
#######################################################
#                                                     #
#                        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   63 (  472),  selected   63 , name one
# Molecule2: number of CA atoms   63 (  472),  selected   63 , 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:    63       1_A - 63_A        3.82     3.82
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    37       1_A - 37_A        1.97     4.76
  LONGEST_CONTINUOUS_SEGMENT:    37       2_A - 38_A        1.97     4.64
  LONGEST_CONTINUOUS_SEGMENT:    37       3_A - 39_A        1.98     4.58
  LCS_AVERAGE:     50.54

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    28       8_A - 35_A        0.96     5.68
  LONGEST_CONTINUOUS_SEGMENT:    28       9_A - 36_A        0.96     5.66
  LCS_AVERAGE:     33.06

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   63
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     G     1_A     G     1_A     10   37   63      3    7    9   13   23   31   36   42   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     2_A     S     2_A     12   37   63      3    8   13   15   23   28   34   38   47   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     3_A     S     3_A     12   37   63      3    8   16   20   29   35   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     F     4_A     F     4_A     12   37   63      3    8   13   22   34   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     12   37   63      5   10   21   28   34   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     12   37   63      5   10   21   26   34   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     7_A     S     7_A     23   37   63      5   16   27   31   34   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     8_A     K     8_A     28   37   63      7   20   28   31   34   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     28   37   63      8   22   28   31   34   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    10_A     G    10_A     28   37   63      8   22   28   31   34   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    11_A     V    11_A     28   37   63      8   22   28   31   34   37   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     28   37   63      4   22   28   31   34   37   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     28   37   63      8   22   28   31   34   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     28   37   63      4   14   28   31   34   37   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     28   37   63      4   19   28   31   34   37   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     28   37   63      3   17   28   31   34   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    17_A     G    17_A     28   37   63      3   22   26   31   34   38   45   47   49   53   58   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    18_A     Y    18_A     28   37   63     10   22   28   31   34   38   45   47   49   53   58   63   63   63   63   63   63   63   63   63 
LCS_GDT     Q    19_A     Q    19_A     28   37   63      3   18   28   31   34   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    20_A     E    20_A     28   37   63      4   22   28   31   34   38   45   47   49   53   58   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     28   37   63     10   22   28   31   34   38   45   47   49   53   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     28   37   63      8   22   28   31   34   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     28   37   63     10   22   28   31   34   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     28   37   63     10   22   28   31   34   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     28   37   63     10   22   28   31   34   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     28   37   63     10   22   28   31   34   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     28   37   63     10   22   28   31   34   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     28   37   63     10   22   28   31   34   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     28   37   63     10   22   28   31   34   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     28   37   63     10   22   28   31   34   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     28   37   63      7   22   28   31   34   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     28   37   63      7   22   28   31   34   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     28   37   63      9   22   28   31   34   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    34_A     H    34_A     28   37   63      7   22   28   31   34   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     28   37   63      8   20   28   31   34   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     28   37   63      6   20   28   31   34   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     21   37   63      5   13   22   31   34   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    38_A     S    38_A     18   37   63      5   10   18   23   31   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     16   37   63      5   10   17   21   28   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A     14   26   63      5   10   16   19   24   32   37   42   49   51   57   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     14   26   63      5   10   16   18   25   27   33   39   46   52   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A      5   26   63      3   11   15   20   23   27   30   37   48   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A      5   24   63      3    4    5   11   17   28   37   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    44_A     K    44_A      7   24   63      3    6    7   14   28   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A      9   23   63      3    7   16   20   28   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    46_A     E    46_A      9   23   63      4    7   14   20   25   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     17   23   63      4    7   17   20   28   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     17   23   63      6   16   17   20   25   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     17   23   63      6   16   17   20   25   36   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     17   23   63      6   16   17   25   33   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    51_A     R    51_A     17   23   63      6   16   17   24   33   38   45   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    52_A     D    52_A     17   23   63      7   16   17   20   29   34   44   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     17   23   63      5   16   17   20   25   33   39   47   49   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     17   23   63      6   16   17   20   25   28   35   41   48   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     17   23   63      7   16   17   20   25   28   31   37   46   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     17   23   63      5   16   17   20   25   28   31   37   46   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     17   23   63      7   16   17   20   25   28   31   37   46   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     17   23   63      5   16   17   20   25   31   35   41   48   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    59_A     N    59_A     17   23   63      7   16   17   20   25   31   35   41   48   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    60_A     P    60_A     17   23   63      7   16   17   20   26   33   35   41   48   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     17   23   63      4   16   17   20   25   28   31   37   46   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     17   23   63      7   16   17   20   25   28   31   37   46   54   59   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     17   23   63      7   16   17   20   25   28   30   35   45   54   59   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  61.20  (  33.06   50.54  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     10     22     28     31     34     38     45     47     49     54     59     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  15.87  34.92  44.44  49.21  53.97  60.32  71.43  74.60  77.78  85.71  93.65 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.29   0.63   0.97   1.18   1.55   2.21   2.46   2.54   2.66   3.36   3.64   3.82   3.82   3.82   3.82   3.82   3.82   3.82   3.82   3.82
GDT RMS_ALL_AT   6.35   5.99   5.49   5.23   4.91   4.79   4.44   4.44   4.38   3.85   3.86   3.82   3.82   3.82   3.82   3.82   3.82   3.82   3.82   3.82

