
#######################################################
#                                                     #
#                        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        1.85     1.85
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.85     1.85
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    27       3_A - 29_A        1.00     2.49
  LONGEST_CONTINUOUS_SEGMENT:    27       7_A - 33_A        0.98     2.42
  LCS_AVERAGE:     33.86

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     19   63   63      3   17   34   44   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H     2_A     H     2_A     22   63   63      7   17   36   51   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I     3_A     I     3_A     27   63   63      7   25   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     4_A     D     4_A     27   63   63      4   22   41   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     27   63   63      7   22   41   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     27   63   63      7   22   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     7_A     K     7_A     27   63   63      7   25   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E     8_A     E     8_A     27   63   63      7   25   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     27   63   63      7   25   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    10_A     N    10_A     27   63   63      8   25   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    11_A     R    11_A     27   63   63      6   25   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     27   63   63      6   25   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     27   63   63      8   25   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     27   63   63      7   25   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     27   63   63      3   17   40   54   57   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     27   63   63      7   25   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    17_A     S    17_A     27   63   63      4   22   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    18_A     A    18_A     27   63   63      3   24   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    19_A     H    19_A     27   63   63      6   25   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    20_A     D    20_A     27   63   63      6   25   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     27   63   63      9   25   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     27   63   63      9   25   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     27   63   63      9   25   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     27   63   63      5   24   40   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     27   63   63      5   24   40   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     27   63   63      5   24   41   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     27   63   63      5   24   40   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     27   63   63      7   24   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     27   63   63      7   24   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     27   63   63      7   24   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     27   63   63      7   16   40   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     27   63   63      6   23   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     27   63   63      7   25   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    34_A     N    34_A     21   63   63      3   18   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     21   63   63      6   23   41   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     21   63   63      9   25   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     21   63   63      9   25   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    38_A     P    38_A     21   63   63      9   25   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     21   63   63      7   25   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A      8   63   63      3    5   10   28   46   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A      8   63   63      3    5   10   19   28   44   53   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A      4   63   63      3    3   10   18   28   43   53   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     12   63   63      3    8   34   53   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    44_A     E    44_A     12   63   63      4   14   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A     12   63   63      6   24   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    46_A     S    46_A     12   63   63      4   19   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     16   63   63      9   25   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     16   63   63      3   23   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     16   63   63      4   22   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     16   63   63      7   25   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    51_A     A    51_A     16   63   63      4   22   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    52_A     N    52_A     16   63   63      8   25   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     16   63   63      9   25   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     16   63   63      6   25   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     16   63   63      7   19   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     16   63   63      4   13   23   44   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     16   63   63      7   19   41   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     16   63   63      7   19   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    59_A     G    59_A     16   63   63      7   23   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    60_A     H    60_A     16   63   63      9   25   42   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     16   63   63      3   22   41   54   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     16   63   63      6   24   39   52   57   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     16   63   63      3    9   10   28   47   54   59   60   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  77.95  (  33.86  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      9     25     42     54     57     58     60     61     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  14.29  39.68  66.67  85.71  90.48  92.06  95.24  96.83 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.41   0.76   1.09   1.28   1.35   1.40   1.54   1.76   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85
GDT RMS_ALL_AT   2.14   1.97   1.88   1.88   1.87   1.87   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85

