
#######################################################
#                                                     #
#                        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   83 (  684),  selected   72 , name one
# Molecule2: number of CA atoms   72 (  603),  selected   72 , 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:    72       2_A - 81_A        4.96     4.96
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49      33_A - 81_A        0.43    12.03
  LCS_AVERAGE:     56.52

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49      33_A - 81_A        0.43    12.03
  LCS_AVERAGE:     55.71

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   72
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     T     2_A     T     2_A      3   23   72      0    3    3    3    3    4    7    9   20   34   39   50   58   61   68   71   72   72   72   72 
LCS_GDT     S     3_A     S     3_A     22   23   72     17   22   23   24   29   32   34   37   42   47   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     L     4_A     L     4_A     22   23   72     21   22   23   24   29   32   34   37   42   47   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     I     5_A     I     5_A     22   23   72     21   22   23   24   29   32   34   37   42   47   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     E     6_A     E     6_A     22   23   72     21   22   23   24   29   32   34   37   42   47   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     E     7_A     E     7_A     22   23   72     21   22   23   24   29   32   34   37   42   47   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     L     8_A     L     8_A     22   23   72     21   22   23   24   29   32   34   37   42   47   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     I     9_A     I     9_A     22   23   72     21   22   23   24   29   32   34   37   42   47   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     R    10_A     R    10_A     22   23   72     21   22   23   24   29   32   34   37   42   47   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     R    11_A     R    11_A     22   23   72     21   22   23   24   29   32   34   37   42   47   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     S    12_A     S    12_A     22   23   72     21   22   23   24   29   32   34   37   42   47   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     E    13_A     E    13_A     22   23   72     21   22   23   24   29   32   34   37   42   47   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     E    14_A     E    14_A     22   23   72     21   22   23   24   29   32   34   37   42   47   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     Q    15_A     Q    15_A     22   23   72     21   22   23   24   29   32   34   37   42   47   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     Q    16_A     Q    16_A     22   23   72     21   22   23   24   29   32   34   37   42   47   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     R    17_A     R    17_A     22   23   72     21   22   23   24   29   32   34   37   42   47   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     R    18_A     R    18_A     22   23   72     21   22   23   24   29   32   34   37   42   47   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     N    19_A     N    19_A     22   23   72     21   22   23   24   29   32   34   37   42   47   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     E    20_A     E    20_A     22   23   72     21   22   23   24   29   32   34   37   42   47   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     E    21_A     E    21_A     22   23   72     21   22   23   24   29   32   34   37   42   47   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     A    22_A     A    22_A     22   23   72     21   22   23   24   29   32   34   37   42   47   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     L    23_A     L    23_A     22   23   72     21   22   23   23   29   32   34   37   41   46   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     R    24_A     R    24_A     22   23   72     21   22   23   24   29   32   34   37   42   47   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     Q    33_A     Q    33_A     49   49   72     41   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     L    34_A     L    34_A     49   49   72     41   48   49   49   49   49   49   49   49   49   51   55   61   67   68   71   72   72   72   72 
LCS_GDT     L    35_A     L    35_A     49   49   72     41   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     S    36_A     S    36_A     49   49   72     41   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     G    37_A     G    37_A     49   49   72     40   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     I    38_A     I    38_A     49   49   72     41   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     V    39_A     V    39_A     49   49   72     41   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     Q    40_A     Q    40_A     49   49   72     40   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     Q    41_A     Q    41_A     49   49   72     41   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     Q    42_A     Q    42_A     49   49   72     41   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     N    43_A     N    43_A     49   49   72     41   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     N    44_A     N    44_A     49   49   72     41   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     L    45_A     L    45_A     49   49   72     41   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     L    46_A     L    46_A     49   49   72     41   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     R    47_A     R    47_A     49   49   72     41   48   49   49   49   49   49   49   49   49   53   60   64   67   68   71   72   72   72   72 
