
#######################################################
#                                                     #
#                        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        0.68     0.68
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.68     0.68
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.68     0.68
  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     11   41   61   67   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     11   59   65   67   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     11   43   65   67   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     12   56   65   67   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     42   62   65   67   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     44   62   65   67   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     28   62   65   67   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     22   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     36   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     26   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     44   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     32   62   65   67   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     47   62   65   67   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     47   62   65   67   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   62   65   67   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     32   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     47   62   65   67   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     26   62   65   67   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     26   62   65   67   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     34   62   65   67   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     22   62   65   67   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     41   62   65   67   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    3   59   67   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     47     62     65     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67 
GDT PERCENT_AT  70.15  92.54  97.01 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.31   0.47   0.57   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68
GDT RMS_ALL_AT   0.77   0.73   0.69   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68

# Checking swapping
#   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    64_A      E    64_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     2_A      S     2_A     2.000     0    0.087   0.649     2.776   73.095   69.048
LGA    P     3_A      P     3_A     1.059     0    0.044   0.081     1.572   83.690   81.497
LGA    E     4_A      E     4_A     1.654     0    0.038   0.724     5.046   77.143   60.317
LGA    E     5_A      E     5_A     1.278     0    0.046   0.412     4.526   85.952   67.354
LGA    Q     6_A      Q     6_A     0.381     0    0.040   0.474     2.350   97.619   86.032
LGA    K     7_A      K     7_A     0.549     0    0.025   0.804     1.693   97.619   86.720
LGA    Q     8_A      Q     8_A     0.678     0    0.039   1.063     5.741   90.476   70.000
LGA    M     9_A      M     9_A     0.715     0    0.043   0.855     2.403   92.857   86.310
LGA    L    10_A      L    10_A     0.575     0    0.050   0.101     1.296   97.619   91.786
LGA    G    11_A      G    11_A     0.432     0    0.027   0.027     0.527   97.619   97.619
LGA    E    12_A      E    12_A     0.487     0    0.036   0.686     2.424   95.238   85.873
LGA    A    13_A      A    13_A     0.397     0    0.062   0.060     0.599   97.619   98.095
LGA    I    14_A      I    14_A     0.323     0    0.014   1.332     3.366  100.000   83.095
LGA    Y    15_A      Y    15_A     0.280     0    0.039   0.279     1.333  100.000   92.976
LGA    P    16_A      P    16_A     0.360     0    0.030   0.356     1.630   97.619   93.401
LGA    K    17_A      K    17_A     0.414     0    0.027   1.067     2.560  100.000   87.196
LGA    V    18_A      V    18_A     0.253     0    0.036   0.993     2.482  100.000   89.932
LGA    A    19_A      A    19_A     0.372     0    0.068   0.067     0.544   97.619   98.095
LGA    A    20_A      A    20_A     0.578     0    0.116   0.119     1.176   90.595   90.571
LGA    S    21_A      S    21_A     0.618     0    0.181   0.661     1.326   97.619   92.222
LGA    Q    22_A      Q    22_A     0.378     0    0.178   0.899     2.476  100.000   85.979
LGA    P    23_A      P    23_A     0.540     0    0.047   0.342     0.779   97.619   97.279
LGA    E    24_A      E    24_A     0.468     0    0.025   0.431     1.253  100.000   91.693
LGA    L    25_A      L    25_A     0.521     0    0.116   0.144     0.979   97.619   94.048
LGA    A    26_A      A    26_A     0.427     0    0.029   0.046     0.455  100.000  100.000
