
#######################################################
#                                                     #
#                        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        2.06     2.06
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    62       1_A - 62_A        1.97     2.06
  LCS_AVERAGE:     98.14

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    28       8_A - 35_A        0.99     3.69
  LCS_AVERAGE:     31.44

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     11   62   63      5   10   20   28   44   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H     2_A     H     2_A     13   62   63      5   12   22   39   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I     3_A     I     3_A     13   62   63      6   15   30   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     4_A     D     4_A     14   62   63      7   15   31   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     22   62   63      7   17   31   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     24   62   63      7   14   25   41   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     7_A     K     7_A     24   62   63      8   17   31   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E     8_A     E     8_A     28   62   63      8   19   31   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     28   62   63      7   19   31   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    10_A     N    10_A     28   62   63      7   19   31   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    11_A     R    11_A     28   62   63      5   19   31   41   52   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     28   62   63      6   19   31   42   54   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     28   62   63      5   16   31   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     28   62   63      8   19   31   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     28   62   63      3   17   31   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     28   62   63      8   19   31   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    17_A     S    17_A     28   62   63      8   19   31   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    18_A     A    18_A     28   62   63      4   17   31   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    19_A     H    19_A     28   62   63      7   17   31   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    20_A     D    20_A     28   62   63      7   19   31   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     28   62   63      8   19   31   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     28   62   63      8   19   31   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     28   62   63      7   19   31   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     28   62   63      5   19   31   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     28   62   63      8   19   31   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     28   62   63      3   19   31   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     28   62   63      3   17   31   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     28   62   63      7   19   31   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     28   62   63      8   19   31   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     28   62   63      4   17   31   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     28   62   63      4   12   25   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     28   62   63      4   14   31   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     28   62   63      8   19   31   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    34_A     N    34_A     28   62   63      5   19   31   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     28   62   63      8   19   31   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     24   62   63      8   15   31   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     19   62   63      8   15   29   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    38_A     P    38_A     12   62   63      7   13   25   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     12   62   63      5   11   24   41   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A     12   62   63      3   11   20   37   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     12   62   63      5   11   20   37   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     12   62   63      8   15   25   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     12   62   63      4   10   20   39   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    44_A     E    44_A      7   62   63      4    9   21   40   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A      7   62   63      4   17   31   42   54   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    46_A     S    46_A      7   62   63      4    6   22   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A      7   62   63      8   15   28   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A      7   62   63      4   14   30   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     12   62   63      5    9   26   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     12   62   63      5    8   21   41   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    51_A     A    51_A     13   62   63      5    8   21   26   53   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    52_A     N    52_A     13   62   63      5    9   21   40   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     13   62   63      3   12   21   41   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     13   62   63      5   12   21   41   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     13   62   63      8   15   24   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     13   62   63      4   12   18   31   43   58   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     13   62   63      5   13   23   41   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     13   62   63      5   12   21   40   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    59_A     G    59_A     13   62   63      5   12   24   41   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    60_A     H    60_A     13   62   63      5   12   22   40   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     13   62   63      4   14   28   42   55   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     13   62   63      4   12   21   36   52   60   62   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     13   51   63      3   12   18   21   28   33   48   59   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  76.53  (  31.44   98.14  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      8     19     31     42     55     60     62     62     62     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  12.70  30.16  49.21  66.67  87.30  95.24  98.41  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    0.35   0.65   1.01   1.44   1.77   1.89   1.97   1.97   1.97   2.06   2.06   2.06   2.06   2.06   2.06   2.06   2.06   2.06   2.06   2.06
GDT RMS_ALL_AT   2.47   3.75   3.26   2.31   2.07   2.07   2.06   2.06   2.06   2.06   2.06   2.06   2.06   2.06   2.06   2.06   2.06   2.06   2.06   2.06