LCS_GDT     A    48_A     A    48_A     49   49   72     41   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     I    49_A     I    49_A     49   49   72     41   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     E    50_A     E    50_A     49   49   72     41   48   49   49   49   49   49   49   49   49   53   60   64   67   68   71   72   72   72   72 
LCS_GDT     A    51_A     A    51_A     49   49   72     41   48   49   49   49   49   49   49   49   49   53   58   64   67   68   71   72   72   72   72 
LCS_GDT     Q    52_A     Q    52_A     49   49   72     41   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     Q    53_A     Q    53_A     49   49   72     40   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     H    54_A     H    54_A     49   49   72     41   48   49   49   49   49   49   49   49   49   53   58   61   67   68   71   72   72   72   72 
LCS_GDT     L    55_A     L    55_A     49   49   72     36   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     L    56_A     L    56_A     49   49   72     34   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     Q    57_A     Q    57_A     49   49   72     41   48   49   49   49   49   49   49   49   49   53   60   64   67   68   71   72   72   72   72 
LCS_GDT     L    58_A     L    58_A     49   49   72     41   48   49   49   49   49   49   49   49   49   53   60   64   67   68   71   72   72   72   72 
LCS_GDT     T    59_A     T    59_A     49   49   72     41   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     V    60_A     V    60_A     49   49   72     41   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     W    61_A     W    61_A     49   49   72     41   48   49   49   49   49   49   49   49   49   53   59   64   67   68   71   72   72   72   72 
LCS_GDT     G    62_A     G    62_A     49   49   72     41   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     I    63_A     I    63_A     49   49   72     41   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     K    64_A     K    64_A     49   49   72     41   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     Q    65_A     Q    65_A     49   49   72     41   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     L    66_A     L    66_A     49   49   72     41   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     Q    67_A     Q    67_A     49   49   72     41   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     A    68_A     A    68_A     49   49   72     41   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     R    69_A     R    69_A     49   49   72     41   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     I    70_A     I    70_A     49   49   72     41   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     L    71_A     L    71_A     49   49   72     41   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     A    72_A     A    72_A     49   49   72     41   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     V    73_A     V    73_A     49   49   72     41   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     E    74_A     E    74_A     49   49   72     41   48   49   49   49   49   49   49   49   49   49   53   63   67   68   71   72   72   72   72 
LCS_GDT     R    75_A     R    75_A     49   49   72     41   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     Y    76_A     Y    76_A     49   49   72     41   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     L    77_A     L    77_A     49   49   72     41   48   49   49   49   49   49   49   49   49   49   53   60   67   68   71   72   72   72   72 
LCS_GDT     R    78_A     R    78_A     49   49   72     41   48   49   49   49   49   49   49   49   49   49   53   59   63   68   71   72   72   72   72 
LCS_GDT     D    79_A     D    79_A     49   49   72     34   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     Q    80_A     Q    80_A     49   49   72     32   48   49   49   49   49   49   49   49   49   55   60   64   67   68   71   72   72   72   72 
LCS_GDT     Q    81_A     Q    81_A     49   49   72      3   42   49   49   49   49   49   49   49   49   49   49   59   59   65   70   72   72   72   72 
LCS_AVERAGE  LCS_A:  70.74  (  55.71   56.52  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     41     48     49     49     49     49     49     49     49     49     55     60     64     67     68     71     72     72     72     72 
GDT PERCENT_AT  56.94  66.67  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  76.39  83.33  88.89  93.06  94.44  98.61 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.29   0.38   0.43   0.43   0.43   0.43   0.43   0.43   0.43   0.43   4.01   4.27   4.44   4.60   4.66   4.88   4.96   4.96   4.96   4.96
GDT RMS_ALL_AT  12.04  12.03  12.03  12.03  12.03  12.03  12.03  12.03  12.03  12.03   5.04   5.03   5.03   5.07   5.07   4.97   4.96   4.96   4.96   4.96