# Checking swapping
#   possible swapping detected:  Y    18_A      Y    18_A
#   possible swapping detected:  E    31_A      E    31_A
#   possible swapping detected:  Y    50_A      Y    50_A
#   possible swapping detected:  D    52_A      D    52_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G     1_A      G     1_A     4.728     0    0.098   0.098     7.513   18.333   18.333
LGA    S     2_A      S     2_A     5.366     0    0.196   0.842     6.760   34.524   28.095
LGA    S     3_A      S     3_A     3.501     0    0.135   0.680     6.438   54.524   46.429
LGA    F     4_A      F     4_A     2.236     0    0.056   0.211     5.276   69.048   48.009
LGA    C     5_A      C     5_A     1.747     0    0.094   0.099     2.207   75.119   73.016
LGA    D     6_A      D     6_A     2.371     0    0.069   1.104     7.492   64.762   43.690
LGA    S     7_A      S     7_A     2.179     0    0.071   0.218     2.949   64.881   64.841
LGA    K     8_A      K     8_A     1.882     0    0.127   0.781     8.419   72.976   52.646
LGA    C     9_A      C     9_A     1.487     0    0.026   0.041     2.130   75.119   78.730
LGA    G    10_A      G    10_A     2.196     0    0.083   0.083     2.595   62.976   62.976
LGA    V    11_A      V    11_A     3.571     0    0.023   1.341     6.233   45.000   42.517
LGA    R    12_A      R    12_A     3.366     0    0.021   1.344     9.662   50.000   32.684
LGA    C    13_A      C    13_A     2.133     0    0.644   0.721     3.213   61.071   65.079
LGA    S    14_A      S    14_A     2.914     0    0.078   0.589     3.515   57.143   57.460
LGA    K    15_A      K    15_A     2.848     0    0.100   0.827     7.634   57.143   40.582
LGA    A    16_A      A    16_A     1.713     0    0.642   0.581     3.093   69.286   70.000
LGA    G    17_A      G    17_A     1.937     0    0.037   0.037     2.887   69.048   69.048
LGA    Y    18_A      Y    18_A     2.134     0    0.298   1.345     7.271   68.810   51.151
LGA    Q    19_A      Q    19_A     1.467     0    0.049   1.085     4.419   83.690   66.878
LGA    E    20_A      E    20_A     2.906     0    0.016   0.805     7.909   57.262   35.926
LGA    R    21_A      R    21_A     3.191     0    0.067   1.127    11.978   55.357   26.710
LGA    C    22_A      C    22_A     1.718     0    0.094   0.117     2.047   70.833   72.937
LGA    L    23_A      L    23_A     1.508     0    0.025   1.203     4.252   75.000   68.452
LGA    K    24_A      K    24_A     2.844     0    0.050   1.173    12.112   59.048   34.233
LGA    Y    25_A      Y    25_A     2.817     0    0.136   0.534     3.780   55.357   53.095
LGA    C    26_A      C    26_A     1.535     0    0.032   0.087     1.809   77.143   77.143
LGA    G    27_A      G    27_A     1.135     0    0.039   0.039     1.350   81.429   81.429
LGA    I    28_A      I    28_A     2.209     0    0.015   0.740     5.762   70.833   55.238
LGA    C    29_A      C    29_A     2.609     0    0.063   0.066     4.014   60.952   55.159
LGA    C    30_A      C    30_A     1.679     0    0.120   0.162     2.047   77.143   75.794
LGA    E    31_A      E    31_A     0.998     0    0.016   0.959     3.755   83.690   75.503
LGA    K    32_A      K    32_A     2.294     0    0.060   1.234     3.223   62.976   64.339
LGA    C    33_A      C    33_A     2.896     0    0.183   0.243     3.676   51.905   54.921
LGA    H    34_A      H    34_A     2.868     0    0.045   0.885     3.431   55.357   65.333
LGA    C    35_A      C    35_A     2.609     0    0.026   0.179     2.926   60.952   59.683
