
#######################################################
#                                                     #
#                        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   97 (  681),  selected   64 , name one
# Molecule2: number of CA atoms   64 (  433),  selected   64 , 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:    64      22_A - 85_A        1.61     1.61
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    64      22_A - 85_A        1.61     1.61
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    62      24_A - 85_A        0.99     1.69
  LCS_AVERAGE:     94.09

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   64
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    22_A     A    22_A      5   64   64      3    5    5    6   25   31   36   40   45   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    23_A     D    23_A      5   64   64      3    5    5    6   25   31   36   40   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    24_A     G    24_A     62   64   64      3    5    5    6   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    25_A     D    25_A     62   64   64      3    5    5   38   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    26_A     G    26_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    27_A     Q    27_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    28_A     G    28_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    29_A     L    29_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Y    30_A     Y    30_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    31_A     A    31_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    32_A     A    32_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     N    33_A     N    33_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     C    34_A     C    34_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    35_A     A    35_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    36_A     A    36_A     62   64   64     32   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     C    37_A     C    37_A     62   64   64     32   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     H    38_A     H    38_A     62   64   64     23   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    39_A     G    39_A     62   64   64     22   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    40_A     A    40_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    41_A     L    41_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    42_A     A    42_A     62   64   64     32   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    43_A     T    43_A     62   64   64     32   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    44_A     S    44_A     62   64   64     32   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     E    45_A     E    45_A     62   64   64     21   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    46_A     K    46_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    47_A     K    47_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    48_A     G    48_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    49_A     T    49_A     62   64   64     21   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    50_A     T    50_A     62   64   64     21   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    51_A     L    51_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    52_A     A    52_A     62   64   64     18   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     R    53_A     R    53_A     62   64   64     17   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    54_A     L    54_A     62   64   64     32   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    55_A     Q    55_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    56_A     S    56_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    57_A     A    57_A     62   64   64     31   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    58_A     V    58_A     62   64   64     31   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    59_A     S    59_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    60_A     A    60_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     N    61_A     N    61_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    62_A     A    62_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    63_A     G    63_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    64_A     G    64_A     62   64   64     17   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     M    65_A     M    65_A     62   64   64     27   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    66_A     G    66_A     62   64   64     31   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     F    67_A     F    67_A     62   64   64     17   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    68_A     L    68_A     62   64   64     17   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    69_A     S    69_A     62   64   64     25   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    70_A     S    70_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    71_A     L    71_A     62   64   64     32   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    72_A     T    72_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    73_A     S    73_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    74_A     A    74_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    75_A     Q    75_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    76_A     L    76_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    77_A     Q    77_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    78_A     A    78_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     I    79_A     I    79_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    80_A     V    80_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    81_A     D    81_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    82_A     V    82_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    83_A     L    83_A     62   64   64     33   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    84_A     A    84_A     62   64   64     32   57   59   59   60   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    85_A     V    85_A     62   64   64      3    4    5    5   43   61   62   62   62   63   64   64   64   64   64   64   64   64   64   64 
LCS_AVERAGE  LCS_A:  98.03  (  94.09  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     33     57     59     59     60     61     62     62     62     63     64     64     64     64     64     64     64     64     64     64 
GDT PERCENT_AT  51.56  89.06  92.19  92.19  93.75  95.31  96.88  96.88  96.88  98.44 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.33   0.55   0.57   0.57   0.67   0.83   0.99   0.99   0.99   1.29   1.61   1.61   1.61   1.61   1.61   1.61   1.61   1.61   1.61   1.61
GDT RMS_ALL_AT   1.75   1.72   1.72   1.72   1.75   1.72   1.69   1.69   1.69   1.64   1.61   1.61   1.61   1.61   1.61   1.61   1.61   1.61   1.61   1.61

