
#######################################################
#                                                     #
#                        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        1.91     1.91
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.91     1.91
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       5_A - 37_A        1.00     2.96
  LCS_AVERAGE:     37.24

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   11   27   48   56   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   15   31   46   56   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   11   27   46   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     F     4_A     F     4_A     31   63   63      3    9   32   48   56   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      5   22   34   48   56   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      4   24   34   48   56   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      4   24   34   48   56   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     12   24   34   48   56   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      9   24   34   48   56   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      4   24   34   48   56   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     11   24   34   48   56   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     12   24   34   48   56   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      7   24   34   48   56   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   18   34   48   56   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      4   19   34   48   56   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      4   21   34   48   56   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      4   21   29   48   56   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      9   24   34   48   56   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      4   16   34   48   56   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     11   24   34   48   56   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     12   24   34   48   56   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     12   24   34   48   56   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     12   24   34   48   56   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     12   24   34   48   56   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     12   24   34   48   56   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     12   24   34   48   56   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     12   24   34   48   56   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     12   24   34   48   56   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     12   24   34   48   56   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     12   24   34   48   56   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     11   24   34   48   56   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     11   24   34   48   56   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     11   24   34   48   56   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     11   24   34   48   56   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     11   23   34   48   56   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      7   23   34   48   56   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     11   21   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    38_A     S    38_A     25   63   63      4   21   32   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     25   63   63      6   23   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A     24   63   63      4   20   34   41   53   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     16   63   63      3   19   27   41   53   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   37   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     11   63   63      5   20   32   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    44_A     K    44_A     11   63   63      5   19   32   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A     10   63   63      5    9   27   45   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    46_A     E    46_A     10   63   63      5   20   31   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     10   63   63      5   20   32   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     10   63   63      5    8   22   36   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     10   63   63      5   11   28   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     10   63   63      5   11   23   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    51_A     R    51_A     10   63   63      5    9   32   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    52_A     D    52_A     11   63   63      9   20   32   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     11   63   63      4   20   32   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     11   63   63      5   17   29   47   56   59   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      5   12   24   39   56   59   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    9   22   37   44   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   12   24   38   52   59   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   12   27   45   56   59   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     11   20   32   48   56   59   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      9   21   34   48   56   59   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    9   34   45   55   59   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   11   32   38   49   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   22   37   45   55   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  79.08  (  37.24  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     24     34     48     56     59     62     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  19.05  38.10  53.97  76.19  88.89  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    0.33   0.58   0.91   1.43   1.63   1.72   1.87   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91
GDT RMS_ALL_AT   3.44   3.39   2.99   2.01   1.93   1.93   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91

