
#######################################################
#                                                     #
#                        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        0.86     0.86
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.86     0.86
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.86     0.86
  LCS_AVERAGE:    100.00

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     67   67   67      5   44   58   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P     3_A     P     3_A     67   67   67      5   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E     4_A     E     4_A     67   67   67      5   18   57   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E     5_A     E     5_A     67   67   67      6   37   57   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q     6_A     Q     6_A     67   67   67     29   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K     7_A     K     7_A     67   67   67     30   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q     8_A     Q     8_A     67   67   67     10   55   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     M     9_A     M     9_A     67   67   67     23   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    10_A     L    10_A     67   67   67     39   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    11_A     G    11_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    12_A     E    12_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    13_A     A    13_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    14_A     I    14_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Y    15_A     Y    15_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    16_A     P    16_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    17_A     K    17_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    18_A     V    18_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    19_A     A    19_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    20_A     A    20_A     67   67   67     35   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    21_A     S    21_A     67   67   67      3   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    22_A     Q    22_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    23_A     P    23_A     67   67   67     35   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    24_A     E    24_A     67   67   67     35   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    25_A     L    25_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    26_A     A    26_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    27_A     G    27_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    28_A     K    28_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    29_A     L    29_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     T    30_A     T    30_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    31_A     G    31_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     M    32_A     M    32_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    33_A     I    33_A     67   67   67     39   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    34_A     L    34_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    35_A     E    35_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    36_A     L    36_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    37_A     P    37_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    38_A     V    38_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     T    39_A     T    39_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    40_A     E    40_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    41_A     L    41_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    42_A     L    42_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     H    43_A     H    43_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    44_A     L    44_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    45_A     L    45_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    46_A     E    46_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    47_A     E    47_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    48_A     S    48_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    49_A     E    49_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    50_A     A    50_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    51_A     L    51_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     D    52_A     D    52_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    53_A     A    53_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    54_A     K    54_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    55_A     V    55_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     N    56_A     N    56_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    57_A     E    57_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    58_A     A    58_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    59_A     L    59_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    60_A     E    60_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    61_A     V    61_A     67   67   67     37   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    62_A     L    62_A     67   67   67     42   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    63_A     K    63_A     67   67   67     18   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    64_A     E    64_A     67   67   67     11   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Y    65_A     Y    65_A     67   67   67     15   56   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    66_A     Q    66_A     67   67   67      5   55   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    67_A     Q    67_A     67   67   67     14   55   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     N    68_A     N    68_A     67   67   67      3   19   41   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_AVERAGE  LCS_A: 100.00  ( 100.00  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     42     56     63     65     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67 
GDT PERCENT_AT  62.69  83.58  94.03  97.01 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.47   0.63   0.73   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86
GDT RMS_ALL_AT   0.96   0.95   0.89   0.87   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86

