
#######################################################
#                                                     #
#                        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        1.87     1.87
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.87     1.87
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       4_A - 36_A        0.96     2.96
  LONGEST_CONTINUOUS_SEGMENT:    33       5_A - 37_A        0.95     2.90
  LCS_AVERAGE:     38.45

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     11   63   63      3    8   38   49   55   59   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    6   28   41   55   59   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   16   31   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     F     4_A     F     4_A     33   63   63      3   13   38   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     33   63   63      4   24   38   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     33   63   63      5   26   38   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     7_A     S     7_A     33   63   63      5   26   35   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     8_A     K     8_A     33   63   63     13   26   38   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     33   63   63     10   26   38   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    10_A     G    10_A     33   63   63     13   26   38   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    11_A     V    11_A     33   63   63     13   26   35   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     33   63   63     13   26   35   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     33   63   63      8   26   38   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     33   63   63      4   22   37   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     33   63   63      3   16   38   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     33   63   63      3   20   38   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    17_A     G    17_A     33   63   63      3   19   29   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    18_A     Y    18_A     33   63   63     13   26   38   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Q    19_A     Q    19_A     33   63   63      3   24   38   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    20_A     E    20_A     33   63   63     12   26   38   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     33   63   63     13   26   38   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     33   63   63     10   26   38   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     33   63   63     13   26   38   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     33   63   63     13   26   38   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     33   63   63     13   26   38   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     33   63   63     13   26   38   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     33   63   63     13   26   38   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     33   63   63     13   26   38   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     33   63   63     13   26   38   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     33   63   63     13   26   38   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     33   63   63     13   26   38   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     33   63   63     13   26   38   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     33   63   63     13   26   38   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    34_A     H    34_A     33   63   63     12   26   38   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     33   63   63     12   26   38   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     33   63   63     12   26   38   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     33   63   63     10   21   38   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    38_A     S    38_A     28   63   63      4   19   38   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     28   63   63     13   26   38   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A     25   63   63      3   16   32   41   51   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     23   63   63      3   19   26   40   51   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     13   63   63      3    7   20   41   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     12   63   63      5   19   37   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    44_A     K    44_A     12   63   63      5   18   37   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A     12   63   63      5   10   27   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    46_A     E    46_A     12   63   63      5   19   32   49   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     12   63   63      5   19   38   49   55   59   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   37   55   59   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   29   49   55   59   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    9   25   49   55   59   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    8   38   49   55   59   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   19   38   49   55   59   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      3   19   38   49   55   59   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   17   32   49   55   59   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      5    9   26   39   55   59   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      5   10   24   37   46   59   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      5   12   25   39   52   59   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      5   11   27   46   55   59   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     10   19   38   49   55   59   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     12   21   38   49   55   59   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      4    8   34   48   55   59   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      4   14   32   39   50   58   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   14   24   38   46   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  79.48  (  38.45  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     26     38     49     55     59     62     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  20.63  41.27  60.32  77.78  87.30  93.65  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    0.31   0.62   1.20   1.39   1.54   1.67   1.82   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87
GDT RMS_ALL_AT   2.86   3.05   2.03   1.93   1.89   1.89   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87

