
#######################################################
#                                                     #
#                        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   73 (  592),  selected   65 , name one
# Molecule2: number of CA atoms   72 (  603),  selected   65 , 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:    65       2_A - 74_A        4.77     4.77
  LCS_AVERAGE:     90.28

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    42      33_A - 74_A        1.02    12.58
  LCS_AVERAGE:     49.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    41      33_A - 73_A        0.96    12.58
  LONGEST_CONTINUOUS_SEGMENT:    41      34_A - 74_A        0.93    12.62
  LCS_AVERAGE:     48.10

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   65
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     23   23   65     18   23   24   25   27   30   33   37   40   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     S     3_A     S     3_A     23   23   65     20   23   24   25   27   30   33   37   40   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     L     4_A     L     4_A     23   23   65     20   23   24   25   27   30   33   37   40   45   50   56   60   61   64   65   65   65   65   65 
LCS_GDT     I     5_A     I     5_A     23   23   65     20   23   24   25   27   30   33   37   40   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     E     6_A     E     6_A     23   23   65     20   23   24   25   27   30   33   37   40   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     E     7_A     E     7_A     23   23   65     20   23   24   25   27   30   33   37   40   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     L     8_A     L     8_A     23   23   65     20   23   24   25   27   30   33   37   40   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     I     9_A     I     9_A     23   23   65     20   23   24   25   27   30   33   37   40   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     R    10_A     R    10_A     23   23   65     20   23   24   25   27   30   33   37   40   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     R    11_A     R    11_A     23   23   65     20   23   24   25   27   30   33   37   40   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     S    12_A     S    12_A     23   23   65     20   23   24   25   27   30   33   37   40   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     E    13_A     E    13_A     23   23   65     20   23   24   25   27   30   33   37   40   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     E    14_A     E    14_A     23   23   65     20   23   24   25   27   30   33   37   40   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     Q    15_A     Q    15_A     23   23   65     20   23   24   25   27   30   33   37   40   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     Q    16_A     Q    16_A     23   23   65     20   23   24   25   27   30   33   37   40   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     R    17_A     R    17_A     23   23   65     20   23   24   25   27   30   33   37   40   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     R    18_A     R    18_A     23   23   65     20   23   24   25   27   30   33   37   40   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     N    19_A     N    19_A     23   23   65     20   23   24   25   27   30   33   37   40   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     E    20_A     E    20_A     23   23   65     20   23   24   25   27   30   33   37   40   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     E    21_A     E    21_A     23   23   65     20   23   24   25   27   30   33   37   40   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     A    22_A     A    22_A     23   23   65     20   23   24   25   27   30   33   37   40   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     L    23_A     L    23_A     23   23   65     20   23   24   25   27   30   33   37   40   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     R    24_A     R    24_A     23   23   65     17   23   24   25   27   30   33   37   40   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     Q    33_A     Q    33_A     41   42   65      4    7   15   40   42   42   42   42   42   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     L    34_A     L    34_A     41   42   65      4   21   39   40   42   42   42   42   42   42   47   53   57   61   64   65   65   65   65   65 
