
#######################################################
#                                                     #
#                        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   68 (  529),  selected   67 , name one
# Molecule2: number of CA atoms   67 (  519),  selected   67 , 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:    67       2_A - 68_A        1.23     1.23
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        1.23     1.23
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    65       3_A - 67_A        0.96     1.26
  LCS_AVERAGE:     96.93

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   67
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     S     2_A     S     2_A     63   67   67      7   13   22   42   60   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P     3_A     P     3_A     65   67   67      7   35   55   61   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E     4_A     E     4_A     65   67   67      5   13   27   56   60   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E     5_A     E     5_A     65   67   67      7   35   55   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q     6_A     Q     6_A     65   67   67     23   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K     7_A     K     7_A     65   67   67     11   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q     8_A     Q     8_A     65   67   67     10   54   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     M     9_A     M     9_A     65   67   67     18   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    10_A     L    10_A     65   67   67     42   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    11_A     G    11_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    12_A     E    12_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    13_A     A    13_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    14_A     I    14_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Y    15_A     Y    15_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    16_A     P    16_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    17_A     K    17_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    18_A     V    18_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    19_A     A    19_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    20_A     A    20_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    21_A     S    21_A     65   67   67      4   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    22_A     Q    22_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    23_A     P    23_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    24_A     E    24_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    25_A     L    25_A     65   67   67     44   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    26_A     A    26_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    27_A     G    27_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    28_A     K    28_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    29_A     L    29_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     T    30_A     T    30_A     65   67   67     30   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    31_A     G    31_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     M    32_A     M    32_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    33_A     I    33_A     65   67   67     34   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    34_A     L    34_A     65   67   67     42   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    35_A     E    35_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    36_A     L    36_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    37_A     P    37_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    38_A     V    38_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     T    39_A     T    39_A     65   67   67     43   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    40_A     E    40_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    41_A     L    41_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    42_A     L    42_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     H    43_A     H    43_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    44_A     L    44_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    45_A     L    45_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    46_A     E    46_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    47_A     E    47_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    48_A     S    48_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    49_A     E    49_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    50_A     A    50_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    51_A     L    51_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     D    52_A     D    52_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    53_A     A    53_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    54_A     K    54_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    55_A     V    55_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     N    56_A     N    56_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    57_A     E    57_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    58_A     A    58_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    59_A     L    59_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    60_A     E    60_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    61_A     V    61_A     65   67   67     45   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    62_A     L    62_A     65   67   67     28   55   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    63_A     K    63_A     65   67   67      6   55   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    64_A     E    64_A     65   67   67     32   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Y    65_A     Y    65_A     65   67   67      5   46   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    66_A     Q    66_A     65   67   67      5    7   54   59   63   64   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    67_A     Q    67_A     65   67   67      3   57   61   62   63   65   66   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     N    68_A     N    68_A     63   67   67      0    3    3    4    8   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_AVERAGE  LCS_A:  98.98  (  96.93  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     45     57     61     62     63     65     66     66     67     67     67     67     67     67     67     67     67     67     67     67 
GDT PERCENT_AT  67.16  85.07  91.04  92.54  94.03  97.01  98.51  98.51 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.33   0.52   0.62   0.71   0.79   1.02   1.08   1.08   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23
GDT RMS_ALL_AT   1.41   1.32   1.32   1.29   1.27   1.24   1.24   1.24   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23

