
#######################################################
#                                                     #
#                        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 (  570),  selected   71 , name one
# Molecule2: number of CA atoms   71 (  553),  selected   71 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    71       1_B - 71_B        1.51     1.51
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    71       1_B - 71_B        1.51     1.51
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    42       2_B - 43_B        1.00     1.88
  LCS_AVERAGE:     54.00

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   71
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_B     G     1_B      6   71   71      4    5   10   39   60   66   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     2_B     S     2_B     42   71   71      5   24   53   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V     3_B     V     3_B     42   71   71     10   30   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     4_B     S     4_B     42   71   71      8   30   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K     5_B     K     5_B     42   71   71      5   15   46   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     W     6_B     W     6_B     42   71   71      8   29   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     7_B     S     7_B     42   71   71     12   30   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T     8_B     T     8_B     42   71   71     10   28   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D     9_B     D     9_B     42   71   71     10   26   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    10_B     E    10_B     42   71   71      9   27   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    11_B     V    11_B     42   71   71     10   26   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    12_B     S    12_B     42   71   71     10   24   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    13_B     E    13_B     42   71   71     10   24   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    14_B     F    14_B     42   71   71     12   26   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    15_B     I    15_B     42   71   71     11   27   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    16_B     Q    16_B     42   71   71     10   26   48   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    17_B     S    17_B     42   71   71     10   26   50   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    18_B     L    18_B     42   71   71     10   26   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    19_B     P    19_B     42   71   71      3   26   48   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    20_B     G    20_B     42   71   71      5   13   36   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     C    21_B     C    21_B     42   71   71      5   13   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    22_B     E    22_B     42   71   71      5   10   51   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    23_B     E    23_B     42   71   71     10   27   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     H    24_B     H    24_B     42   71   71     14   31   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    25_B     G    25_B     42   71   71     12   31   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    26_B     K    26_B     42   71   71     14   31   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    27_B     V    27_B     42   71   71     12   30   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    28_B     F    28_B     42   71   71     15   31   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    29_B     K    29_B     42   71   71     15   31   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    30_B     D    30_B     42   71   71     12   30   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    31_B     E    31_B     42   71   71     12   30   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    32_B     Q    32_B     42   71   71     12   30   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    33_B     I    33_B     42   71   71     12   30   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    34_B     D    34_B     42   71   71      6   30   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    35_B     G    35_B     42   71   71     15   30   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    36_B     E    36_B     42   71   71      5   29   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    37_B     A    37_B     42   71   71      8   30   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    38_B     F    38_B     42   71   71      5   30   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    39_B     L    39_B     42   71   71     16   31   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    40_B     L    40_B     42   71   71     10   30   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    41_B     M    41_B     42   71   71     16   31   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    42_B     T    42_B     42   71   71     16   31   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    43_B     Q    43_B     42   71   71     16   31   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    44_B     T    44_B     34   71   71     16   31   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    45_B     D    45_B     34   71   71     16   31   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    46_B     I    46_B     34   71   71      5   31   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    47_B     V    47_B     34   71   71      5   31   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    48_B     K    48_B     34   71   71      5   13   36   58   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    49_B     I    49_B     34   71   71      5    9   12   42   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    50_B     M    50_B     34   71   71      5   24   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    51_B     S    51_B     34   71   71     14   31   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    52_B     I    52_B     34   71   71      5   29   53   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    53_B     K    53_B     34   71   71     16   31   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    54_B     E    54_B     34   71   71     16   31   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    55_B     G    55_B     34   71   71     16   31   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    56_B     P    56_B     34   71   71     16   31   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    57_B     A    57_B     34   71   71     16   31   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    58_B     E    58_B     34   71   71     16   31   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    59_B     K    59_B     34   71   71     16   31   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    60_B     I    60_B     34   71   71     16   31   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    61_B     F    61_B     34   71   71     16   31   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     N    62_B     N    62_B     34   71   71     16   31   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    63_B     S    63_B     34   71   71     15   31   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    64_B     I    64_B     34   71   71     15   31   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    65_B     L    65_B     34   71   71     15   31   54   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    66_B     M    66_B     34   71   71     15   31   53   62   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    67_B     F    67_B     34   71   71     12   31   48   61   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    68_B     K    68_B     34   71   71     10   31   45   61   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    69_B     A    69_B     34   71   71     10   31   45   61   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    70_B     A    70_B     34   71   71     10   19   41   54   65   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    71_B     E    71_B     34   71   71     10   15   37   52   62   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_AVERAGE  LCS_A:  84.67  (  54.00  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     16     31     54     62     66     69     71     71     71     71     71     71     71     71     71     71     71     71     71     71 
GDT PERCENT_AT  22.54  43.66  76.06  87.32  92.96  97.18 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.30   0.64   1.06   1.19   1.30   1.42   1.51   1.51   1.51   1.51   1.51   1.51   1.51   1.51   1.51   1.51   1.51   1.51   1.51   1.51
GDT RMS_ALL_AT   1.73   1.89   1.56   1.58   1.55   1.52   1.51   1.51   1.51   1.51   1.51   1.51   1.51   1.51   1.51   1.51   1.51   1.51   1.51   1.51