# Checking swapping
#   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    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     2.095     0    0.054   0.102     3.437   67.262   63.968
LGA    P     3_A      P     3_A     0.618     0    0.067   0.078     1.248   90.595   87.959
LGA    E     4_A      E     4_A     2.141     0    0.050   0.809     6.466   70.833   51.111
LGA    E     5_A      E     5_A     2.053     0    0.071   0.368     5.278   75.119   55.820
LGA    Q     6_A      Q     6_A     0.922     0    0.025   1.066     2.916   88.214   83.810
LGA    K     7_A      K     7_A     0.838     0    0.038   0.931     2.604   90.476   81.058
LGA    Q     8_A      Q     8_A     1.276     0    0.032   1.004     5.297   83.690   69.153
LGA    M     9_A      M     9_A     0.993     0    0.025   0.771     3.495   88.214   79.821
LGA    L    10_A      L    10_A     0.380     0    0.045   0.126     0.579  100.000   98.810
LGA    G    11_A      G    11_A     0.272     0    0.031   0.031     0.388  100.000  100.000
LGA    E    12_A      E    12_A     0.383     0    0.052   0.975     3.641   95.238   82.910
LGA    A    13_A      A    13_A     0.508     0    0.068   0.066     0.792   92.857   92.381
LGA    I    14_A      I    14_A     0.380     0    0.016   0.977     2.607  100.000   85.833
LGA    Y    15_A      Y    15_A     0.357     0    0.045   0.374     2.239  100.000   87.857
LGA    P    16_A      P    16_A     0.437     0    0.025   0.343     1.640   95.238   92.041
LGA    K    17_A      K    17_A     0.548     0    0.029   1.083     4.190   90.476   77.196
LGA    V    18_A      V    18_A     0.417     0    0.038   1.089     2.368   95.238   87.211
LGA    A    19_A      A    19_A     0.606     0    0.071   0.070     0.982   90.476   92.381
LGA    A    20_A      A    20_A     0.923     0    0.110   0.113     1.549   83.810   85.143
LGA    S    21_A      S    21_A     1.149     0    0.162   0.651     1.782   88.214   84.524
LGA    Q    22_A      Q    22_A     0.630     0    0.148   0.860     2.984   90.476   79.947
LGA    P    23_A      P    23_A     1.087     0    0.051   0.349     1.269   83.690   85.306
LGA    E    24_A      E    24_A     1.121     0    0.054   0.765     2.752   85.952   76.984
LGA    L    25_A      L    25_A     0.938     0    0.088   0.122     1.167   90.476   87.083
LGA    A    26_A      A    26_A     0.694     0    0.024   0.042     0.776   92.857   92.381
LGA    G    27_A      G    27_A     0.615     0    0.021   0.021     0.714   92.857   92.857
LGA    K    28_A      K    28_A     0.653     0    0.026   0.619     3.131   90.476   81.058
LGA    L    29_A      L    29_A     0.453     0    0.048   1.438     4.140   95.238   76.964
LGA    T    30_A      T    30_A     0.504     0    0.050   0.112     0.799   95.238   93.197
LGA    G    31_A      G    31_A     0.495     0    0.029   0.029     0.528   97.619   97.619
LGA    M    32_A      M    32_A     0.503     0    0.034   0.185     1.385   97.619   91.786
LGA    I    33_A      I    33_A     0.518     0    0.018   0.162     1.009   92.857   90.536
LGA    L    34_A      L    34_A     0.480     0    0.084   0.117     0.988  100.000   95.238
LGA    E    35_A      E    35_A     0.333     0    0.027   1.080     3.928  100.000   77.090
LGA    L    36_A      L    36_A     0.253     0    0.031   0.181     0.895  100.000   97.619
LGA    P    37_A      P    37_A     0.503     0    0.038   0.360     1.226   97.619   93.265
LGA    V    38_A      V    38_A     0.558     0    0.027   0.918     2.745   92.857   84.558
LGA    T    39_A      T    39_A     0.450     0    0.054   1.110     2.771   97.619   86.395
LGA    E    40_A      E    40_A     0.063     0    0.029   0.567     1.776  100.000   92.804
LGA    L    41_A      L    41_A     0.353     0    0.029   0.082     0.464  100.000  100.000
LGA    L    42_A      L    42_A     0.474     0    0.034   1.404     2.972   97.619   84.702
LGA    H    43_A      H    43_A     0.392     0    0.033   0.312     1.086  100.000   93.429
LGA    L    44_A      L    44_A     0.317     0    0.061   0.096     0.412  100.000  100.000
LGA    L    45_A      L    45_A     0.473     0    0.055   0.193     1.120   95.238   94.107
LGA    E    46_A      E    46_A     0.620     0    0.077   0.771     3.125   90.476   78.519
LGA    E    47_A      E    47_A     0.536     0    0.053   1.051     3.455   92.857   77.037
LGA    S    48_A      S    48_A     0.210     0    0.027   0.635     2.073  100.000   94.127
LGA    E    49_A      E    49_A     0.577     0    0.108   0.851     4.070   97.619   81.005
LGA    A    50_A      A    50_A     0.247     0    0.029   0.041     0.303  100.000  100.000
LGA    L    51_A      L    51_A     0.184     0    0.042   0.156     0.443  100.000  100.000
LGA    D    52_A      D    52_A     0.241     0    0.036   0.111     0.614  100.000   98.810
LGA    A    53_A      A    53_A     0.464     0    0.045   0.046     0.568  100.000   98.095
LGA    K    54_A      K    54_A     0.324     0    0.032   0.675     1.674   97.619   90.794
LGA    V    55_A      V    55_A     0.290     0    0.031   0.124     0.462  100.000  100.000
LGA    N    56_A      N    56_A     0.394     0    0.030   0.060     0.761  100.000   96.429
LGA    E    57_A      E    57_A     0.397     0    0.040   0.500     1.760  100.000   93.810
LGA    A    58_A      A    58_A     0.437     0    0.026   0.036     0.506   97.619   98.095
LGA    L    59_A      L    59_A     0.315     0    0.039   0.903     3.162   97.619   90.238
LGA    E    60_A      E    60_A     0.743     0    0.068   0.631     2.759   90.476   78.254
LGA    V    61_A      V    61_A     0.786     0    0.018   0.900     2.165   88.214   82.993
LGA    L    62_A      L    62_A     0.687     0    0.029   1.413     3.454   90.476   77.143
LGA    K    63_A      K    63_A     0.985     0    0.046   0.824     3.930   85.952   73.175
LGA    E    64_A      E    64_A     1.242     0    0.064   0.861     5.345   81.548   62.434
LGA    Y    65_A      Y    65_A     1.299     0    0.054   0.369     3.825   79.286   66.786
LGA    Q    66_A      Q    66_A     1.157     0    0.172   0.442     3.534   88.214   76.455
LGA    Q    67_A      Q    67_A     1.155     0    0.534   1.398     4.460   77.262   65.291
LGA    N    68_A      N    68_A     2.872     0    0.338   1.211     4.480   47.143   45.357

# 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):     0.855          0.898                  1.626           92.159   85.205

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   68   67    4.0     67    0.86    95.149    98.049     7.012

LGA_LOCAL      RMSD:   0.855  Number of atoms:   67  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.855  Number of assigned atoms:   67 
Std_ASGN_ATOMS RMSD:   0.855  Standard rmsd on all 67 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.166487 * X  +  -0.283101 * Y  +  -0.944530 * Z  +  17.297680
  Y_new =  -0.886065 * X  +  -0.463237 * Y  +  -0.017337 * Z  +  14.980090
  Z_new =  -0.432633 * X  +   0.839801 * Y  +  -0.327968 * Z  +   1.813660 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.385067  0.447411  1.943113   [DEG:  -79.3585   25.6348  111.3322 ]
ZXZ: -1.552443  1.904949 -0.475703   [DEG:  -88.9484  109.1455  -27.2558 ]
 
# END of job