LGA    G    27_A      G    27_A     0.568     0    0.023   0.023     0.568   90.476   90.476
LGA    K    28_A      K    28_A     0.540     0    0.018   1.463     7.539   95.238   70.688
LGA    L    29_A      L    29_A     0.283     0    0.036   1.006     2.874  100.000   90.060
LGA    T    30_A      T    30_A     0.510     0    0.036   0.082     0.890   92.857   91.837
LGA    G    31_A      G    31_A     0.633     0    0.033   0.033     0.633   95.238   95.238
LGA    M    32_A      M    32_A     0.345     0    0.022   0.766     2.526  100.000   94.643
LGA    I    33_A      I    33_A     0.254     0    0.016   0.157     0.571  100.000   97.619
LGA    L    34_A      L    34_A     0.427     0    0.089   0.103     1.282  100.000   92.976
LGA    E    35_A      E    35_A     0.342     0    0.021   1.276     5.168  100.000   74.974
LGA    L    36_A      L    36_A     0.458     0    0.025   1.014     3.071  100.000   88.155
LGA    P    37_A      P    37_A     0.813     0    0.047   0.357     1.157   90.476   87.891
LGA    V    38_A      V    38_A     0.610     0    0.027   0.128     1.208   95.238   91.905
LGA    T    39_A      T    39_A     0.283     0    0.044   0.060     0.525   97.619   98.639
LGA    E    40_A      E    40_A     0.284     0    0.040   0.763     1.875  100.000   92.804
LGA    L    41_A      L    41_A     0.289     0    0.039   0.128     1.199  100.000   92.976
LGA    L    42_A      L    42_A     0.438     0    0.042   1.018     3.691   97.619   86.012
LGA    H    43_A      H    43_A     0.680     0    0.034   0.271     2.088   92.857   83.524
LGA    L    44_A      L    44_A     0.338     0    0.033   1.080     2.813  100.000   90.060
LGA    L    45_A      L    45_A     0.317     0    0.068   0.245     1.190   97.619   95.298
LGA    E    46_A      E    46_A     0.579     0    0.082   0.402     1.091   90.476   90.529
LGA    E    47_A      E    47_A     0.502     0    0.071   1.061     3.081   97.619   80.582
LGA    S    48_A      S    48_A     0.225     0    0.037   0.627     2.061  100.000   92.540
LGA    E    49_A      E    49_A     0.626     0    0.101   1.311     4.195   97.619   71.799
LGA    A    50_A      A    50_A     0.498     0    0.027   0.037     0.547  100.000   98.095
LGA    L    51_A      L    51_A     0.271     0    0.038   0.209     0.866  100.000   98.810
LGA    D    52_A      D    52_A     0.553     0    0.036   1.005     4.096   90.476   77.381
LGA    A    53_A      A    53_A     0.712     0    0.050   0.050     0.877   90.476   90.476
LGA    K    54_A      K    54_A     0.478     0    0.032   0.762     2.951   95.238   83.175
LGA    V    55_A      V    55_A     0.503     0    0.030   0.118     0.671   92.857   91.837
LGA    N    56_A      N    56_A     0.521     0    0.023   1.129     3.046   95.238   85.595
LGA    E    57_A      E    57_A     0.357     0    0.050   0.611     1.821  100.000   89.788
LGA    A    58_A      A    58_A     0.342     0    0.035   0.042     0.440  100.000  100.000
LGA    L    59_A      L    59_A     0.200     0    0.036   0.627     2.377  100.000   92.083
LGA    E    60_A      E    60_A     0.484     0    0.050   1.021     4.576   95.238   76.667
LGA    V    61_A      V    61_A     0.567     0    0.034   0.144     0.865   92.857   91.837
LGA    L    62_A      L    62_A     0.458     0    0.028   0.100     0.709   95.238   96.429
LGA    K    63_A      K    63_A     0.827     0    0.038   1.169     4.359   88.214   74.392
LGA    E    64_A      E    64_A     1.011     0    0.037   1.104     5.694   83.690   62.804
LGA    Y    65_A      Y    65_A     0.882     0    0.079   0.216     1.436   88.214   85.952
LGA    Q    66_A      Q    66_A     0.863     0    0.141   0.141     2.620   92.857   79.153
LGA    Q    67_A      Q    67_A     0.640     0    0.155   1.028     4.721   88.214   69.947
LGA    N    68_A      N    68_A     2.198     0    0.452   0.724     6.463   48.690   52.024

# 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):     0.680          0.785                  1.543           94.533   86.788

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   68   67    4.0     67    0.68    98.134    99.188     8.592

LGA_LOCAL      RMSD:   0.680  Number of atoms:   67  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.680  Number of assigned atoms:   67 
Std_ASGN_ATOMS RMSD:   0.680  Standard rmsd on all 67 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.496045 * X  +   0.672042 * Y  +  -0.549817 * Z  +   8.541007
  Y_new =   0.724798 * X  +   0.669158 * Y  +   0.164000 * Z  +  18.011812
  Z_new =   0.478129 * X  +  -0.317155 * Y  +  -0.819027 * Z  +   0.699736 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.170969 -0.498523 -2.772140   [DEG:  124.3874  -28.5633 -158.8319 ]
ZXZ: -1.860675  2.530510  2.156482   [DEG: -106.6088  144.9875  123.5573 ]
 
# END of job
