
#######################################################
#                                                     #
#                        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        0.97     2.95
  LONGEST_CONTINUOUS_SEGMENT:    33       5_A - 37_A        0.95     2.89
  LCS_AVERAGE:     38.15

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      8   63   63      0   10   28   49   56   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   15   33   48   56   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   11   33   48   56   60   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   10   34   49   56   60   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      5   21   34   49   56   60   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      4   25   34   49   56   60   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      4   25   34   49   56   60   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     12   25   34   49   56   60   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      9   24   34   49   56   60   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      4   25   34   49   56   60   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      9   25   34   49   56   60   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     12   25   34   49   56   60   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      6   25   34   49   56   60   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   20   34   49   56   60   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      4   17   34   49   56   60   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      4   22   34   49   56   60   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      4   22   29   49   56   60   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     11   25   34   49   56   60   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      4   16   34   49   56   60   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     11   25   34   49   56   60   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     12   25   34   49   56   60   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      6   25   34   49   56   60   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     12   25   34   49   56   60   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     12   25   34   49   56   60   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     12   25   34   49   56   60   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     12   25   34   49   56   60   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     12   25   34   49   56   60   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     12   25   34   49   56   60   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     12   25   34   49   56   60   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     12   25   34   49   56   60   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     11   25   34   49   56   60   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     11   25   34   49   56   60   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     12   25   34   49   56   60   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     11   25   34   49   56   60   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     11   24   34   49   56   60   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     11   25   34   49   56   60   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     11   22   34   49   56   60   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      5   22   34   49   56   60   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      6   25   34   49   56   60   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      4   19   33   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     22   63   63      3   19   28   41   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    8   23   40   56   60   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      6   22   34   49   56   60   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   19   34   49   56   60   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   28   47   56   60   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   20   32   49   56   60   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   21   34   49   56   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    7   22   36   56   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   49   56   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    9   25   49   56   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    8   34   49   56   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      7   21   34   49   56   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      4   20   34   49   56   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      4   18   31   49   56   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     11   63   63      4   13   26   39   56   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     11   63   63      6   12   25   37   45   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     11   63   63      6   13   25   39   53   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     11   63   63      6   11   28   47   56   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    59_A     N    59_A     11   63   63     10   21   34   49   56   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    60_A     P    60_A     11   63   63     11   22   34   49   56   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     11   63   63      6   10   34   48   56   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     11   63   63      3   15   31   39   52   58   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     11   63   63      3   11   25   38   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  79.38  (  38.15  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     12     25     34     49     56     60     62     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  19.05  39.68  53.97  77.78  88.89  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    0.33   0.64   0.94   1.41   1.57   1.72   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   3.27   3.03   2.66   1.94   1.90   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   1.87

