
#######################################################
#                                                     #
#                        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        0.71     0.71
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.71     0.71
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.71     0.71
  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   19   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     36   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     41   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     30   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     29   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     36   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     14   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     42   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     36   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     36   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     36   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     42   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     43   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     40   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     44   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   54   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    4    7   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    0.32   0.46   0.60   0.63   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71
GDT RMS_ALL_AT   0.79   0.77   0.73   0.72   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71

# Checking swapping
#   possible swapping detected:  E     4_A      E     4_A
#   possible swapping detected:  E     5_A      E     5_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     1.791     0    0.070   0.151     2.105   75.119   73.016
LGA    P     3_A      P     3_A     0.376     0    0.019   0.039     0.697   95.238   94.558
LGA    E     4_A      E     4_A     1.220     0    0.029   0.721     3.891   83.690   69.206
LGA    E     5_A      E     5_A     1.241     0    0.053   0.599     4.783   85.952   68.095
LGA    Q     6_A      Q     6_A     0.433     0    0.018   0.385     1.113   97.619   93.704
LGA    K     7_A      K     7_A     0.773     0    0.028   0.621     3.494   92.857   76.032
LGA    Q     8_A      Q     8_A     0.981     0    0.057   0.763     4.611   90.476   72.169
LGA    M     9_A      M     9_A     0.652     0    0.022   0.678     2.051   92.857   86.190
LGA    L    10_A      L    10_A     0.575     0    0.038   0.080     1.372   92.857   88.274
LGA    G    11_A      G    11_A     0.695     0    0.021   0.021     0.698   90.476   90.476
LGA    E    12_A      E    12_A     0.385     0    0.025   0.797     3.389   97.619   86.296
LGA    A    13_A      A    13_A     0.254     0    0.022   0.025     0.480  100.000  100.000
LGA    I    14_A      I    14_A     0.227     0    0.017   0.055     0.271  100.000  100.000
LGA    Y    15_A      Y    15_A     0.196     0    0.024   0.241     0.483  100.000  100.000
LGA    P    16_A      P    16_A     0.551     0    0.012   0.312     1.193   92.857   91.905
LGA    K    17_A      K    17_A     0.255     0    0.014   0.831     3.258  100.000   90.370
LGA    V    18_A      V    18_A     0.288     0    0.010   0.065     0.379  100.000  100.000
LGA    A    19_A      A    19_A     0.435     0    0.020   0.019     0.832   95.238   96.190
LGA    A    20_A      A    20_A     0.668     0    0.131   0.146     0.774   90.476   90.476
LGA    S    21_A      S    21_A     0.953     0    0.124   0.647     2.228   85.952   83.175
LGA    Q    22_A      Q    22_A     1.013     0    0.074   0.669     1.777   88.214   86.508
LGA    P    23_A      P    23_A     0.300     0    0.045   0.049     0.842   97.619   94.558
LGA    E    24_A      E    24_A     0.332     0    0.032   0.647     2.355   97.619   91.852
LGA    L    25_A      L    25_A     0.409     0    0.027   0.048     0.637  100.000   95.238
LGA    A    26_A      A    26_A     0.272     0    0.018   0.017     0.336  100.000  100.000
LGA    G    27_A      G    27_A     0.427     0    0.051   0.051     0.620   97.619   97.619
LGA    K    28_A      K    28_A     0.331     0    0.006   1.128     5.656  100.000   74.815
LGA    L    29_A      L    29_A     0.122     0    0.030   0.085     0.518  100.000   98.810
LGA    T    30_A      T    30_A     0.216     0    0.021   0.072     0.430  100.000  100.000