# Checking swapping
#   possible swapping detected:  D    23_A      D    23_A
#   possible swapping detected:  D    25_A      D    25_A
#   possible swapping detected:  Y    30_A      Y    30_A
#   possible swapping detected:  E    45_A      E    45_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    22_A      A    22_A     8.637     0    0.027   0.034    10.890    6.310    5.048
LGA    D    23_A      D    23_A     6.835     0    0.019   1.105    11.714   21.548   12.143
LGA    G    24_A      G    24_A     3.734     0    0.691   0.691     3.792   50.357   50.357
LGA    D    25_A      D    25_A     3.000     0    0.211   0.989     5.972   49.762   36.190
LGA    G    26_A      G    26_A     0.539     0    0.058   0.058     0.719   95.238   95.238
LGA    Q    27_A      Q    27_A     0.285     0    0.014   1.491     5.932  100.000   77.884
LGA    G    28_A      G    28_A     0.089     0    0.006   0.006     0.225  100.000  100.000
LGA    L    29_A      L    29_A     0.360     0    0.004   1.250     2.967  100.000   90.238
LGA    Y    30_A      Y    30_A     0.325     0    0.024   0.075     0.373  100.000  100.000
LGA    A    31_A      A    31_A     0.309     0    0.009   0.013     0.446  100.000  100.000
LGA    A    32_A      A    32_A     0.308     0    0.066   0.073     0.516   97.619   98.095
LGA    N    33_A      N    33_A     0.433     0    0.040   0.102     0.667  100.000   97.619
LGA    C    34_A      C    34_A     0.396     0    0.006   0.083     0.477  100.000  100.000
LGA    A    35_A      A    35_A     0.526     0    0.041   0.049     0.858   92.857   94.286
LGA    A    36_A      A    36_A     0.677     0    0.013   0.016     0.903   90.476   90.476
LGA    C    37_A      C    37_A     0.808     0    0.017   0.025     0.991   90.476   90.476
LGA    H    38_A      H    38_A     0.956     0    0.011   0.131     1.275   85.952   85.952
LGA    G    39_A      G    39_A     1.065     0    0.065   0.065     1.075   85.952   85.952
LGA    A    40_A      A    40_A     0.270     0    0.038   0.058     0.435  100.000  100.000
LGA    L    41_A      L    41_A     0.417     0    0.035   0.077     0.775  100.000   96.429
LGA    A    42_A      A    42_A     0.540     0    0.021   0.022     0.578   92.857   92.381
LGA    T    43_A      T    43_A     0.576     0    0.108   0.097     0.780   90.476   90.476
LGA    S    44_A      S    44_A     0.611     0    0.018   0.025     0.717   95.238   93.651
LGA    E    45_A      E    45_A     0.895     0    0.091   0.732     4.877   92.857   66.243
LGA    K    46_A      K    46_A     0.164     0    0.038   0.137     1.661  100.000   89.788
LGA    K    47_A      K    47_A     0.456     0    0.058   0.128     0.946   97.619   93.651
LGA    G    48_A      G    48_A     0.314     0    0.031   0.031     0.757   95.238   95.238
LGA    T    49_A      T    49_A     0.833     0    0.006   0.098     1.168   90.476   89.184
LGA    T    50_A      T    50_A     0.868     0    0.027   0.063     1.434   90.476   86.599
LGA    L    51_A      L    51_A     0.555     0    0.020   0.107     1.041   90.476   90.536
LGA    A    52_A      A    52_A     0.894     0    0.012   0.013     1.069   90.476   88.667
LGA    R    53_A      R    53_A     0.990     0    0.010   1.122     3.058   90.476   79.610
LGA    L    54_A      L    54_A     0.529     0    0.014   0.106     0.647   92.857   95.238
LGA    Q    55_A      Q    55_A     0.332     0    0.013   0.218     0.645  100.000   96.825
LGA    S    56_A      S    56_A     0.525     0    0.027   0.640     2.141   92.857   87.778
LGA    A    57_A      A    57_A     0.669     0    0.024   0.028     0.726   90.476   90.476