LCS_GDT     L    35_A     L    35_A     41   42   65     14   35   39   40   42   42   42   42   42   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     S    36_A     S    36_A     41   42   65      4   24   39   40   42   42   42   42   42   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     G    37_A     G    37_A     41   42   65     14   35   39   40   42   42   42   42   42   44   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     I    38_A     I    38_A     41   42   65     14   35   39   40   42   42   42   42   42   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     V    39_A     V    39_A     41   42   65     16   35   39   40   42   42   42   42   42   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     Q    40_A     Q    40_A     41   42   65     10   35   39   40   42   42   42   42   42   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     Q    41_A     Q    41_A     41   42   65     14   35   39   40   42   42   42   42   42   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     Q    42_A     Q    42_A     41   42   65     16   35   39   40   42   42   42   42   42   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     N    43_A     N    43_A     41   42   65     16   35   39   40   42   42   42   42   42   42   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     N    44_A     N    44_A     41   42   65     16   35   39   40   42   42   42   42   42   42   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     L    45_A     L    45_A     41   42   65     16   35   39   40   42   42   42   42   42   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     L    46_A     L    46_A     41   42   65     16   35   39   40   42   42   42   42   42   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     R    47_A     R    47_A     41   42   65     16   35   39   40   42   42   42   42   42   42   51   54   58   61   64   65   65   65   65   65 
LCS_GDT     A    48_A     A    48_A     41   42   65     16   35   39   40   42   42   42   42   42   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     I    49_A     I    49_A     41   42   65     16   35   39   40   42   42   42   42   42   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     E    50_A     E    50_A     41   42   65     16   35   39   40   42   42   42   42   42   42   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     A    51_A     A    51_A     41   42   65     16   35   39   40   42   42   42   42   42   42   51   54   57   61   64   65   65   65   65   65 
LCS_GDT     Q    52_A     Q    52_A     41   42   65     16   35   39   40   42   42   42   42   42   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     Q    53_A     Q    53_A     41   42   65     16   35   39   40   42   42   42   42   42   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     H    54_A     H    54_A     41   42   65     16   35   39   40   42   42   42   42   42   42   51   54   57   61   64   65   65   65   65   65 
LCS_GDT     L    55_A     L    55_A     41   42   65     16   35   39   40   42   42   42   42   42   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     L    56_A     L    56_A     41   42   65     16   35   39   40   42   42   42   42   42   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     Q    57_A     Q    57_A     41   42   65      6   35   39   40   42   42   42   42   42   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     L    58_A     L    58_A     41   42   65      6   35   39   40   42   42   42   42   42   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     T    59_A     T    59_A     41   42   65     11   35   39   40   42   42   42   42   42   45   50   56   60   61   64   65   65   65   65   65 
LCS_GDT     V    60_A     V    60_A     41   42   65     11   35   39   40   42   42   42   42   42   45   49   56   60   61   64   65   65   65   65   65 
LCS_GDT     W    61_A     W    61_A     41   42   65     14   35   39   40   42   42   42   42   42   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     G    62_A     G    62_A     41   42   65      9   35   39   40   42   42   42   42   42   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     I    63_A     I    63_A     41   42   65      9   35   39   40   42   42   42   42   42   45   49   56   60   61   64   65   65   65   65   65 
LCS_GDT     K    64_A     K    64_A     41   42   65     14   35   39   40   42   42   42   42   42   42   48   56   60   61   64   65   65   65   65   65 
LCS_GDT     Q    65_A     Q    65_A     41   42   65     14   35   39   40   42   42   42   42   42   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     L    66_A     L    66_A     41   42   65     14   35   39   40   42   42   42   42   42   45   49   56   60   61   64   65   65   65   65   65 
LCS_GDT     Q    67_A     Q    67_A     41   42   65     14   35   39   40   42   42   42   42   42   42   44   54   60   61   64   65   65   65   65   65 
LCS_GDT     A    68_A     A    68_A     41   42   65      9   29   39   40   42   42   42   42   42   42   49   56   60   61   64   65   65   65   65   65 
LCS_GDT     R    69_A     R    69_A     41   42   65      6   12   39   40   42   42   42   42   42   45   51   56   60   61   64   65   65   65   65   65 
LCS_GDT     I    70_A     I    70_A     41   42   65      6   35   39   40   42   42   42   42   42   45   48   55   60   61   64   65   65   65   65   65 
LCS_GDT     L    71_A     L    71_A     41   42   65      3   15   39   40   42   42   42   42   42   42   47   55   60   61   64   65   65   65   65   65 
LCS_GDT     A    72_A     A    72_A     41   42   65      3   35   39   40   42   42   42   42   42   45   50   56   60   61   64   65   65   65   65   65 
LCS_GDT     V    73_A     V    73_A     41   42   65      3   35   39   40   42   42   42   42   42   45   49   55   60   61   64   65   65   65   65   65 
LCS_GDT     E    74_A     E    74_A     41   42   65      3    3   14   17   42   42   42   42   42   42   42   44   51   60   64   65   65   65   65   65 
LCS_AVERAGE  LCS_A:  62.46  (  48.10   49.00   90.28 )