LGA    G    31_A      G    31_A     0.528     0    0.070   0.070     0.528   97.619   97.619
LGA    M    32_A      M    32_A     0.160     0    0.037   0.155     0.909  100.000   98.810
LGA    I    33_A      I    33_A     0.316     0    0.067   0.080     0.407  100.000  100.000
LGA    L    34_A      L    34_A     0.302     0    0.069   0.116     0.825   95.238   97.619
LGA    E    35_A      E    35_A     0.543     0    0.079   1.040     4.869   90.595   67.989
LGA    L    36_A      L    36_A     0.840     0    0.035   0.097     0.897   90.476   90.476
LGA    P    37_A      P    37_A     1.135     0    0.079   0.072     1.367   83.690   82.721
LGA    V    38_A      V    38_A     1.004     0    0.019   0.099     1.540   85.952   82.789
LGA    T    39_A      T    39_A     1.005     0    0.025   0.964     3.223   88.214   77.347
LGA    E    40_A      E    40_A     0.602     0    0.041   0.852     3.761   92.857   79.735
LGA    L    41_A      L    41_A     0.511     0    0.025   0.126     0.949   95.238   94.048
LGA    L    42_A      L    42_A     0.603     0    0.041   0.056     1.049   95.238   91.726
LGA    H    43_A      H    43_A     0.283     0    0.028   0.583     2.101  100.000   87.381
LGA    L    44_A      L    44_A     0.204     0    0.050   0.108     0.743   97.619   96.429
LGA    L    45_A      L    45_A     0.685     0    0.070   0.119     0.873   92.857   91.667
LGA    E    46_A      E    46_A     0.604     0    0.085   0.875     2.802   90.476   75.661
LGA    E    47_A      E    47_A     0.573     0    0.046   1.078     3.548   90.476   76.720
LGA    S    48_A      S    48_A     0.522     0    0.047   0.158     1.133   92.857   90.556
LGA    E    49_A      E    49_A     0.524     0    0.099   0.761     1.791   95.238   86.667
LGA    A    50_A      A    50_A     0.357     0    0.015   0.017     0.410  100.000  100.000
LGA    L    51_A      L    51_A     0.152     0    0.025   0.111     0.614  100.000   98.810
LGA    D    52_A      D    52_A     0.404     0    0.016   0.452     1.751  100.000   89.702
LGA    A    53_A      A    53_A     0.545     0    0.058   0.067     0.662   90.476   90.476
LGA    K    54_A      K    54_A     0.385     0    0.026   0.595     1.870  100.000   91.799
LGA    V    55_A      V    55_A     0.192     0    0.032   0.052     0.261  100.000  100.000
LGA    N    56_A      N    56_A     0.248     0    0.034   0.158     0.842  100.000   96.429
LGA    E    57_A      E    57_A     0.355     0    0.028   0.134     0.821  100.000   96.825
LGA    A    58_A      A    58_A     0.284     0    0.020   0.025     0.314  100.000  100.000
LGA    L    59_A      L    59_A     0.373     0    0.028   0.255     0.704  100.000   97.619
LGA    E    60_A      E    60_A     0.411     0    0.077   1.078     4.415  100.000   82.698
LGA    V    61_A      V    61_A     0.351     0    0.019   0.094     0.450  100.000  100.000
LGA    L    62_A      L    62_A     0.477     0    0.019   0.731     2.151  100.000   90.000
LGA    K    63_A      K    63_A     0.686     0    0.014   0.225     1.782   90.476   85.503
LGA    E    64_A      E    64_A     0.513     0    0.016   0.946     2.840   90.476   78.413
LGA    Y    65_A      Y    65_A     0.316     0    0.032   0.408     1.699  100.000   92.381
LGA    Q    66_A      Q    66_A     0.880     0    0.063   0.272     3.490   88.333   73.704
LGA    Q    67_A      Q    67_A     1.586     0    0.264   0.497     4.180   77.143   63.915
LGA    N    68_A      N    68_A     2.664     0    0.643   1.100     6.267   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):     0.713          0.776                  1.401           93.982   88.332

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   67   67    4.0     67    0.71    97.388    98.966     8.243

LGA_LOCAL      RMSD:   0.713  Number of atoms:   67  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.713  Number of assigned atoms:   67 
Std_ASGN_ATOMS RMSD:   0.713  Standard rmsd on all 67 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.116379 * X  +   0.959209 * Y  +   0.257632 * Z  +  46.828991
  Y_new =  -0.611243 * X  +   0.135283 * Y  +  -0.779795 * Z  +  12.453424
  Z_new =  -0.782840 * X  +  -0.248228 * Y  +   0.570565 * Z  +  -7.692019 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.758942  0.899217 -0.410357   [DEG: -100.7800   51.5213  -23.5117 ]
ZXZ:  0.319094  0.963602 -1.877854   [DEG:   18.2827   55.2103 -107.5931 ]
 
# END of job