LGA    V    58_A      V    58_A     0.656     0    0.025   1.340     3.115   90.476   82.177
LGA    S    59_A      S    59_A     0.500     0    0.039   0.528     2.179   95.238   90.952
LGA    A    60_A      A    60_A     0.515     0    0.012   0.018     0.602   95.238   94.286
LGA    N    61_A      N    61_A     0.403     0    0.024   0.128     0.939  100.000   96.429
LGA    A    62_A      A    62_A     0.306     0    0.034   0.044     0.745   97.619   98.095
LGA    G    63_A      G    63_A     0.550     0    0.034   0.034     0.961   92.857   92.857
LGA    G    64_A      G    64_A     0.727     0    0.073   0.073     1.105   88.214   88.214
LGA    M    65_A      M    65_A     0.641     0    0.044   0.210     1.089   90.476   89.345
LGA    G    66_A      G    66_A     0.554     0    0.015   0.015     0.783   90.476   90.476
LGA    F    67_A      F    67_A     1.191     0    0.023   0.148     2.081   83.690   78.398
LGA    L    68_A      L    68_A     1.201     0    0.092   1.247     3.919   85.952   75.774
LGA    S    69_A      S    69_A     0.738     0    0.039   0.043     0.924   90.476   90.476
LGA    S    70_A      S    70_A     0.637     0    0.020   0.069     1.093   90.595   90.556
LGA    L    71_A      L    71_A     0.609     0    0.032   1.243     3.072   90.476   82.202
LGA    T    72_A      T    72_A     0.531     0    0.011   0.027     0.597   95.238   95.918
LGA    S    73_A      S    73_A     0.464     0    0.015   0.632     2.723  100.000   91.270
LGA    A    74_A      A    74_A     0.142     0    0.021   0.024     0.241  100.000  100.000
LGA    Q    75_A      Q    75_A     0.257     0    0.029   0.138     0.766  100.000   96.825
LGA    L    76_A      L    76_A     0.295     0    0.009   1.242     2.581  100.000   90.238
LGA    Q    77_A      Q    77_A     0.287     0    0.008   0.144     0.458  100.000  100.000
LGA    A    78_A      A    78_A     0.245     0    0.010   0.012     0.337  100.000  100.000
LGA    I    79_A      I    79_A     0.324     0    0.022   0.037     0.382  100.000  100.000
LGA    V    80_A      V    80_A     0.286     0    0.015   1.343     2.782  100.000   88.844
LGA    D    81_A      D    81_A     0.492     0    0.017   0.019     0.864  100.000   95.238
LGA    V    82_A      V    82_A     0.485     0    0.042   1.229     2.948   97.619   86.122
LGA    L    83_A      L    83_A     0.368     0    0.020   1.244     2.807   97.619   89.048
LGA    A    84_A      A    84_A     0.575     0    0.632   0.568     1.405   88.333   90.667
LGA    V    85_A      V    85_A     4.184     0    0.480   0.807     7.404   30.833   23.401

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       64     256    256  100.00     433    433  100.00                64
SUMMARY(RMSD_GDC):     1.613          1.600                  2.024           89.857   86.258

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   97   64    4.0     62    0.99    94.531    96.745     5.681

LGA_LOCAL      RMSD:   0.991  Number of atoms:   62  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.687  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   1.613  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.757615 * X  +  -0.645674 * Y  +   0.095521 * Z  +  25.909439
  Y_new =  -0.526353 * X  +  -0.690921 * Y  +  -0.495561 * Z  + -14.125228
  Z_new =   0.385969 * X  +   0.325166 * Y  +  -0.863305 * Z  + -14.745896 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.607194 -0.396258  2.781374   [DEG:  -34.7897  -22.7039  159.3610 ]
ZXZ:  0.190419  2.612578  0.870691   [DEG:   10.9102  149.6897   49.8869 ]
 
# END of job