# Checking swapping
#   possible swapping detected:  E     7_A      E     7_A
#   possible swapping detected:  E    13_A      E    13_A
#   possible swapping detected:  E    50_A      E    50_A
#   possible swapping detected:  E    74_A      E    74_A
#   possible swapping detected:  Y    76_A      Y    76_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    T     2_A      T     2_A    25.370     0    0.098   1.041    26.250    0.000    0.000
LGA    S     3_A      S     3_A    25.954     0    0.657   0.771    25.979    0.000    0.000
LGA    L     4_A      L     4_A    24.077     0    0.045   0.082    25.319    0.000    0.000
LGA    I     5_A      I     5_A    17.598     0    0.036   0.053    19.789    0.000    0.000
LGA    E     6_A      E     6_A    21.904     0    0.047   1.048    26.518    0.000    0.000
LGA    E     7_A      E     7_A    25.097     0    0.016   0.133    30.913    0.000    0.000
LGA    L     8_A      L     8_A    19.258     0    0.047   0.081    21.170    0.000    0.000
LGA    I     9_A      I     9_A    17.290     0    0.064   0.119    19.341    0.000    0.000
LGA    R    10_A      R    10_A    23.688     0    0.056   1.498    34.865    0.000    0.000
LGA    R    11_A      R    11_A    22.463     0    0.008   1.500    28.823    0.000    0.000
LGA    S    12_A      S    12_A    16.205     0    0.043   0.671    18.260    0.000    0.000
LGA    E    13_A      E    13_A    20.404     0    0.032   1.311    24.011    0.000    0.000
LGA    E    14_A      E    14_A    24.273     0    0.011   0.343    29.687    0.000    0.000
LGA    Q    15_A      Q    15_A    18.990     0    0.042   0.066    20.641    0.000    0.000
LGA    Q    16_A      Q    16_A    16.774     0    0.030   0.154    18.852    0.000    0.000
LGA    R    17_A      R    17_A    23.262     0    0.032   1.156    30.987    0.000    0.000
LGA    R    18_A      R    18_A    22.173     0    0.013   1.085    27.901    0.000    0.000
LGA    N    19_A      N    19_A    15.760     0    0.021   0.082    17.882    0.000    0.000
LGA    E    20_A      E    20_A    19.716     0    0.000   1.015    22.606    0.000    0.000
LGA    E    21_A      E    21_A    24.205     0    0.017   0.891    31.289    0.000    0.000
LGA    A    22_A      A    22_A    19.054     0    0.068   0.077    20.647    0.000    0.000
LGA    L    23_A      L    23_A    16.819     0    0.041   0.171    19.070    0.000    0.000
LGA    R    24_A      R    24_A    23.430     0    0.301   1.124    29.387    0.000    0.000
LGA    Q    33_A      Q    33_A     0.109     0    0.088   0.613     3.864   97.619   80.529
LGA    L    34_A      L    34_A     0.402     0    0.045   0.104     1.130  100.000   92.976
LGA    L    35_A      L    35_A     0.238     0    0.010   0.489     2.309  100.000   91.012
LGA    S    36_A      S    36_A     0.508     0    0.033   0.687     2.634   92.857   86.508
LGA    G    37_A      G    37_A     0.548     0    0.050   0.050     0.548   97.619   97.619
LGA    I    38_A      I    38_A     0.188     0    0.041   0.060     0.456  100.000  100.000
LGA    V    39_A      V    39_A     0.479     0    0.021   0.052     0.598   95.238   93.197
LGA    Q    40_A      Q    40_A     0.697     0    0.011   0.931     2.838   90.476   81.111
LGA    Q    41_A      Q    41_A     0.466     0    0.027   0.318     1.207   97.619   93.704
LGA    Q    42_A      Q    42_A     0.341     0    0.069   0.340     1.341  100.000   96.878
LGA    N    43_A      N    43_A     0.386     0    0.022   0.458     1.968  100.000   93.036
LGA    N    44_A      N    44_A     0.299     0    0.020   0.035     0.481  100.000  100.000
LGA    L    45_A      L    45_A     0.121     0    0.019   0.187     0.658  100.000   98.810
LGA    L    46_A      L    46_A     0.207     0    0.054   0.076     0.670  100.000   97.619
LGA    R    47_A      R    47_A     0.173     0    0.034   1.179     4.569  100.000   82.641
LGA    A    48_A      A    48_A     0.090     0    0.040   0.043     0.253  100.000  100.000
LGA    I    49_A      I    49_A     0.240     0    0.043   0.086     0.383  100.000  100.000