# Checking swapping
#   possible swapping detected:  D     6_A      D     6_A
#   possible swapping detected:  Y    25_A      Y    25_A
#   possible swapping detected:  E    31_A      E    31_A
#   possible swapping detected:  D    45_A      D    45_A
#   possible swapping detected:  E    46_A      E    46_A
#   possible swapping detected:  Y    50_A      Y    50_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G     1_A      G     1_A     1.451     0    0.108   0.108     2.259   79.524   79.524
LGA    S     2_A      S     2_A     2.470     0    0.183   0.757     4.113   68.810   60.397
LGA    S     3_A      S     3_A     2.127     0    0.140   0.383     3.132   68.810   63.730
LGA    F     4_A      F     4_A     1.533     0    0.064   0.224     3.614   72.857   62.424
LGA    C     5_A      C     5_A     1.834     0    0.099   0.802     2.754   72.857   70.238
LGA    D     6_A      D     6_A     1.784     0    0.090   0.994     5.580   72.857   55.774
LGA    S     7_A      S     7_A     2.132     0    0.109   0.189     2.441   68.810   67.460
LGA    K     8_A      K     8_A     1.427     0    0.120   0.769     5.881   79.286   67.831
LGA    C     9_A      C     9_A     1.386     0    0.070   0.075     1.686   79.286   80.000
LGA    G    10_A      G    10_A     1.312     0    0.069   0.069     1.354   81.429   81.429
LGA    V    11_A      V    11_A     1.816     0    0.021   0.046     2.123   72.857   70.544
LGA    R    12_A      R    12_A     1.696     0    0.055   1.364     8.283   72.857   52.554
LGA    C    13_A      C    13_A     0.898     0    0.565   0.650     2.341   81.786   83.175
LGA    S    14_A      S    14_A     1.334     0    0.071   0.580     1.855   79.286   78.571
LGA    K    15_A      K    15_A     1.285     0    0.072   0.617     3.920   81.429   69.259
LGA    A    16_A      A    16_A     1.259     0    0.652   0.593     2.745   75.357   76.571
LGA    G    17_A      G    17_A     2.606     0    0.020   0.020     2.761   60.952   60.952
LGA    Y    18_A      Y    18_A     2.019     0    0.283   1.333     7.739   68.929   50.357
LGA    Q    19_A      Q    19_A     1.244     0    0.059   1.121     3.801   83.690   74.550
LGA    E    20_A      E    20_A     1.796     0    0.024   0.542     3.887   72.976   62.011
LGA    R    21_A      R    21_A     2.270     0    0.044   1.290    12.162   66.786   34.502
LGA    C    22_A      C    22_A     1.466     0    0.090   0.136     1.689   77.143   78.571
LGA    L    23_A      L    23_A     1.227     0    0.014   0.282     2.210   81.429   79.345
LGA    K    24_A      K    24_A     1.961     0    0.048   1.192    10.413   70.833   45.238
LGA    Y    25_A      Y    25_A     2.060     0    0.148   0.553     3.300   66.905   65.794
LGA    C    26_A      C    26_A     1.032     0    0.020   0.120     1.289   85.952   85.952
LGA    G    27_A      G    27_A     0.868     0    0.017   0.017     1.197   85.952   85.952
LGA    I    28_A      I    28_A     1.715     0    0.014   0.742     4.815   79.286   66.012
LGA    C    29_A      C    29_A     1.309     0    0.107   0.118     1.992   85.952   81.587
LGA    C    30_A      C    30_A     0.802     0    0.109   0.111     1.126   88.214   90.556
LGA    E    31_A      E    31_A     0.755     0    0.030   0.351     1.983   90.476   83.598
LGA    K    32_A      K    32_A     1.113     0    0.022   1.000     2.492   81.429   76.720
LGA    C    33_A      C    33_A     1.010     0    0.151   0.184     1.771   79.286   84.603
LGA    H    34_A      H    34_A     1.237     0    0.157   1.200     3.170   81.548   71.095
LGA    C    35_A      C    35_A     1.161     0    0.023   0.138     1.435   81.429   81.429
LGA    V    36_A      V    36_A     1.216     0    0.064   0.286     2.380   81.429   76.599
LGA    P    37_A      P    37_A     0.887     0    0.017   0.244     1.055   88.214   89.252
LGA    S    38_A      S    38_A     1.259     0    0.233   0.681     4.927   81.548   70.397
LGA    G    39_A      G    39_A     1.595     0    0.082   0.082     2.616   69.048   69.048
LGA    T    40_A      T    40_A     2.969     0    0.466   0.379     4.139   52.262   53.401
LGA    Y    41_A      Y    41_A     3.138     0    0.140   1.267    10.973   57.381   30.397
LGA    G    42_A      G    42_A     2.500     0    0.638   0.638     4.390   55.952   55.952
LGA    N    43_A      N    43_A     1.348     0    0.257   0.921     4.747   83.690   65.774
LGA    K    44_A      K    44_A     1.168     0    0.065   0.930     7.815   77.143   56.878
LGA    D    45_A      D    45_A     2.070     0    0.161   1.035     6.330   70.833   52.560
LGA    E    46_A      E    46_A     1.593     0    0.147   0.209     2.827   79.405   69.630
LGA    C    47_A      C    47_A     0.857     0    0.088   0.596     2.472   81.548   78.730
LGA    P    48_A      P    48_A     2.151     0    0.183   0.361     2.710   70.833   70.680
LGA    C    49_A      C    49_A     1.790     0    0.089   0.204     2.073   72.976   73.016
LGA    Y    50_A      Y    50_A     1.892     0    0.107   0.752     4.874   72.857   56.548
LGA    R    51_A      R    51_A     1.251     0    0.034   1.204     5.535   83.690   65.195
LGA    D    52_A      D    52_A     0.222     0    0.141   0.743     3.147   92.857   81.190
LGA    L    53_A      L    53_A     1.105     0    0.068   0.597     3.130   83.690   73.452
LGA    K    54_A      K    54_A     1.454     0    0.016   0.927     3.289   75.119   69.577
LGA    N    55_A      N    55_A     2.695     0    0.054   0.235     3.034   57.262   59.107
LGA    S    56_A      S    56_A     3.893     0    0.102   0.751     7.036   43.452   36.825
LGA    K    57_A      K    57_A     3.452     0    0.023   0.758     6.158   50.000   37.937
LGA    G    58_A      G    58_A     2.245     0    0.045   0.045     2.535   66.905   66.905
LGA    N    59_A      N    59_A     0.606     0    0.023   0.248     2.063   92.976   88.571
LGA    P    60_A      P    60_A     1.478     0    0.090   0.271     2.625   77.143   71.905
LGA    K    61_A      K    61_A     2.417     0    0.044   0.977     3.301   59.167   64.180
LGA    C    62_A      C    62_A     3.344     0    0.114   0.468     4.057   48.452   46.825
LGA    P    63_A      P    63_A     3.737     0    0.448   0.422     4.388   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):     1.871          1.886                  2.903           74.072   67.511

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    1.87    79.762    89.529     3.196

LGA_LOCAL      RMSD:   1.871  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.871  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.871  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.726017 * X  +   0.590291 * Y  +   0.352784 * Z  +  -7.644685
  Y_new =  -0.593595 * X  +   0.796948 * Y  +  -0.111886 * Z  +   2.313457
  Z_new =  -0.347196 * X  +  -0.128180 * Y  +   0.928991 * Z  +  -5.743411 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.685384  0.354579 -0.137112   [DEG:  -39.2696   20.3159   -7.8559 ]
ZXZ:  1.263680  0.379118 -1.924460   [DEG:   72.4035   21.7219 -110.2635 ]
 
# END of job