# Checking swapping
#   possible swapping detected:  D     9_B      D     9_B
#   possible swapping detected:  E    13_B      E    13_B
#   possible swapping detected:  F    14_B      F    14_B
#   possible swapping detected:  E    36_B      E    36_B
#   possible swapping detected:  F    38_B      F    38_B
#   possible swapping detected:  E    54_B      E    54_B
#   possible swapping detected:  E    58_B      E    58_B
#   possible swapping detected:  F    67_B      F    67_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G     1_B      G     1_B     3.290     0    0.214   0.214     4.266   56.190   56.190
LGA    S     2_B      S     2_B     1.446     0    0.064   0.710     3.908   75.119   70.873
LGA    V     3_B      V     3_B     1.337     0    0.101   0.101     2.253   81.429   75.442
LGA    S     4_B      S     4_B     0.868     0    0.683   0.852     2.858   88.452   83.571
LGA    K     5_B      K     5_B     2.493     0    0.068   0.792     7.740   68.810   44.339
LGA    W     6_B      W     6_B     1.417     0    0.050   0.284     2.854   79.286   71.395
LGA    S     7_B      S     7_B     0.862     0    0.039   0.036     1.027   88.214   88.968
LGA    T     8_B      T     8_B     0.988     0    0.009   0.079     1.337   88.214   85.306
LGA    D     9_B      D     9_B     0.938     0    0.014   0.737     3.214   88.214   77.857
LGA    E    10_B      E    10_B     1.037     0    0.030   0.326     2.358   85.952   79.683
LGA    V    11_B      V    11_B     1.066     0    0.026   0.109     1.596   83.690   81.497
LGA    S    12_B      S    12_B     1.480     0    0.036   0.090     1.810   79.286   77.143
LGA    E    13_B      E    13_B     1.672     0    0.017   0.773     5.473   75.000   58.571
LGA    F    14_B      F    14_B     1.325     0    0.016   1.383     7.356   81.429   54.113
LGA    I    15_B      I    15_B     1.087     0    0.006   0.655     1.643   81.429   80.357
LGA    Q    16_B      Q    16_B     2.079     0    0.052   0.166     3.641   66.786   60.741
LGA    S    17_B      S    17_B     2.340     0    0.012   0.021     2.459   64.762   64.762
LGA    L    18_B      L    18_B     1.559     0    0.159   0.221     1.717   72.857   77.143
LGA    P    19_B      P    19_B     1.874     0    0.647   0.815     3.174   68.929   65.034
LGA    G    20_B      G    20_B     2.807     0    0.018   0.018     2.807   60.952   60.952
LGA    C    21_B      C    21_B     1.911     0    0.066   0.098     2.215   72.976   71.587
LGA    E    22_B      E    22_B     2.140     0    0.057   1.120     4.747   68.810   57.989
LGA    E    23_B      E    23_B     1.597     0    0.067   0.819     5.028   77.143   61.429
LGA    H    24_B      H    24_B     0.452     0    0.031   0.131     0.883   97.619   93.333
LGA    G    25_B      G    25_B     0.584     0    0.026   0.026     0.692   92.857   92.857
LGA    K    26_B      K    26_B     0.770     0    0.015   0.754     1.563   90.476   85.503
LGA    V    27_B      V    27_B     1.132     0    0.058   1.029     3.686   85.952   79.864
LGA    F    28_B      F    28_B     0.621     0    0.009   0.396     1.322   90.476   89.697
LGA    K    29_B      K    29_B     0.640     0    0.010   0.793     2.494   88.214   83.915
LGA    D    30_B      D    30_B     1.328     0    0.054   0.077     1.529   81.429   80.357
LGA    E    31_B      E    31_B     1.437     0    0.015   0.104     1.850   81.429   77.619
LGA    Q    32_B      Q    32_B     1.356     0    0.024   0.796     4.215   81.429   69.365
LGA    I    33_B      I    33_B     1.102     0    0.093   0.629     1.598   83.690   82.619
LGA    D    34_B      D    34_B     1.242     0    0.029   0.158     2.110   83.690   78.333
LGA    G    35_B      G    35_B     0.743     0    0.061   0.061     0.982   90.476   90.476
LGA    E    36_B      E    36_B     1.332     0    0.034   0.915     3.244   81.429   75.079
LGA    A    37_B      A    37_B     1.237     0    0.058   0.056     1.314   81.429   81.429
LGA    F    38_B      F    38_B     1.187     0    0.024   1.088     4.234   81.429   73.983