LGA    E    50_A      E    50_A     0.250     0    0.067   0.135     0.766  100.000   96.825
LGA    A    51_A      A    51_A     0.229     0    0.016   0.021     0.360  100.000  100.000
LGA    Q    52_A      Q    52_A     0.514     0    0.022   0.289     0.994   92.857   91.534
LGA    Q    53_A      Q    53_A     0.539     0    0.023   0.218     1.310   90.476   89.471
LGA    H    54_A      H    54_A     0.435     0    0.010   1.334     5.675   97.619   68.333
LGA    L    55_A      L    55_A     0.708     0    0.034   1.394     3.923   90.476   78.155
LGA    L    56_A      L    56_A     0.834     0    0.016   1.365     3.294   90.476   82.083
LGA    Q    57_A      Q    57_A     0.503     0    0.028   1.413     5.127   95.238   74.127
LGA    L    58_A      L    58_A     0.218     0    0.033   0.193     0.737  100.000   97.619
LGA    T    59_A      T    59_A     0.432     0    0.042   0.072     0.596  100.000   97.279
LGA    V    60_A      V    60_A     0.360     0    0.010   0.036     0.571  100.000   98.639
LGA    W    61_A      W    61_A     0.250     0    0.080   1.291     8.979  100.000   52.789
LGA    G    62_A      G    62_A     0.104     0    0.048   0.048     0.269  100.000  100.000
LGA    I    63_A      I    63_A     0.217     0    0.026   0.074     0.420  100.000  100.000
LGA    K    64_A      K    64_A     0.314     0    0.039   1.140     6.403  100.000   75.344
LGA    Q    65_A      Q    65_A     0.155     0    0.042   1.376     5.285  100.000   78.360
LGA    L    66_A      L    66_A     0.139     0    0.025   0.062     0.409  100.000  100.000
LGA    Q    67_A      Q    67_A     0.156     0    0.014   0.058     0.307  100.000  100.000
LGA    A    68_A      A    68_A     0.267     0    0.012   0.022     0.324  100.000  100.000
LGA    R    69_A      R    69_A     0.241     0    0.014   0.149     0.728  100.000   99.134
LGA    I    70_A      I    70_A     0.362     0    0.064   1.368     4.101  100.000   83.155
LGA    L    71_A      L    71_A     0.345     0    0.022   0.049     0.537  100.000   98.810
LGA    A    72_A      A    72_A     0.144     0    0.021   0.035     0.191  100.000  100.000
LGA    V    73_A      V    73_A     0.101     0    0.017   0.061     0.325  100.000  100.000
LGA    E    74_A      E    74_A     0.190     0    0.016   0.089     0.514  100.000   98.942
LGA    R    75_A      R    75_A     0.333     0    0.079   0.232     1.531  100.000   93.203
LGA    Y    76_A      Y    76_A     0.245     0    0.019   0.155     0.747  100.000   96.825
LGA    L    77_A      L    77_A     0.330     0    0.038   0.093     0.569   97.619   97.619
LGA    R    78_A      R    78_A     0.383     0    0.048   1.166     4.311   97.619   76.104
LGA    D    79_A      D    79_A     0.587     0    0.029   0.110     0.796   92.857   91.667
LGA    Q    80_A      Q    80_A     0.732     0    0.033   0.117     1.309   85.952   87.460
LGA    Q    81_A      Q    81_A     1.430     0    0.455   0.506     3.121   71.429   76.032

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       72     288    288  100.00     603    603  100.00                72
SUMMARY(RMSD_GDC):     4.961          4.480                  7.302           66.306   62.016

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   83   72    4.0     49    0.43    75.347    69.180     9.261

LGA_LOCAL      RMSD:   0.429  Number of atoms:   49  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  12.031  Number of assigned atoms:   72 
Std_ASGN_ATOMS RMSD:   4.961  Standard rmsd on all 72 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.298558 * X  +  -0.905813 * Y  +  -0.300609 * Z  +  -1.790491
  Y_new =   0.594678 * X  +  -0.422917 * Y  +   0.683740 * Z  +   5.780000
  Z_new =  -0.746473 * X  +   0.025370 * Y  +   0.664932 * Z  +  68.924149 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.036083  0.842746  0.038136   [DEG:  116.6589   48.2858    2.1851 ]
ZXZ: -2.727376  0.843394 -1.536822   [DEG: -156.2671   48.3229  -88.0534 ]
 
# END of job