LGA    V    36_A      V    36_A     1.949     0    0.211   1.340     4.139   68.810   63.129
LGA    P    37_A      P    37_A     1.864     0    0.020   0.284     3.877   72.857   64.150
LGA    S    38_A      S    38_A     2.055     0    0.168   0.431     2.671   64.881   62.302
LGA    G    39_A      G    39_A     3.301     0    0.102   0.102     4.454   45.357   45.357
LGA    T    40_A      T    40_A     5.348     0    0.570   1.236     9.110   23.095   18.367
LGA    Y    41_A      Y    41_A     6.149     0    0.619   1.296     7.947   15.714   14.683
LGA    G    42_A      G    42_A     5.609     0    0.176   0.176     6.054   25.357   25.357
LGA    N    43_A      N    43_A     4.106     0    0.154   1.017     4.637   38.810   44.940
LGA    K    44_A      K    44_A     3.016     0    0.045   0.901     3.658   50.119   59.312
LGA    D    45_A      D    45_A     3.098     0    0.097   0.879     3.573   51.786   50.952
LGA    E    46_A      E    46_A     3.401     0    0.176   0.433     3.897   51.786   47.831
LGA    C    47_A      C    47_A     2.432     0    0.038   0.648     4.315   60.952   58.968
LGA    P    48_A      P    48_A     3.318     0    0.168   0.388     4.524   53.571   47.483
LGA    C    49_A      C    49_A     3.214     0    0.113   0.221     4.710   55.476   49.444
LGA    Y    50_A      Y    50_A     1.749     0    0.134   0.844     5.363   70.833   57.817
LGA    R    51_A      R    51_A     1.763     0    0.025   1.288     6.878   65.119   53.203
LGA    D    52_A      D    52_A     3.730     0    0.117   0.768     4.690   42.262   42.024
LGA    L    53_A      L    53_A     4.602     0    0.077   0.890     5.558   29.048   39.643
LGA    K    54_A      K    54_A     7.242     0    0.020   0.910    10.691    9.167    5.661
LGA    N    55_A      N    55_A     9.839     0    0.067   0.222    11.188    0.952    0.476
LGA    S    56_A      S    56_A    10.927     0    0.101   0.528    12.873    0.000    0.000
LGA    K    57_A      K    57_A    10.488     0    0.047   0.745    12.175    0.476    0.212
LGA    G    58_A      G    58_A     8.632     0    0.057   0.057     9.360    4.048    4.048
LGA    N    59_A      N    59_A     8.319     0    0.056   1.034    10.631    4.881    3.393
LGA    P    60_A      P    60_A     6.823     0    0.124   0.325     7.766   10.119   12.109
LGA    K    61_A      K    61_A     8.259     0    0.024   1.365     8.792    4.881    6.190
LGA    C    62_A      C    62_A     7.562     0    0.075   0.380     7.728    7.143   10.556
LGA    P    63_A      P    63_A     8.490     0    0.463   0.568     9.167    5.952    4.694

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       63     252    252  100.00     472    472  100.00                63
SUMMARY(RMSD_GDC):     3.817          3.832                  4.516           49.875   45.403

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     47    2.54    64.683    64.411     1.777

LGA_LOCAL      RMSD:   2.545  Number of atoms:   47  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.438  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   3.817  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.428512 * X  +  -0.900028 * Y  +  -0.079544 * Z  +  -9.592957
  Y_new =   0.871526 * X  +  -0.388501 * Y  +  -0.299181 * Z  +   1.930995
  Z_new =   0.238369 * X  +  -0.197528 * Y  +   0.950875 * Z  +  -7.129164 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.027766 -0.240686 -0.204820   [DEG:  116.1824  -13.7903  -11.7353 ]
ZXZ: -0.259861  0.314746  2.262773   [DEG:  -14.8889   18.0336  129.6474 ]
 
# END of job