LGA    L    39_B      L    39_B     0.637     0    0.118   1.376     3.723   88.214   77.262
LGA    L    40_B      L    40_B     1.015     0    0.039   0.045     1.844   88.214   81.607
LGA    M    41_B      M    41_B     0.511     0    0.062   0.183     1.034   90.476   90.536
LGA    T    42_B      T    42_B     0.809     0    0.013   0.026     0.874   90.476   90.476
LGA    Q    43_B      Q    43_B     1.089     0    0.014   1.005     3.845   85.952   71.005
LGA    T    44_B      T    44_B     1.063     0    0.024   0.101     1.396   85.952   84.014
LGA    D    45_B      D    45_B     0.853     0    0.016   0.202     1.303   85.952   83.690
LGA    I    46_B      I    46_B     1.145     0    0.076   0.077     1.547   79.286   80.357
LGA    V    47_B      V    47_B     1.384     0    0.022   0.077     2.087   77.143   75.374
LGA    K    48_B      K    48_B     2.506     0    0.023   0.956     8.096   61.071   44.074
LGA    I    49_B      I    49_B     2.760     0    0.009   0.099     4.263   60.952   52.202
LGA    M    50_B      M    50_B     1.358     0    0.035   0.287     4.314   83.810   71.964
LGA    S    51_B      S    51_B     1.054     0    0.089   0.086     1.602   83.690   81.508
LGA    I    52_B      I    52_B     1.572     0    0.105   1.190     2.969   75.000   68.036
LGA    K    53_B      K    53_B     1.298     0    0.035   0.642     1.949   81.429   79.524
LGA    E    54_B      E    54_B     1.317     0    0.021   0.744     3.276   81.429   72.434
LGA    G    55_B      G    55_B     1.393     0    0.069   0.069     1.456   81.429   81.429
LGA    P    56_B      P    56_B     1.084     0    0.041   0.056     1.201   81.429   81.429
LGA    A    57_B      A    57_B     0.982     0    0.021   0.020     1.081   88.214   88.667
LGA    E    58_B      E    58_B     0.985     0    0.010   0.805     3.906   88.214   74.021
LGA    K    59_B      K    59_B     1.045     0    0.008   0.108     1.754   85.952   80.582
LGA    I    60_B      I    60_B     0.709     0    0.033   0.054     1.092   92.857   90.536
LGA    F    61_B      F    61_B     0.461     0    0.063   0.142     1.285   97.619   90.649
LGA    N    62_B      N    62_B     0.556     0    0.026   0.052     1.029   90.476   89.345
LGA    S    63_B      S    63_B     1.001     0    0.016   0.040     1.272   85.952   84.444
LGA    I    64_B      I    64_B     0.737     0    0.011   0.081     1.073   88.214   91.726
LGA    L    65_B      L    65_B     0.635     0    0.028   0.121     1.109   88.214   92.917
LGA    M    66_B      M    66_B     1.316     0    0.025   0.796     4.109   79.405   66.190
LGA    F    67_B      F    67_B     1.720     0    0.032   0.483     2.223   72.976   74.459
LGA    K    68_B      K    68_B     1.852     0    0.045   0.905     3.511   68.810   62.540
LGA    A    69_B      A    69_B     2.119     0    0.072   0.074     2.522   64.881   66.476
LGA    A    70_B      A    70_B     3.084     0    0.144   0.155     3.528   50.119   51.524
LGA    E    71_B      E    71_B     3.419     0    0.016   0.671     3.888   48.333   51.005

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       71     284    284  100.00     553    553  100.00                71
SUMMARY(RMSD_GDC):     1.511          1.496                  2.019           80.255   75.512

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   73   71    4.0     71    1.51    82.746    92.241     4.408

LGA_LOCAL      RMSD:   1.511  Number of atoms:   71  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.511  Number of assigned atoms:   71 
Std_ASGN_ATOMS RMSD:   1.511  Standard rmsd on all 71 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.036158 * X  +  -0.923267 * Y  +  -0.382454 * Z  +  25.046589
  Y_new =  -0.997985 * X  +  -0.053325 * Y  +   0.034378 * Z  +  41.106594
  Z_new =  -0.052135 * X  +   0.380441 * Y  +  -0.923335 * Z  + -10.218330 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.534581  0.052158  2.750760   [DEG:  -87.9250    2.9885  157.6069 ]
ZXZ: -1.660444  2.747472 -0.136190   [DEG:  -95.1364  157.4186   -7.8031 ]
 
# END of job