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     20     35     39     40     42     42     42     42     42     45     51     56     60     61     64     65     65     65     65     65 
GDT PERCENT_AT  27.78  48.61  54.17  55.56  58.33  58.33  58.33  58.33  58.33  62.50  70.83  77.78  83.33  84.72  88.89  90.28  90.28  90.28  90.28  90.28
GDT RMS_LOCAL    0.27   0.71   0.79   0.85   1.02   1.02   1.02   1.02   1.02   3.32   4.16   4.22   4.40   4.47   4.69   4.77   4.77   4.77   4.77   4.77
GDT RMS_ALL_AT   9.26  12.62  12.65  12.62  12.58  12.58  12.58  12.58  12.58   5.08   5.45   4.85   4.77   4.77   4.78   4.77   4.77   4.77   4.77   4.77

# Checking swapping
#   possible swapping detected:  E     6_A      E     6_A
#   possible swapping detected:  E    50_A      E    50_A
#   possible swapping detected:  E    74_A      E    74_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    T     2_A      T     2_A    20.243     0    0.523   0.546    21.788    0.000    0.000
LGA    S     3_A      S     3_A    25.757     0    0.065   0.093    30.162    0.000    0.000
LGA    L     4_A      L     4_A    23.714     0    0.029   1.457    26.276    0.000    0.000
LGA    I     5_A      I     5_A    17.536     0    0.034   1.413    19.592    0.000    0.000
LGA    E     6_A      E     6_A    21.633     0    0.065   1.047    26.950    0.000    0.000
LGA    E     7_A      E     7_A    24.598     0    0.039   0.956    30.803    0.000    0.000
LGA    L     8_A      L     8_A    18.910     0    0.056   0.913    20.716    0.000    0.000
LGA    I     9_A      I     9_A    17.180     0    0.026   1.225    19.205    0.000    0.000
LGA    R    10_A      R    10_A    23.427     0    0.041   1.439    34.030    0.000    0.000
LGA    R    11_A      R    11_A    22.223     0    0.027   0.780    26.774    0.000    0.000
LGA    S    12_A      S    12_A    16.327     0    0.030   0.645    18.221    0.000    0.000
LGA    E    13_A      E    13_A    20.380     0    0.042   1.259    26.102    0.000    0.000
LGA    E    14_A      E    14_A    24.156     0    0.030   1.218    29.462    0.000    0.000
LGA    Q    15_A      Q    15_A    19.195     0    0.034   0.293    20.686    0.000    0.000
LGA    Q    16_A      Q    16_A    17.177     0    0.034   1.062    19.222    0.000    0.000
LGA    R    17_A      R    17_A    23.463     0    0.028   1.306    29.757    0.000    0.000
LGA    R    18_A      R    18_A    22.569     0    0.025   0.914    27.317    0.000    0.000
LGA    N    19_A      N    19_A    16.604     0    0.046   1.186    18.560    0.000    0.000
LGA    E    20_A      E    20_A    19.865     0    0.020   1.105    24.399    0.000    0.000
LGA    E    21_A      E    21_A    24.477     0    0.030   0.950    30.689    0.000    0.000
LGA    A    22_A      A    22_A    20.155     0    0.030   0.036    21.412    0.000    0.000
LGA    L    23_A      L    23_A    17.684     0    0.101   1.079    19.690    0.000    0.000
LGA    R    24_A      R    24_A    23.549     0    0.261   1.591    31.886    0.000    0.000
LGA    Q    33_A      Q    33_A     2.762     0    0.035   0.762     4.639   60.952   52.063
LGA    L    34_A      L    34_A     1.758     0    0.049   0.216     2.210   77.381   74.167
LGA    L    35_A      L    35_A     0.429     0    0.060   1.085     4.591   97.619   74.940
LGA    S    36_A      S    36_A     1.229     0    0.077   0.735     2.521   81.548   76.032
LGA    G    37_A      G    37_A     0.840     0    0.047   0.047     0.955   95.238   95.238
LGA    I    38_A      I    38_A     0.111     0    0.027   0.138     0.924  100.000   97.619
LGA    V    39_A      V    39_A     0.523     0    0.028   0.077     1.006   92.857   90.544
LGA    Q    40_A      Q    40_A     0.800     0    0.043   0.888     2.391   90.476   83.598
LGA    Q    41_A      Q    41_A     0.325     0    0.090   0.603     1.557   95.238   87.672
LGA    Q    42_A      Q    42_A     0.592     0    0.042   1.063     3.610   90.476   84.233
