
#######################################################
#                                                     #
#                        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        2.09     2.09
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        2.00     2.10
  LCS_AVERAGE:     94.61

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    32       5_A - 36_A        0.97     3.60
  LCS_AVERAGE:     36.38

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      9   60   63      3    6   28   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     2_A     S     2_A     12   60   63      3   16   29   44   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     3_A     S     3_A     12   60   63      3   12   24   40   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     F     4_A     F     4_A     12   60   63      3    9   30   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     32   60   63      4   21   32   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     32   60   63      5   23   32   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     7_A     S     7_A     32   60   63      4   23   32   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     8_A     K     8_A     32   60   63     10   23   32   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     32   60   63      8   23   32   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    10_A     G    10_A     32   60   63      4   23   32   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    11_A     V    11_A     32   60   63     10   23   32   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     32   60   63     10   23   32   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     32   60   63      9   23   32   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     32   60   63      4   20   32   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     32   60   63      3   10   30   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     32   60   63      4   23   32   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    17_A     G    17_A     32   60   63      4   21   30   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    18_A     Y    18_A     32   60   63      9   23   32   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Q    19_A     Q    19_A     32   60   63      4   17   32   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    20_A     E    20_A     32   60   63      8   23   32   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     32   60   63      9   23   32   45   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     32   60   63      8   23   32   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     32   60   63     11   23   32   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     32   60   63     10   23   32   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     32   60   63     10   23   32   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     32   60   63     10   23   32   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     32   60   63     11   23   32   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     32   60   63     10   23   32   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     32   60   63     11   23   32   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     32   60   63     11   23   32   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     32   60   63     11   23   32   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     32   60   63     11   23   32   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     32   60   63     11   23   32   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    34_A     H    34_A     32   60   63     11   22   32   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     32   60   63     11   21   32   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     32   60   63      9   21   32   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     25   60   63     11   21   30   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    38_A     S    38_A     25   60   63      4   21   28   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     25   60   63      9   20   32   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A     24   60   63      4   18   32   39   51   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     16   60   63      3   18   23   34   48   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     13   60   63      3   11   19   37   51   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     12   60   63      4   19   28   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    44_A     K    44_A     12   60   63      3   17   28   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A     12   60   63      3   10   24   37   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    46_A     E    46_A     12   60   63      4   15   28   41   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     12   60   63      4   15   28   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     12   60   63      4    8   20   34   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     12   60   63      4   11   28   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     12   60   63      4   11   24   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    51_A     R    51_A     12   60   63      4   11   27   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    52_A     D    52_A     12   60   63      4   19   28   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     12   60   63      3   17   28   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     12   60   63      4   15   25   41   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     12   60   63      3   10   24   34   50   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     12   60   63      6   11   24   33   41   51   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     12   60   63      6   11   24   33   43   51   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     12   60   63      6   10   24   37   51   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    59_A     N    59_A     11   60   63      6   17   26   42   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    60_A     P    60_A     11   60   63     11   21   30   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     11   58   63      6   10   28   45   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     11   55   63      6   21   32   38   49   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     11   42   63      3   15   30   38   45   52   59   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  77.00  (  36.38   94.61  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     11     23     32     45     53     58     61     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  17.46  36.51  50.79  71.43  84.13  92.06  96.83 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.33   0.62   0.91   1.43   1.65   1.85   2.01   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09
GDT RMS_ALL_AT   2.48   3.86   3.70   2.42   2.19   2.11   2.10   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09