# Checking swapping
#   possible swapping detected:  E     4_A      E     4_A
#   possible swapping detected:  E     5_A      E     5_A
#   possible swapping detected:  E    12_A      E    12_A
#   possible swapping detected:  E    35_A      E    35_A
#   possible swapping detected:  E    40_A      E    40_A
#   possible swapping detected:  E    46_A      E    46_A
#   possible swapping detected:  E    47_A      E    47_A
#   possible swapping detected:  E    57_A      E    57_A
#   possible swapping detected:  E    60_A      E    60_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     2_A      S     2_A     3.989     0    0.053   0.070     4.837   46.905   41.746
LGA    P     3_A      P     3_A     2.491     0    0.082   0.256     3.469   60.952   57.279
LGA    E     4_A      E     4_A     3.442     0    0.042   1.334     8.669   55.476   34.974
LGA    E     5_A      E     5_A     2.213     0    0.022   1.088     4.916   73.452   55.556
LGA    Q     6_A      Q     6_A     0.684     0    0.031   0.504     2.080   92.976   86.825
LGA    K     7_A      K     7_A     0.996     0    0.033   0.595     4.026   90.476   70.899
LGA    Q     8_A      Q     8_A     1.208     0    0.022   1.224     5.260   85.952   65.608
LGA    M     9_A      M     9_A     0.800     0    0.035   0.953     2.274   95.238   85.179
LGA    L    10_A      L    10_A     0.361     0    0.023   0.844     3.663   97.619   81.071
LGA    G    11_A      G    11_A     0.621     0    0.038   0.038     0.775   92.857   92.857
LGA    E    12_A      E    12_A     0.550     0    0.071   0.906     1.921   92.857   87.672
LGA    A    13_A      A    13_A     0.634     0    0.061   0.059     0.951   90.476   90.476
LGA    I    14_A      I    14_A     0.682     0    0.019   1.011     2.906   90.476   77.976
LGA    Y    15_A      Y    15_A     0.655     0    0.039   0.236     0.868   90.476   90.476
LGA    P    16_A      P    16_A     0.731     0    0.027   0.351     2.022   90.476   85.510
LGA    K    17_A      K    17_A     0.646     0    0.032   0.502     2.844   92.857   84.868
LGA    V    18_A      V    18_A     0.368     0    0.043   0.108     0.540   97.619   97.279
LGA    A    19_A      A    19_A     0.264     0    0.066   0.064     0.456  100.000  100.000
LGA    A    20_A      A    20_A     0.511     0    0.119   0.121     1.139   90.595   90.571
LGA    S    21_A      S    21_A     0.975     0    0.216   0.209     1.666   95.238   87.778
LGA    Q    22_A      Q    22_A     0.482     0    0.137   1.170     3.039   92.857   82.063
LGA    P    23_A      P    23_A     0.635     0    0.071   0.077     0.943   90.476   90.476
LGA    E    24_A      E    24_A     0.639     0    0.021   1.022     4.153   90.476   70.317
LGA    L    25_A      L    25_A     0.688     0    0.104   0.100     1.795   95.238   87.321
LGA    A    26_A      A    26_A     0.460     0    0.020   0.039     0.573   97.619   96.190
LGA    G    27_A      G    27_A     0.683     0    0.026   0.026     0.683   90.476   90.476
LGA    K    28_A      K    28_A     0.605     0    0.019   0.539     2.264   95.238   85.820
LGA    L    29_A      L    29_A     0.402     0    0.039   0.094     1.101   95.238   91.726
LGA    T    30_A      T    30_A     0.668     0    0.047   0.908     2.783   90.476   80.952
LGA    G    31_A      G    31_A     0.759     0    0.029   0.029     0.759   90.476   90.476
LGA    M    32_A      M    32_A     0.465     0    0.025   0.662     1.676   97.619   89.583
LGA    I    33_A      I    33_A     0.412     0    0.017   0.179     1.017  100.000   94.107
LGA    L    34_A      L    34_A     0.534     0    0.079   0.844     2.186   97.619   87.500
LGA    E    35_A      E    35_A     0.363     0    0.030   0.723     2.898  100.000   81.799
LGA    L    36_A      L    36_A     0.513     0    0.036   0.827     2.142   92.857   87.619
LGA    P    37_A      P    37_A     0.862     0    0.051   0.121     1.141   90.476   89.184