# Checking swapping
#   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

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     1_A      A     1_A     3.440     0    0.120   0.170     3.804   53.571   51.524
LGA    H     2_A      H     2_A     2.129     0    0.041   0.756     3.082   71.190   64.429
LGA    I     3_A      I     3_A     0.500     0    0.047   1.009     2.929   85.952   79.643
LGA    D     4_A      D     4_A     1.585     0    0.043   1.079     4.290   75.238   64.762
LGA    C     5_A      C     5_A     2.179     0    0.087   0.194     2.407   66.786   67.460
LGA    D     6_A      D     6_A     2.352     0    0.017   0.698     3.873   64.762   61.131
LGA    K     7_A      K     7_A     1.484     0    0.079   0.532     2.265   77.143   78.730
LGA    E     8_A      E     8_A     1.455     0    0.066   0.404     2.045   77.143   76.772
LGA    C     9_A      C     9_A     1.929     0    0.049   0.053     1.968   72.857   72.857
LGA    N    10_A      N    10_A     1.918     0    0.099   0.234     2.359   68.810   66.786
LGA    R    11_A      R    11_A     2.887     0    0.011   1.522     5.405   57.143   45.887
LGA    R    12_A      R    12_A     2.462     0    0.040   0.867     2.969   62.857   63.550
LGA    C    13_A      C    13_A     1.888     0    0.205   0.233     3.368   77.381   70.714
LGA    S    14_A      S    14_A     1.454     0    0.026   0.660     1.952   83.810   83.095
LGA    K    15_A      K    15_A     1.594     0    0.121   1.087     3.890   77.143   65.397
LGA    A    16_A      A    16_A     1.227     0    0.020   0.028     1.777   77.143   79.810
LGA    S    17_A      S    17_A     1.999     0    0.014   0.677     3.485   70.833   65.079
LGA    A    18_A      A    18_A     1.992     0    0.057   0.057     2.323   72.857   71.238
LGA    H    19_A      H    19_A     1.253     0    0.136   0.324     1.838   77.143   81.524
LGA    D    20_A      D    20_A     1.570     0    0.176   0.167     2.264   79.286   73.036
LGA    R    21_A      R    21_A     1.824     0    0.067   1.171     8.760   75.000   45.065
LGA    C    22_A      C    22_A     1.272     0    0.128   0.182     1.737   81.429   80.000
LGA    L    23_A      L    23_A     0.941     0    0.112   1.275     4.639   90.476   77.560
LGA    K    24_A      K    24_A     2.157     0    0.063   0.478     6.461   66.786   50.000
LGA    Y    25_A      Y    25_A     2.216     0    0.022   0.541     2.739   64.762   65.516
LGA    C    26_A      C    26_A     1.854     0    0.060   0.200     1.977   72.857   72.857
LGA    G    27_A      G    27_A     1.711     0    0.120   0.120     2.518   66.905   66.905
LGA    I    28_A      I    28_A     1.971     0    0.043   0.676     5.161   72.857   61.131
LGA    C    29_A      C    29_A     1.832     0    0.038   0.726     1.911   72.857   72.857
LGA    C    30_A      C    30_A     1.787     0    0.038   0.067     2.333   72.857   70.159
LGA    E    31_A      E    31_A     1.891     0    0.034   0.474     4.117   72.857   59.841
LGA    K    32_A      K    32_A     1.359     0    0.063   0.719     3.039   81.429   76.032
LGA    C    33_A      C    33_A     1.117     0    0.593   0.520     3.382   71.429   69.286
LGA    N    34_A      N    34_A     0.854     0    0.175   0.715     3.489   85.952   76.726
LGA    C    35_A      C    35_A     1.296     0    0.033   0.506     2.491   85.952   80.238
LGA    V    36_A      V    36_A     0.916     0    0.079   1.336     2.866   88.214   78.367
LGA    P    37_A      P    37_A     0.850     0    0.011   0.117     0.952   90.476   90.476
LGA    P    38_A      P    38_A     1.203     0    0.027   0.123     1.308   83.690   84.014
LGA    G    39_A      G    39_A     1.661     0    0.127   0.127     1.661   75.000   75.000
LGA    T    40_A      T    40_A     2.582     0    0.526   0.513     5.032   49.524   56.054
LGA    Y    41_A      Y    41_A     2.471     0    0.123   1.270     4.528   66.786   56.310
LGA    G    42_A      G    42_A     1.382     0    0.276   0.276     2.592   73.214   73.214
LGA    N    43_A      N    43_A     2.090     0    0.261   1.185     7.024   72.976   49.940
LGA    E    44_A      E    44_A     2.450     0    0.074   1.020     3.609   68.810   65.979
LGA    D    45_A      D    45_A     2.763     0    0.104   0.742     3.295   59.167   54.583
LGA    S    46_A      S    46_A     2.369     0    0.023   0.746     2.795   64.881   63.571
LGA    C    47_A      C    47_A     0.961     0    0.054   0.388     2.517   90.595   82.063
LGA    P    48_A      P    48_A     1.072     0    0.047   0.307     1.700   81.548   79.048
LGA    C    49_A      C    49_A     1.217     0    0.066   0.271     2.596   77.381   73.254
LGA    Y    50_A      Y    50_A     2.155     0    0.019   1.114     4.510   66.786   62.659
LGA    A    51_A      A    51_A     3.095     0    0.210   0.231     3.633   51.905   51.524
LGA    N    52_A      N    52_A     2.309     0    0.079   0.386     2.748   64.762   63.810
LGA    L    53_A      L    53_A     1.818     0    0.048   0.988     2.887   70.833   70.952
LGA    K    54_A      K    54_A     2.102     0    0.134   1.263     3.301   72.976   68.783
LGA    N    55_A      N    55_A     1.465     0    0.030   0.192     2.506   73.452   76.369
LGA    S    56_A      S    56_A     3.675     0    0.105   0.394     6.202   46.905   39.365
LGA    K    57_A      K    57_A     1.589     0    0.127   0.748     3.092   70.833   72.275
LGA    G    58_A      G    58_A     2.309     0    0.112   0.112     2.919   64.881   64.881
LGA    G    59_A      G    59_A     1.994     0    0.106   0.106     2.151   68.810   68.810
LGA    H    60_A      H    60_A     2.530     0    0.101   1.315     9.706   62.857   35.619
LGA    K    61_A      K    61_A     2.018     0    0.035   0.748     2.680   62.857   76.349
LGA    C    62_A      C    62_A     3.061     0    0.216   0.275     4.585   45.476   53.413
LGA    P    63_A      P    63_A     5.237     0    0.227   0.362     6.025   37.619   32.993

# 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):     2.061          2.041                  2.548           71.217   67.100

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     62    1.97    73.810    86.515     2.994

LGA_LOCAL      RMSD:   1.971  Number of atoms:   62  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.063  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   2.061  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.838797 * X  +  -0.358377 * Y  +   0.409859 * Z  + -12.139479
  Y_new =  -0.525617 * X  +   0.729295 * Y  +  -0.438012 * Z  +   1.256803
  Z_new =  -0.141935 * X  +  -0.582833 * Y  +  -0.800100 * Z  + -11.995171 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.581821  0.142416 -2.512027   [DEG: -147.9274    8.1598 -143.9286 ]
ZXZ:  0.752206  2.498259 -2.902716   [DEG:   43.0982  143.1397 -166.3134 ]
 
# END of job