# Checking swapping
#   possible swapping detected:  F     4_A      F     4_A
#   possible swapping detected:  E    31_A      E    31_A
#   possible swapping detected:  D    45_A      D    45_A
#   possible swapping detected:  E    46_A      E    46_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     2.116     0    0.101   0.101     2.739   71.190   71.190
LGA    S     2_A      S     2_A     2.431     0    0.146   0.760     3.551   66.786   60.079
LGA    S     3_A      S     3_A     2.636     0    0.161   0.479     3.735   60.952   56.190
LGA    F     4_A      F     4_A     1.665     0    0.037   0.733     5.919   70.833   52.165
LGA    C     5_A      C     5_A     2.133     0    0.122   0.637     2.933   66.786   64.841
LGA    D     6_A      D     6_A     2.122     0    0.095   0.397     3.215   64.762   61.964
LGA    S     7_A      S     7_A     2.601     0    0.107   0.234     2.849   60.952   60.952
LGA    K     8_A      K     8_A     1.653     0    0.083   0.723     3.405   72.857   72.222
LGA    C     9_A      C     9_A     1.642     0    0.067   0.090     1.818   72.857   74.286
LGA    G    10_A      G    10_A     1.631     0    0.093   0.093     1.655   75.000   75.000
LGA    V    11_A      V    11_A     2.221     0    0.020   0.100     2.550   64.762   63.673
LGA    R    12_A      R    12_A     2.010     0    0.034   1.171     7.074   66.786   51.602
LGA    C    13_A      C    13_A     1.219     0    0.662   0.751     2.438   79.524   77.302
LGA    S    14_A      S    14_A     1.509     0    0.053   0.603     2.012   77.143   74.365
LGA    K    15_A      K    15_A     1.783     0    0.303   0.831     4.187   72.857   63.704
LGA    A    16_A      A    16_A     1.431     0    0.616   0.555     3.137   71.429   73.429
LGA    G    17_A      G    17_A     2.339     0    0.057   0.057     2.501   64.881   64.881
LGA    Y    18_A      Y    18_A     2.322     0    0.356   1.349     7.318   64.881   48.294
LGA    Q    19_A      Q    19_A     1.356     0    0.047   1.455     4.481   81.429   70.106
LGA    E    20_A      E    20_A     2.451     0    0.029   0.673     5.446   62.976   46.931
LGA    R    21_A      R    21_A     2.834     0    0.049   1.139     9.153   59.048   30.519
LGA    C    22_A      C    22_A     1.727     0    0.078   0.171     1.950   72.857   74.286
LGA    L    23_A      L    23_A     1.365     0    0.031   1.008     4.615   77.143   67.798
LGA    K    24_A      K    24_A     2.125     0    0.046   1.283    10.142   66.786   43.280
LGA    Y    25_A      Y    25_A     2.321     0    0.114   0.489     4.063   62.857   55.119
LGA    C    26_A      C    26_A     1.267     0    0.021   0.171     1.431   81.429   81.429
LGA    G    27_A      G    27_A     1.000     0    0.018   0.018     1.363   85.952   85.952
LGA    I    28_A      I    28_A     1.739     0    0.017   1.311     6.489   77.143   60.595
LGA    C    29_A      C    29_A     1.433     0    0.112   0.646     4.059   83.690   74.127
LGA    C    30_A      C    30_A     0.933     0    0.063   0.715     2.359   88.214   84.683
LGA    E    31_A      E    31_A     0.888     0    0.078   0.921     3.586   85.952   74.550
LGA    K    32_A      K    32_A     1.178     0    0.054   1.022     6.084   83.690   66.243
LGA    C    33_A      C    33_A     1.219     0    0.126   0.163     1.950   79.286   81.508
LGA    H    34_A      H    34_A     1.424     0    0.132   1.068     3.902   79.286   70.333
LGA    C    35_A      C    35_A     1.358     0    0.029   0.201     1.872   81.429   78.571
LGA    V    36_A      V    36_A     1.265     0    0.068   0.281     2.425   81.429   76.599
LGA    P    37_A      P    37_A     0.900     0    0.034   0.329     1.039   88.214   90.544
LGA    S    38_A      S    38_A     1.289     0    0.271   0.528     3.631   81.548   72.381
LGA    G    39_A      G    39_A     1.771     0    0.042   0.042     2.586   66.905   66.905
LGA    T    40_A      T    40_A     3.109     0    0.539   0.426     4.165   50.476   53.605
LGA    Y    41_A      Y    41_A     3.236     0    0.204   1.209    10.144   55.476   30.516
LGA    G    42_A      G    42_A     2.630     0    0.670   0.670     4.599   50.714   50.714
LGA    N    43_A      N    43_A     1.176     0    0.167   0.977     4.432   83.690   67.560
LGA    K    44_A      K    44_A     1.375     0    0.020   0.955     7.645   77.143   56.878
LGA    D    45_A      D    45_A     2.389     0    0.095   0.344     4.034   66.786   56.012
LGA    E    46_A      E    46_A     2.023     0    0.085   0.611     3.246   70.952   65.079
LGA    C    47_A      C    47_A     1.291     0    0.052   0.620     2.647   72.976   71.746
LGA    P    48_A      P    48_A     2.214     0    0.167   0.416     2.607   70.833   70.680
LGA    C    49_A      C    49_A     1.599     0    0.103   0.226     1.872   77.143   78.651
LGA    Y    50_A      Y    50_A     1.650     0    0.126   0.847     5.361   75.000   55.873
LGA    R    51_A      R    51_A     0.997     0    0.022   1.397     7.188   85.952   59.913
LGA    D    52_A      D    52_A     0.186     0    0.048   0.709     3.105  100.000   85.774
LGA    L    53_A      L    53_A     0.973     0    0.109   0.914     4.939   85.952   72.262
LGA    K    54_A      K    54_A     1.662     0    0.042   1.229     6.152   70.952   59.365
LGA    N    55_A      N    55_A     2.940     0    0.087   0.105     3.373   55.476   57.262
LGA    S    56_A      S    56_A     4.328     0    0.046   0.176     5.533   37.262   33.651
LGA    K    57_A      K    57_A     4.319     0    0.211   0.851     7.090   37.262   28.360
LGA    G    58_A      G    58_A     2.918     0    0.044   0.044     3.253   59.167   59.167
LGA    N    59_A      N    59_A     1.210     0    0.027   0.549     3.494   88.571   78.036
LGA    P    60_A      P    60_A     1.450     0    0.083   0.345     3.104   77.143   69.728
LGA    K    61_A      K    61_A     2.515     0    0.057   1.079     3.499   57.500   60.212
LGA    C    62_A      C    62_A     3.537     0    0.118   0.542     4.403   43.452   42.381
LGA    P    63_A      P    63_A     4.011     0    0.478   0.486     4.211   38.690   41.633

# 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):     2.095          2.103                  3.045           70.811   63.868

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    2.09    76.984    86.253     2.870

LGA_LOCAL      RMSD:   2.095  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.095  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   2.095  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.864179 * X  +  -0.370563 * Y  +  -0.340407 * Z  +   2.950355
  Y_new =  -0.256291 * X  +  -0.258027 * Y  +   0.931524 * Z  +  -1.118253
  Z_new =  -0.433023 * X  +   0.892247 * Y  +   0.128010 * Z  +  -0.967714 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.853284  0.447843  1.428300   [DEG: -163.4811   25.6595   81.8355 ]
ZXZ: -2.791238  1.442434 -0.451832   [DEG: -159.9262   82.6454  -25.8881 ]
 
# END of job