# Checking swapping
#   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:  Y    50_A      Y    50_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     1_A      A     1_A     3.105     0    0.051   0.083     3.949   51.905   56.095
LGA    H     2_A      H     2_A     2.212     0    0.067   1.195     5.226   71.190   57.381
LGA    I     3_A      I     3_A     0.297     0    0.660   1.580     3.159   78.214   69.702
LGA    D     4_A      D     4_A     1.458     0    0.170   0.968     3.227   77.143   71.131
LGA    C     5_A      C     5_A     1.464     0    0.091   0.125     1.860   81.429   78.571
LGA    D     6_A      D     6_A     1.235     0    0.064   0.649     3.070   85.952   78.690
LGA    K     7_A      K     7_A     0.489     0    0.056   0.998     3.109   95.238   84.233
LGA    E     8_A      E     8_A     0.369     0    0.058   0.362     0.803   95.238   95.767
LGA    C     9_A      C     9_A     0.773     0    0.057   0.077     1.376   90.476   87.460
LGA    N    10_A      N    10_A     0.443     0    0.079   0.647     2.342   95.238   88.512
LGA    R    11_A      R    11_A     0.895     0    0.026   1.212     8.636   90.476   52.468
LGA    R    12_A      R    12_A     0.785     0    0.037   1.248     5.296   90.476   75.455
LGA    C    13_A      C    13_A     0.714     0    0.226   0.245     2.868   88.214   81.905
LGA    S    14_A      S    14_A     0.956     0    0.043   0.662     2.943   82.024   79.286
LGA    K    15_A      K    15_A     2.636     0    0.140   1.017     4.544   64.881   57.884
LGA    A    16_A      A    16_A     1.584     0    0.672   0.619     4.035   61.905   67.619
LGA    S    17_A      S    17_A     1.333     0    0.084   0.498     3.639   81.429   72.302
LGA    A    18_A      A    18_A     1.590     0    0.051   0.051     1.963   75.000   74.571
LGA    H    19_A      H    19_A     1.339     0    0.100   1.352     5.988   75.119   55.619
LGA    D    20_A      D    20_A     1.442     0    0.118   0.886     4.599   81.429   65.417
LGA    R    21_A      R    21_A     1.527     0    0.077   1.056     3.173   77.143   71.082
LGA    C    22_A      C    22_A     1.134     0    0.107   0.166     1.345   81.429   84.444
LGA    L    23_A      L    23_A     0.997     0    0.127   0.202     1.237   88.214   84.821
LGA    K    24_A      K    24_A     2.219     0    0.101   0.920     3.454   66.786   65.926
LGA    Y    25_A      Y    25_A     2.327     0    0.011   0.717     3.533   64.762   63.095
LGA    C    26_A      C    26_A     1.819     0    0.064   0.206     2.071   70.833   71.587
LGA    G    27_A      G    27_A     1.864     0    0.168   0.168     2.705   66.905   66.905
LGA    I    28_A      I    28_A     1.558     0    0.050   0.688     4.149   79.286   69.583
LGA    C    29_A      C    29_A     1.606     0    0.088   0.175     2.176   77.143   74.365
LGA    C    30_A      C    30_A     1.609     0    0.028   0.086     1.979   77.143   75.714
LGA    E    31_A      E    31_A     1.629     0    0.015   0.239     3.372   75.000   66.085
LGA    K    32_A      K    32_A     1.210     0    0.018   1.232     6.851   81.429   60.265
LGA    C    33_A      C    33_A     0.877     0    0.593   0.522     3.781   74.286   75.397
LGA    N    34_A      N    34_A     1.384     0    0.198   0.291     3.835   83.690   68.036
LGA    C    35_A      C    35_A     1.487     0    0.048   0.880     1.938   81.429   78.571
LGA    V    36_A      V    36_A     0.906     0    0.155   0.191     1.120   85.952   86.599
LGA    P    37_A      P    37_A     0.886     0    0.028   0.115     0.985   90.476   90.476
LGA    P    38_A      P    38_A     1.020     0    0.038   0.103     1.313   88.214   85.306
LGA    G    39_A      G    39_A     1.260     0    0.192   0.192     2.264   75.119   75.119
LGA    T    40_A      T    40_A     3.922     0    0.584   0.529     5.687   41.667   40.748
LGA    Y    41_A      Y    41_A     4.923     0    0.211   1.111    10.012   35.714   17.222
LGA    G    42_A      G    42_A     4.873     0    0.587   0.587     5.456   30.238   30.238
LGA    N    43_A      N    43_A     1.917     0    0.348   0.335     2.522   68.929   80.893
LGA    E    44_A      E    44_A     1.753     0    0.135   0.976     2.840   72.976   67.619
LGA    D    45_A      D    45_A     0.489     0    0.279   0.769     3.567   92.857   79.345
LGA    S    46_A      S    46_A     1.182     0    0.147   0.242     2.015   85.952   80.238
LGA    C    47_A      C    47_A     1.153     0    0.037   0.538     2.759   81.548   76.032
LGA    P    48_A      P    48_A     1.551     0    0.065   0.350     1.787   77.143   77.755
LGA    C    49_A      C    49_A     1.779     0    0.029   0.261     3.022   72.976   67.778
LGA    Y    50_A      Y    50_A     1.310     0    0.023   1.142     7.871   79.286   53.413
LGA    A    51_A      A    51_A     1.578     0    0.125   0.142     2.116   72.976   72.952
LGA    N    52_A      N    52_A     1.004     0    0.181   0.374     1.747   85.952   82.619
LGA    L    53_A      L    53_A     1.041     0    0.050   1.020     3.279   85.952   79.762
LGA    K    54_A      K    54_A     0.890     0    0.077   1.203     4.822   90.476   74.709
LGA    N    55_A      N    55_A     1.307     0    0.036   0.142     1.898   79.405   78.274
LGA    S    56_A      S    56_A     2.838     0    0.173   0.665     5.679   55.595   48.968
LGA    K    57_A      K    57_A     1.667     0    0.145   0.556     4.100   72.857   67.196
LGA    G    58_A      G    58_A     1.414     0    0.080   0.080     1.415   81.429   81.429
LGA    G    59_A      G    59_A     0.617     0    0.030   0.030     0.960   92.857   92.857
LGA    H    60_A      H    60_A     1.150     0    0.167   1.132     7.517   83.690   53.857
LGA    K    61_A      K    61_A     1.894     0    0.068   0.774     2.334   68.810   75.979
LGA    C    62_A      C    62_A     2.392     0    0.439   0.905     3.940   55.714   57.619
LGA    P    63_A      P    63_A     4.461     0    0.261   0.408     6.640   54.762   39.388

# 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):     1.845          1.874                  2.636           76.476   70.481

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     61    1.76    80.556    90.198     3.279

LGA_LOCAL      RMSD:   1.760  Number of atoms:   61  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.851  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.845  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.028367 * X  +  -0.959995 * Y  +  -0.278577 * Z  +   4.070988
  Y_new =   0.431193 * X  +  -0.239675 * Y  +   0.869844 * Z  +   1.270695
  Z_new =  -0.901814 * X  +  -0.144795 * Y  +   0.407145 * Z  +  -0.526318 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.505105  1.123948 -0.341686   [DEG:   86.2362   64.3975  -19.5772 ]
ZXZ: -2.831653  1.151471 -1.729997   [DEG: -162.2418   65.9744  -99.1216 ]
 
# END of job
