
#######################################################
#                                                     #
#                        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   67 (  519),  selected   67 , name one
# Molecule2: number of CA atoms   67 (  519),  selected   67 , 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:    67       2_A - 68_A        0.72     0.72
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.72     0.72
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.72     0.72
  LCS_AVERAGE:    100.00

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   67
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     S     2_A     S     2_A     67   67   67     11   18   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P     3_A     P     3_A     67   67   67     40   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E     4_A     E     4_A     67   67   67     12   60   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E     5_A     E     5_A     67   67   67     12   60   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q     6_A     Q     6_A     67   67   67     43   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K     7_A     K     7_A     67   67   67     22   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q     8_A     Q     8_A     67   67   67     14   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     M     9_A     M     9_A     67   67   67     30   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    10_A     L    10_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    11_A     G    11_A     67   67   67     43   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    12_A     E    12_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    13_A     A    13_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    14_A     I    14_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Y    15_A     Y    15_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    16_A     P    16_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    17_A     K    17_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    18_A     V    18_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    19_A     A    19_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    20_A     A    20_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    21_A     S    21_A     67   67   67     19   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    22_A     Q    22_A     67   67   67     11   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    23_A     P    23_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    24_A     E    24_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    25_A     L    25_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    26_A     A    26_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    27_A     G    27_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    28_A     K    28_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    29_A     L    29_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     T    30_A     T    30_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    31_A     G    31_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     M    32_A     M    32_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    33_A     I    33_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    34_A     L    34_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    35_A     E    35_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    36_A     L    36_A     67   67   67     44   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    37_A     P    37_A     67   67   67     30   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    38_A     V    38_A     67   67   67     30   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     T    39_A     T    39_A     67   67   67     30   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    40_A     E    40_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    41_A     L    41_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    42_A     L    42_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     H    43_A     H    43_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    44_A     L    44_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    45_A     L    45_A     67   67   67     44   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    46_A     E    46_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    47_A     E    47_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    48_A     S    48_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    49_A     E    49_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    50_A     A    50_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    51_A     L    51_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     D    52_A     D    52_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    53_A     A    53_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    54_A     K    54_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    55_A     V    55_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     N    56_A     N    56_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    57_A     E    57_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    58_A     A    58_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    59_A     L    59_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    60_A     E    60_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    61_A     V    61_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    62_A     L    62_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    63_A     K    63_A     67   67   67     36   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    64_A     E    64_A     67   67   67     41   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Y    65_A     Y    65_A     67   67   67     46   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    66_A     Q    66_A     67   67   67     45   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    67_A     Q    67_A     67   67   67     16   49   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     N    68_A     N    68_A     67   67   67      3    5    6   12   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_AVERAGE  LCS_A: 100.00  ( 100.00  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     46     61     65     66     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67 
GDT PERCENT_AT  68.66  91.04  97.01  98.51 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.31   0.46   0.60   0.63   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72
GDT RMS_ALL_AT   0.79   0.78   0.73   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72