LGA    N    43_A      N    43_A     0.752     0    0.027   0.915     4.948   90.476   74.762
LGA    N    44_A      N    44_A     0.711     0    0.049   0.531     1.605   90.476   87.143
LGA    L    45_A      L    45_A     0.788     0    0.027   1.145     3.132   90.476   83.214
LGA    L    46_A      L    46_A     0.919     0    0.044   1.257     3.674   90.476   79.286
LGA    R    47_A      R    47_A     0.812     0    0.026   1.144     4.175   90.476   79.307
LGA    A    48_A      A    48_A     0.822     0    0.041   0.067     0.822   90.476   90.476
LGA    I    49_A      I    49_A     0.726     0    0.043   1.390     4.481   90.476   78.393
LGA    E    50_A      E    50_A     0.706     0    0.056   1.001     2.367   90.476   80.899
LGA    A    51_A      A    51_A     0.732     0    0.022   0.036     0.902   90.476   90.476
LGA    Q    52_A      Q    52_A     0.769     0    0.035   0.855     2.774   90.476   81.905
LGA    Q    53_A      Q    53_A     0.635     0    0.045   0.490     2.179   90.476   84.656
LGA    H    54_A      H    54_A     0.806     0    0.023   1.223     6.621   90.476   61.476
LGA    L    55_A      L    55_A     0.942     0    0.040   0.248     1.355   90.476   88.214
LGA    L    56_A      L    56_A     0.812     0    0.033   0.900     2.501   90.476   84.048
LGA    Q    57_A      Q    57_A     0.764     0    0.032   1.240     3.667   90.476   82.222
LGA    L    58_A      L    58_A     0.645     0    0.061   1.015     2.332   90.476   84.048
LGA    T    59_A      T    59_A     0.631     0    0.087   1.130     2.669   90.476   83.197
LGA    V    60_A      V    60_A     0.899     0    0.025   0.138     1.349   88.214   86.599
LGA    W    61_A      W    61_A     0.710     0    0.044   1.391     6.151   90.476   68.265
LGA    G    62_A      G    62_A     0.873     0    0.034   0.034     0.889   90.476   90.476
LGA    I    63_A      I    63_A     0.847     0    0.039   0.587     1.145   90.476   89.345
LGA    K    64_A      K    64_A     0.759     0    0.034   1.345     9.487   90.476   60.582
LGA    Q    65_A      Q    65_A     0.778     0    0.049   0.627     2.325   88.214   79.841
LGA    L    66_A      L    66_A     0.794     0    0.044   0.200     1.176   90.476   88.214
LGA    Q    67_A      Q    67_A     0.951     0    0.028   0.620     2.117   85.952   78.730
LGA    A    68_A      A    68_A     1.506     0    0.046   0.046     1.742   77.143   76.286
LGA    R    69_A      R    69_A     1.449     0    0.062   1.293     5.611   81.429   68.701
LGA    I    70_A      I    70_A     0.622     0    0.023   0.146     1.347   90.476   89.345
LGA    L    71_A      L    71_A     1.206     0    0.032   1.088     4.201   83.690   74.881
LGA    A    72_A      A    72_A     0.905     0    0.038   0.040     1.041   88.214   88.667
LGA    V    73_A      V    73_A     0.926     0    0.044   1.238     2.915   83.810   78.231
LGA    E    74_A      E    74_A     2.393     0    0.623   0.757     5.870   64.881   45.820

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       65     260    260  100.00     535    535  100.00                72
SUMMARY(RMSD_GDC):     4.765          4.273                  6.719           51.448   46.859

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   73   72    4.0     42    1.02    63.194    59.617     3.752

LGA_LOCAL      RMSD:   1.019  Number of atoms:   42  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  12.580  Number of assigned atoms:   65 
Std_ASGN_ATOMS RMSD:   4.765  Standard rmsd on all 65 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.012158 * X  +   0.616472 * Y  +  -0.787283 * Z  +  -2.917193
  Y_new =   0.809720 * X  +  -0.468030 * Y  +  -0.353979 * Z  +   1.163792
  Z_new =  -0.586690 * X  +  -0.633175 * Y  +  -0.504860 * Z  + 126.234688 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.555782  0.626965 -2.243917   [DEG:   89.1397   35.9225 -128.5670 ]
ZXZ: -1.148257  2.100016 -2.394283   [DEG:  -65.7903  120.3221 -137.1823 ]
 
# END of job
