.813     2.779   75.476   71.310
LGA    K    54_A      K    54_A     1.280     0    0.041   0.923     4.452   81.429   67.884
LGA    N    55_A      N    55_A     1.652     0    0.062   0.227     1.943   72.857   73.929
LGA    S    56_A      S    56_A     2.004     0    0.159   0.486     3.648   68.810   63.889
LGA    K    57_A      K    57_A     1.593     0    0.041   0.770     4.047   77.143   62.487
LGA    G    58_A      G    58_A     0.781     0    0.059   0.059     0.996   90.476   90.476
LGA    N    59_A      N    59_A     0.522     0    0.130   0.295     1.707   90.476   89.464
LGA    P    60_A      P    60_A     1.620     0    0.113   0.330     3.444   72.976   66.259
LGA    K    61_A      K    61_A     2.685     0    0.063   1.390     3.762   53.810   54.974
LGA    C    62_A      C    62_A     3.748     0    0.458   1.061     5.707   36.548   39.127
LGA    P    63_A      P    63_A     6.062     0    0.416   0.373     7.438   26.667   21.156

# 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):     1.940          1.950                  2.799           73.460   66.980

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     62    1.80    79.365    89.007     3.261

LGA_LOCAL      RMSD:   1.801  Number of atoms:   62  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.943  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.940  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.048675 * X  +   0.995621 * Y  +  -0.079808 * Z  +   0.333110
  Y_new =  -0.930312 * X  +  -0.074273 * Y  +  -0.359170 * Z  +   6.091154
  Z_new =  -0.363524 * X  +   0.056763 * Y  +   0.929854 * Z  +   4.442498 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.623070  0.372048  0.060970   [DEG:  -92.9951   21.3168    3.4933 ]
ZXZ: -0.218648  0.376781 -1.415900   [DEG:  -12.5276   21.5880  -81.1251 ]
 
# END of job