# Checking swapping
#   possible swapping detected:  F     4_A      F     4_A
#   possible swapping detected:  Y    18_A      Y    18_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     1.868     0    0.053   0.053     2.898   75.476   75.476
LGA    S     2_A      S     2_A     2.271     0    0.209   0.783     3.882   68.810   61.429
LGA    S     3_A      S     3_A     2.217     0    0.139   0.680     5.653   68.810   58.968
LGA    F     4_A      F     4_A     1.717     0    0.077   0.216     3.810   72.857   60.390
LGA    C     5_A      C     5_A     1.864     0    0.113   0.795     2.670   72.857   70.238
LGA    D     6_A      D     6_A     1.795     0    0.111   1.107     5.910   72.857   55.774
LGA    S     7_A      S     7_A     2.139     0    0.134   0.244     2.503   64.881   64.841
LGA    K     8_A      K     8_A     1.409     0    0.115   0.735     5.594   79.286   67.831
LGA    C     9_A      C     9_A     1.506     0    0.055   0.066     1.776   75.000   77.143
LGA    G    10_A      G    10_A     1.494     0    0.119   0.119     1.541   79.286   79.286
LGA    V    11_A      V    11_A     1.852     0    0.064   0.078     2.098   72.857   71.701
LGA    R    12_A      R    12_A     1.642     0    0.056   1.362     8.089   75.000   53.333
LGA    C    13_A      C    13_A     1.020     0    0.640   0.716     2.490   79.524   81.667
LGA    S    14_A      S    14_A     1.389     0    0.095   0.624     2.086   79.286   77.222
LGA    K    15_A      K    15_A     1.264     0    0.115   0.647     4.331   81.429   68.571
LGA    A    16_A      A    16_A     1.209     0    0.619   0.556     2.845   75.357   76.571
LGA    G    17_A      G    17_A     2.185     0    0.039   0.039     2.545   64.881   64.881
LGA    Y    18_A      Y    18_A     1.844     0    0.287   1.353     7.732   75.000   52.738
LGA    Q    19_A      Q    19_A     1.408     0    0.120   1.126     4.059   85.952   74.021
LGA    E    20_A      E    20_A     1.716     0    0.028   0.780     4.466   72.976   59.048
LGA    R    21_A      R    21_A     2.251     0    0.049   1.161    10.091   66.786   36.364
LGA    C    22_A      C    22_A     1.482     0    0.067   0.088     1.719   77.143   77.143
LGA    L    23_A      L    23_A     1.100     0    0.055   0.284     2.223   81.429   78.274
LGA    K    24_A      K    24_A     1.920     0    0.064   1.132     9.991   70.833   45.291
LGA    Y    25_A      Y    25_A     2.114     0    0.120   0.640     3.484   68.810   66.429
LGA    C    26_A      C    26_A     1.092     0    0.044   0.105     1.299   83.690   84.444
LGA    G    27_A      G    27_A     0.907     0    0.055   0.055     1.460   85.952   85.952
LGA    I    28_A      I    28_A     1.750     0    0.046   0.753     4.804   75.000   63.869
LGA    C    29_A      C    29_A     1.360     0    0.097   0.115     1.861   83.690   80.079
LGA    C    30_A      C    30_A     0.797     0    0.131   0.142     1.132   88.214   90.556
LGA    E    31_A      E    31_A     0.675     0    0.020   0.876     3.928   90.476   78.519
LGA    K    32_A      K    32_A     1.054     0    0.059   0.886     2.024   88.214   79.735
LGA    C    33_A      C    33_A     1.081     0    0.227   0.236     2.010   77.262   80.159
LGA    H    34_A      H    34_A     1.304     0    0.095   1.232     3.131   79.286   70.952
LGA    C    35_A      C    35_A     1.264     0    0.080   0.605     2.359   81.429   77.222
LGA    V    36_A      V    36_A     1.130     0    0.069   0.290     2.243   81.429   77.823
LGA    P    37_A      P    37_A     0.914     0    0.037   0.319     1.224   88.214   89.252
LGA    S    38_A      S    38_A     1.348     0    0.232   0.658     5.076   83.810   71.032
LGA    G    39_A      G    39_A     1.687     0    0.071   0.071     2.408   68.810   68.810
LGA    T    40_A      T    40_A     2.875     0    0.489   0.402     3.966   53.810   55.306
LGA    Y    41_A      Y    41_A     3.102     0    0.148   0.316     4.030   57.381   48.095
LGA    G    42_A      G    42_A     2.320     0    0.636   0.636     4.572   54.524   54.524
LGA    N    43_A      N    43_A     1.173     0    0.186   0.826     4.326   83.690   67.560
LGA    K    44_A      K    44_A     1.278     0    0.040   1.054     8.039   77.143   57.407
LGA    D    45_A      D    45_A     2.116     0    0.095   1.032     3.778   70.833   62.262
LGA    E    46_A      E    46_A     1.461     0    0.131   0.166     2.644   81.548   72.275
LGA    C    47_A      C    47_A     0.860     0    0.100   0.233     2.349   79.524   77.381
LGA    P    48_A      P    48_A     2.275     0    0.249   0.439     2.838   68.810   69.524
LGA    C    49_A      C    49_A     1.836     0    0.094   0.220     2.177   72.976   73.016
LGA    Y    50_A      Y    50_A     1.866     0    0.085   0.805     5.369   72.857   53.611
LGA    R    51_A      R    51_A     1.187     0    0.039   1.238     5.837   83.690   63.939
LGA    D    52_A      D    52_A     0.179     0    0.089   0.779     3.443   92.857   80.179
LGA    L    53_A      L    53_A     1.060     0    0.032   0.708     4.151   83.690   72.798
LGA    K    54_A      K    54_A     1.440     0    0.035   1.275     6.263   75.119   62.116
LGA    N    55_A      N    55_A     2.655     0    0.092   0.272     3.014   57.262   61.012
LGA    S    56_A      S    56_A     3.885     0    0.157   0.565     6.098   42.024   37.063
LGA    K    57_A      K    57_A     3.449     0    0.037   0.772     6.260   50.000   38.466
LGA    G    58_A      G    58_A     2.181     0    0.038   0.038     2.455   68.810   68.810
LGA    N    59_A      N    59_A     0.738     0    0.041   0.250     2.176   92.976   87.440
LGA    P    60_A      P    60_A     1.653     0    0.076   0.317     2.814   75.000   70.680
LGA    K    61_A      K    61_A     2.418     0    0.036   0.955     3.256   59.167   60.794
LGA    C    62_A      C    62_A     3.337     0    0.113   0.527     4.300   48.452   46.825
LGA    P    63_A      P    63_A     3.695     0    0.293   0.278     4.192   41.786   43.401

# 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):     1.867          1.889                  2.766           73.917   67.262

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    1.87    79.365    89.133     3.203

LGA_LOCAL      RMSD:   1.867  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.867  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.867  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.303720 * X  +   0.830122 * Y  +   0.467602 * Z  +  -8.723296
  Y_new =   0.273037 * X  +   0.546037 * Y  +  -0.792020 * Z  +   2.256557
  Z_new =  -0.912801 * X  +  -0.112879 * Y  +  -0.392496 * Z  +  -4.795031 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.409343  1.150090 -2.861557   [DEG:  138.0452   65.8953 -163.9551 ]
ZXZ:  0.533325  1.974140 -1.693834   [DEG:   30.5573  113.1099  -97.0495 ]
 
# END of job