# 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     1.917     0    0.056   0.056     3.071   73.690   73.690
LGA    S     2_A      S     2_A     2.302     0    0.213   0.796     3.876   68.810   61.429
LGA    S     3_A      S     3_A     2.283     0    0.157   0.481     3.912   68.810   61.429
LGA    F     4_A      F     4_A     1.738     0    0.081   0.235     3.873   72.857   60.390
LGA    C     5_A      C     5_A     1.828     0    0.112   0.793     2.649   72.857   70.238
LGA    D     6_A      D     6_A     1.821     0    0.118   1.123     5.979   72.857   55.774
LGA    S     7_A      S     7_A     2.180     0    0.132   0.243     2.549   62.857   63.492
LGA    K     8_A      K     8_A     1.454     0    0.114   0.767     5.715   77.143   66.878
LGA    C     9_A      C     9_A     1.594     0    0.052   0.061     1.857   75.000   77.143
LGA    G    10_A      G    10_A     1.602     0    0.109   0.109     1.638   75.000   75.000
LGA    V    11_A      V    11_A     1.981     0    0.059   0.078     2.252   70.833   68.231
LGA    R    12_A      R    12_A     1.761     0    0.063   1.365     8.155   72.857   52.554
LGA    C    13_A      C    13_A     1.087     0    0.641   0.719     2.479   79.524   80.159
LGA    S    14_A      S    14_A     1.476     0    0.085   0.626     2.071   79.286   75.794
LGA    K    15_A      K    15_A     1.306     0    0.111   0.656     4.276   81.429   68.571
LGA    A    16_A      A    16_A     1.289     0    0.626   0.563     2.805   75.357   76.571
LGA    G    17_A      G    17_A     2.429     0    0.042   0.042     2.858   62.857   62.857
LGA    Y    18_A      Y    18_A     1.925     0    0.305   1.376     7.524   72.976   52.063
LGA    Q    19_A      Q    19_A     1.464     0    0.140   0.987     2.759   83.690   73.280
LGA    E    20_A      E    20_A     1.754     0    0.028   0.807     4.478   72.976   59.048
LGA    R    21_A      R    21_A     2.282     0    0.051   1.161    10.208   66.786   36.277
LGA    C    22_A      C    22_A     1.490     0    0.064   0.085     1.711   77.143   77.143
LGA    L    23_A      L    23_A     1.132     0    0.056   0.289     2.274   81.429   78.274
LGA    K    24_A      K    24_A     1.932     0    0.062   1.125     9.965   70.833   45.291
LGA    Y    25_A      Y    25_A     2.134     0    0.119   0.616     3.556   68.810   65.238
LGA    C    26_A      C    26_A     1.079     0    0.048   0.104     1.347   83.690   84.444
LGA    G    27_A      G    27_A     0.916     0    0.046   0.046     1.488   85.952   85.952
LGA    I    28_A      I    28_A     1.838     0    0.039   0.752     4.922   75.000   63.036
LGA    C    29_A      C    29_A     1.405     0    0.103   0.123     1.935   83.690   80.079
LGA    C    30_A      C    30_A     0.808     0    0.142   0.157     1.148   88.214   90.556
LGA    E    31_A      E    31_A     0.709     0    0.021   0.861     4.028   90.476   76.138
LGA    K    32_A      K    32_A     1.028     0    0.077   0.794     1.818   88.214   82.593
LGA    C    33_A      C    33_A     1.005     0    0.228   0.230     2.014   77.262   81.667
LGA    H    34_A      H    34_A     1.276     0    0.098   1.292     3.484   79.286   70.190
LGA    C    35_A      C    35_A     1.271     0    0.070   0.611     2.379   81.429   77.222
LGA    V    36_A      V    36_A     1.179     0    0.068   0.294     2.271   81.429   77.823
LGA    P    37_A      P    37_A     1.004     0    0.045   0.320     1.336   85.952   86.599
LGA    S    38_A      S    38_A     1.334     0    0.232   0.656     5.073   81.548   69.524
LGA    G    39_A      G    39_A     1.751     0    0.075   0.075     2.536   66.905   66.905
LGA    T    40_A      T    40_A     2.982     0    0.484   0.398     4.080   52.262   52.449
LGA    Y    41_A      Y    41_A     3.188     0    0.146   0.314     4.087   57.381   48.095
LGA    G    42_A      G    42_A     2.541     0    0.631   0.631     4.712   50.714   50.714
LGA    N    43_A      N    43_A     1.226     0    0.188   0.866     4.242   83.690   67.560
LGA    K    44_A      K    44_A     1.244     0    0.046   1.014     8.176   77.143   56.614
LGA    D    45_A      D    45_A     2.172     0    0.089   1.031     3.906   70.833   62.262
LGA    E    46_A      E    46_A     1.512     0    0.126   0.172     2.715   79.405   70.476
LGA    C    47_A      C    47_A     0.892     0    0.102   0.238     2.432   79.524   77.381
LGA    P    48_A      P    48_A     2.295     0    0.244   0.440     2.854   68.810   69.524
LGA    C    49_A      C    49_A     1.860     0    0.075   0.212     2.199   72.976   73.016
LGA    Y    50_A      Y    50_A     1.801     0    0.087   0.828     5.304   72.857   54.563
LGA    R    51_A      R    51_A     1.125     0    0.051   1.243     5.953   83.690   63.939
LGA    D    52_A      D    52_A     0.110     0    0.102   0.781     3.504  100.000   82.917
LGA    L    53_A      L    53_A     1.045     0    0.028   0.746     3.311   83.690   73.452
LGA    K    54_A      K    54_A     1.439     0    0.044   1.283     6.184   75.119   62.116
LGA    N    55_A      N    55_A     2.632     0    0.086   0.260     3.033   57.262   61.012
LGA    S    56_A      S    56_A     3.972     0    0.151   0.557     6.079   40.476   35.079
LGA    K    57_A      K    57_A     3.489     0    0.036   0.773     6.168   50.000   38.466
LGA    G    58_A      G    58_A     2.264     0    0.037   0.037     2.545   66.905   66.905
LGA    N    59_A      N    59_A     0.915     0    0.042   0.349     2.820   90.595   83.036
LGA    P    60_A      P    60_A     1.788     0    0.076   0.314     3.017   75.000   68.503
LGA    K    61_A      K    61_A     2.501     0    0.041   0.964     3.250   57.262   58.307
LGA    C    62_A      C    62_A     3.337     0    0.104   0.514     4.265   48.452   46.825
LGA    P    63_A      P    63_A     3.727     0    0.312   0.297     4.200   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):     1.913          1.935                  2.787           73.358   66.606

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    1.91    78.571    88.798     3.130

LGA_LOCAL      RMSD:   1.913  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.913  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.913  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.473914 * X  +   0.684898 * Y  +   0.553463 * Z  +  -9.537782
  Y_new =   0.623282 * X  +   0.183086 * Y  +  -0.760263 * Z  +   2.323708
  Z_new =  -0.622033 * X  +   0.705262 * Y  +  -0.340118 * Z  +  -5.346094 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.920703  0.671337  2.020149   [DEG:   52.7524   38.4648  115.7460 ]
ZXZ:  0.629264  1.917838 -0.722775   [DEG:   36.0542  109.8840  -41.4119 ]
 
# END of job