LGA    V    38_A      V    38_A     0.868     0    0.033   1.248     3.265   90.476   78.912
LGA    T    39_A      T    39_A     0.854     0    0.031   1.100     3.344   90.476   78.639
LGA    E    40_A      E    40_A     0.607     0    0.039   0.706     2.451   95.238   83.862
LGA    L    41_A      L    41_A     0.494     0    0.028   0.975     2.504   95.238   87.857
LGA    L    42_A      L    42_A     0.622     0    0.042   0.196     1.638   92.857   87.202
LGA    H    43_A      H    43_A     0.172     0    0.035   0.923     2.704  100.000   87.667
LGA    L    44_A      L    44_A     0.398     0    0.069   0.106     0.831  100.000   95.238
LGA    L    45_A      L    45_A     0.606     0    0.055   0.262     1.691   92.857   89.464
LGA    E    46_A      E    46_A     0.667     0    0.050   0.730     2.628   88.214   78.995
LGA    E    47_A      E    47_A     0.633     0    0.102   0.825     3.010   90.476   78.307
LGA    S    48_A      S    48_A     0.148     0    0.029   0.064     0.267  100.000  100.000
LGA    E    49_A      E    49_A     0.372     0    0.108   0.921     2.886  100.000   85.344
LGA    A    50_A      A    50_A     0.082     0    0.036   0.045     0.261  100.000  100.000
LGA    L    51_A      L    51_A     0.252     0    0.045   0.212     0.713  100.000   98.810
LGA    D    52_A      D    52_A     0.258     0    0.038   1.205     4.904  100.000   80.714
LGA    A    53_A      A    53_A     0.308     0    0.036   0.038     0.385  100.000  100.000
LGA    K    54_A      K    54_A     0.315     0    0.037   0.240     0.488  100.000  100.000
LGA    V    55_A      V    55_A     0.207     0    0.021   0.128     0.457  100.000  100.000
LGA    N    56_A      N    56_A     0.313     0    0.036   0.094     0.469  100.000  100.000
LGA    E    57_A      E    57_A     0.475     0    0.048   0.541     1.927  100.000   91.799
LGA    A    58_A      A    58_A     0.474     0    0.049   0.049     0.657   95.238   96.190
LGA    L    59_A      L    59_A     0.332     0    0.024   0.895     3.358   95.238   85.655
LGA    E    60_A      E    60_A     0.752     0    0.040   1.370     5.703   90.476   72.063
LGA    V    61_A      V    61_A     0.781     0    0.030   0.139     1.113   88.214   87.891
LGA    L    62_A      L    62_A     1.270     0    0.068   0.973     3.482   79.286   77.560
LGA    K    63_A      K    63_A     1.543     0    0.022   0.938     2.297   77.143   75.873
LGA    E    64_A      E    64_A     1.007     0    0.042   0.300     2.800   81.548   73.280
LGA    Y    65_A      Y    65_A     1.877     0    0.031   0.292     6.785   66.905   46.944
LGA    Q    66_A      Q    66_A     2.837     0    0.154   1.115     5.807   66.905   46.349
LGA    Q    67_A      Q    67_A     1.102     0    0.176   1.082     7.110   71.190   52.116
LGA    N    68_A      N    68_A     5.192     0    0.500   1.134     9.592   25.119   14.702

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       67     268    268  100.00     519    519  100.00                67
SUMMARY(RMSD_GDC):     1.228          1.229                  2.036           89.600   81.965

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   68   67    4.0     66    1.08    94.030    96.891     5.609

LGA_LOCAL      RMSD:   1.077  Number of atoms:   66  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.243  Number of assigned atoms:   67 
Std_ASGN_ATOMS RMSD:   1.228  Standard rmsd on all 67 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.978737 * X  +  -0.073050 * Y  +   0.191671 * Z  +   8.101828
  Y_new =  -0.153488 * X  +  -0.359060 * Y  +  -0.920607 * Z  +  15.525075
  Z_new =   0.136072 * X  +  -0.930451 * Y  +   0.340213 * Z  +   7.929588 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.986037 -0.136495 -1.220254   [DEG: -171.0873   -7.8206  -69.9154 ]
ZXZ:  0.205269  1.223653  2.996379   [DEG:   11.7610   70.1101  171.6799 ]
 
# END of job