# Checking swapping
#   possible swapping detected:  E     4_A      E     4_A
#   possible swapping detected:  E    12_A      E    12_A
#   possible swapping detected:  Y    15_A      Y    15_A
#   possible swapping detected:  E    40_A      E    40_A
#   possible swapping detected:  E    47_A      E    47_A
#   possible swapping detected:  E    57_A      E    57_A
#   possible swapping detected:  E    60_A      E    60_A
#   possible swapping detected:  Y    65_A      Y    65_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     2_A      S     2_A     1.830     0    0.025   0.048     2.239   75.119   71.667
LGA    P     3_A      P     3_A     0.371     0    0.035   0.058     0.713   95.238   93.197
LGA    E     4_A      E     4_A     1.238     0    0.033   0.717     3.832   83.690   69.206
LGA    E     5_A      E     5_A     1.265     0    0.039   0.816     4.779   85.952   68.889
LGA    Q     6_A      Q     6_A     0.426     0    0.011   0.398     1.118   97.619   95.820
LGA    K     7_A      K     7_A     0.791     0    0.030   0.626     3.505   92.857   75.291
LGA    Q     8_A      Q     8_A     1.022     0    0.062   0.763     4.643   88.214   71.164
LGA    M     9_A      M     9_A     0.666     0    0.045   0.670     2.072   92.857   86.190
LGA    L    10_A      L    10_A     0.590     0    0.049   0.090     1.373   92.857   88.274
LGA    G    11_A      G    11_A     0.712     0    0.047   0.047     0.712   90.476   90.476
LGA    E    12_A      E    12_A     0.413     0    0.039   0.777     3.348   97.619   86.296
LGA    A    13_A      A    13_A     0.257     0    0.023   0.029     0.498  100.000  100.000
LGA    I    14_A      I    14_A     0.207     0    0.032   0.071     0.256  100.000  100.000
LGA    Y    15_A      Y    15_A     0.226     0    0.022   0.227     0.466  100.000  100.000
LGA    P    16_A      P    16_A     0.569     0    0.014   0.307     1.201   92.857   91.905
LGA    K    17_A      K    17_A     0.234     0    0.049   0.857     3.279   97.619   89.312
LGA    V    18_A      V    18_A     0.273     0    0.016   0.080     0.400  100.000  100.000
LGA    A    19_A      A    19_A     0.455     0    0.039   0.037     0.969   95.238   96.190
LGA    A    20_A      A    20_A     0.624     0    0.106   0.126     0.788   90.476   90.476
LGA    S    21_A      S    21_A     0.880     0    0.120   0.654     2.254   88.214   84.683
LGA    Q    22_A      Q    22_A     0.956     0    0.061   0.680     1.740   92.857   87.566
LGA    P    23_A      P    23_A     0.316     0    0.030   0.036     0.840   97.619   94.558
LGA    E    24_A      E    24_A     0.348     0    0.046   0.636     2.316   97.619   91.852
LGA    L    25_A      L    25_A     0.390     0    0.074   0.096     0.610  100.000   95.238
LGA    A    26_A      A    26_A     0.205     0    0.027   0.025     0.317  100.000  100.000
LGA    G    27_A      G    27_A     0.435     0    0.043   0.043     0.621   97.619   97.619
LGA    K    28_A      K    28_A     0.346     0    0.034   1.144     5.648  100.000   74.815
LGA    L    29_A      L    29_A     0.113     0    0.041   0.091     0.518  100.000   98.810
LGA    T    30_A      T    30_A     0.241     0    0.041   0.126     0.531   97.619   98.639
LGA    G    31_A      G    31_A     0.563     0    0.057   0.057     0.563   97.619   97.619
LGA    M    32_A      M    32_A     0.150     0    0.017   0.162     0.968  100.000   97.619
LGA    I    33_A      I    33_A     0.299     0    0.049   0.077     0.424  100.000  100.000
LGA    L    34_A      L    34_A     0.314     0    0.052   0.112     0.751   95.238   97.619
LGA    E    35_A      E    35_A     0.557     0    0.054   1.034     4.767   90.595   67.989
LGA    L    36_A      L    36_A     0.818     0    0.038   0.093     0.863   90.476   90.476
LGA    P    37_A      P    37_A     1.148     0    0.092   0.098     1.351   83.690   82.721
LGA    V    38_A      V    38_A     1.029     0    0.050   0.113     1.505   85.952   82.789
LGA    T    39_A      T    39_A     1.018     0    0.034   0.962     3.216   85.952   76.054
LGA    E    40_A      E    40_A     0.567     0    0.066   0.864     3.659   95.238   80.794
LGA    L    41_A      L    41_A     0.494     0    0.060   0.123     0.917   95.238   94.048
LGA    L    42_A      L    42_A     0.620     0    0.028   0.046     1.027   92.857   90.536
LGA    H    43_A      H    43_A     0.293     0    0.021   0.605     2.223  100.000   86.571
LGA    L    44_A      L    44_A     0.199     0    0.074   0.114     0.765   97.619   96.429
LGA    L    45_A      L    45_A     0.687     0    0.032   0.104     0.857   92.857   91.667
LGA    E    46_A      E    46_A     0.610     0    0.071   0.867     2.871   90.476   75.661
LGA    E    47_A      E    47_A     0.543     0    0.042   1.094     3.496   90.476   77.460
LGA    S    48_A      S    48_A     0.508     0    0.022   0.106     1.049   97.619   93.730
LGA    E    49_A      E    49_A     0.515     0    0.098   0.756     1.750   95.238   86.667
LGA    A    50_A      A    50_A     0.320     0    0.031   0.030     0.417  100.000  100.000
LGA    L    51_A      L    51_A     0.148     0    0.022   0.111     0.598  100.000   98.810
LGA    D    52_A      D    52_A     0.407     0    0.020   0.383     1.580  100.000   90.774
LGA    A    53_A      A    53_A     0.526     0    0.074   0.090     0.667   92.857   92.381
LGA    K    54_A      K    54_A     0.355     0    0.041   0.584     1.887  100.000   91.799
LGA    V    55_A      V    55_A     0.196     0    0.017   0.057     0.291  100.000  100.000
LGA    N    56_A      N    56_A     0.236     0    0.034   0.169     0.869  100.000   96.429
LGA    E    57_A      E    57_A     0.330     0    0.017   0.089     0.799  100.000   96.825
LGA    A    58_A      A    58_A     0.264     0    0.064   0.062     0.304  100.000  100.000
LGA    L    59_A      L    59_A     0.378     0    0.051   0.230     0.727   97.619   96.429
LGA    E    60_A      E    60_A     0.428     0    0.120   1.098     4.442  100.000   82.698
LGA    V    61_A      V    61_A     0.339     0    0.032   0.103     0.445  100.000  100.000
LGA    L    62_A      L    62_A     0.493     0    0.059   0.750     2.139   95.238   89.821
LGA    K    63_A      K    63_A     0.716     0    0.013   0.230     1.728   90.476   86.508
LGA    E    64_A      E    64_A     0.543     0    0.029   0.959     2.896   95.238   80.529
LGA    Y    65_A      Y    65_A     0.338     0    0.058   0.445     1.852   97.619   91.587
LGA    Q    66_A      Q    66_A     0.866     0    0.161   0.317     3.484   86.190   72.751
LGA    Q    67_A      Q    67_A     1.579     0    0.211   0.443     4.195   77.143   63.915
LGA    N    68_A      N    68_A     2.684     0    0.123   0.997     6.271   44.881   34.464

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       67     268    268  100.00     519    519  100.00                67
SUMMARY(RMSD_GDC):     0.716          0.770                  1.402           93.950   88.363

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   67   67    4.0     67    0.72    97.388    98.966     8.215

LGA_LOCAL      RMSD:   0.716  Number of atoms:   67  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.716  Number of assigned atoms:   67 
Std_ASGN_ATOMS RMSD:   0.716  Standard rmsd on all 67 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.116136 * X  +   0.959236 * Y  +   0.257641 * Z  +  46.827969
  Y_new =  -0.611342 * X  +   0.135403 * Y  +  -0.779697 * Z  +  12.453138
  Z_new =  -0.782799 * X  +  -0.248058 * Y  +   0.570696 * Z  +  -7.690900 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.758528  0.899151 -0.410023   [DEG: -100.7562   51.5175  -23.4926 ]
ZXZ:  0.319142  0.963443 -1.877672   [DEG:   18.2855   55.2012 -107.5827 ]
 
# END of job
