
#######################################################
#                                                     #
#                        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        0.70     0.70
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.70     0.70
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.70     0.70
  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     13   43   64   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     24   50   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     24   50   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     15   51   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     27   61   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     45   61   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     38   61   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     36   61   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     52   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     56   61   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     40   61   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      5    5   39   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     56     61     65     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67 
GDT PERCENT_AT  83.58  91.04  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    0.25   0.35   0.56   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70
GDT RMS_ALL_AT   0.85   0.80   0.72   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70

# 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:  Y    15_A      Y    15_A
#   possible swapping detected:  E    40_A      E    40_A
#   possible swapping detected:  E    49_A      E    49_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     2.273     0    0.020   0.075     2.352   68.810   67.460
LGA    P     3_A      P     3_A     1.640     0    0.009   0.034     1.956   77.143   75.306
LGA    E     4_A      E     4_A     1.374     0    0.024   0.649     4.044   79.286   62.646
LGA    E     5_A      E     5_A     1.321     0    0.066   0.507     3.911   83.690   68.413
LGA    Q     6_A      Q     6_A     1.120     0    0.016   0.309     1.550   85.952   81.534
LGA    K     7_A      K     7_A     0.368     0    0.027   0.622     1.801   97.619   89.788
LGA    Q     8_A      Q     8_A     0.546     0    0.062   0.790     4.170   97.619   79.524
LGA    M     9_A      M     9_A     0.553     0    0.028   0.824     1.644   95.238   88.393
LGA    L    10_A      L    10_A     0.502     0    0.033   0.082     0.664   95.238   96.429
LGA    G    11_A      G    11_A     0.503     0    0.050   0.050     0.623   92.857   92.857
LGA    E    12_A      E    12_A     0.637     0    0.012   0.802     2.875   90.476   83.757
LGA    A    13_A      A    13_A     0.451     0    0.024   0.039     0.555   97.619   96.190
LGA    I    14_A      I    14_A     0.359     0    0.020   0.047     0.380  100.000  100.000
LGA    Y    15_A      Y    15_A     0.385     0    0.009   0.255     0.823  100.000   94.444
LGA    P    16_A      P    16_A     0.312     0    0.018   0.310     1.333  100.000   97.347
LGA    K    17_A      K    17_A     0.373     0    0.019   0.685     2.419  100.000   92.011
LGA    V    18_A      V    18_A     0.449     0    0.007   0.103     0.491  100.000  100.000
LGA    A    19_A      A    19_A     0.411     0    0.019   0.020     0.568   97.619   98.095
LGA    A    20_A      A    20_A     0.388     0    0.057   0.077     0.603   97.619   98.095
LGA    S    21_A      S    21_A     0.199     0    0.070   0.101     0.416  100.000  100.000
LGA    Q    22_A      Q    22_A     0.212     0    0.051   0.206     0.644  100.000   98.942
LGA    P    23_A      P    23_A     0.263     0    0.065   0.065     0.564   97.619   98.639
LGA    E    24_A      E    24_A     0.467     0    0.066   0.537     1.646   95.238   92.751
LGA    L    25_A      L    25_A     0.380     0    0.032   0.060     0.649  100.000   96.429
LGA    A    26_A      A    26_A     0.311     0    0.027   0.035     0.534  100.000   98.095
LGA    G    27_A      G    27_A     0.328     0    0.011   0.011     0.382  100.000  100.000
LGA    K    28_A      K    28_A     0.408     0    0.020   0.715     4.037  100.000   85.185
LGA    L    29_A      L    29_A     0.191     0    0.027   0.065     0.470  100.000  100.000
LGA    T    30_A      T    30_A     0.270     0    0.013   0.067     0.412  100.000  100.000
LGA    G    31_A      G    31_A     0.520     0    0.033   0.033     0.520   97.619   97.619
LGA    M    32_A      M    32_A     0.351     0    0.029   0.085     0.493  100.000  100.000
LGA    I    33_A      I    33_A     0.172     0    0.038   0.085     0.360  100.000  100.000
LGA    L    34_A      L    34_A     0.228     0    0.024   0.083     0.365  100.000  100.000
LGA    E    35_A      E    35_A     0.484     0    0.009   0.728     3.065   95.238   74.603
LGA    L    36_A      L    36_A     0.402     0    0.035   0.079     0.577   95.238   97.619
LGA    P    37_A      P    37_A     0.567     0    0.071   0.317     1.435   90.476   90.544
LGA    V    38_A      V    38_A     0.854     0    0.022   0.045     1.173   90.476   87.891
LGA    T    39_A      T    39_A     0.918     0    0.025   1.008     3.412   90.476   79.728
LGA    E    40_A      E    40_A     0.575     0    0.055   0.823     3.612   90.476   79.735
LGA    L    41_A      L    41_A     0.452     0    0.028   0.060     0.567   95.238   97.619
LGA    L    42_A      L    42_A     0.710     0    0.047   0.064     0.988   90.476   90.476
LGA    H    43_A      H    43_A     0.756     0    0.024   1.147     2.811   90.476   81.095
LGA    L    44_A      L    44_A     0.559     0    0.013   0.082     0.586   90.476   91.667
LGA    L    45_A      L    45_A     0.501     0    0.025   0.092     0.543   92.857   95.238
LGA    E    46_A      E    46_A     0.622     0    0.029   0.844     3.219   90.476   74.868
LGA    E    47_A      E    47_A     0.681     0    0.082   1.080     4.074   92.857   77.196
LGA    S    48_A      S    48_A     0.613     0    0.029   0.621     2.841   90.476   84.921
LGA    E    49_A      E    49_A     0.484     0    0.080   0.204     0.709   97.619   95.767
LGA    A    50_A      A    50_A     0.189     0    0.004   0.014     0.254  100.000  100.000
LGA    L    51_A      L    51_A     0.264     0    0.018   0.087     0.721  100.000   96.429
LGA    D    52_A      D    52_A     0.253     0    0.010   0.158     0.744  100.000   96.429
LGA    A    53_A      A    53_A     0.335     0    0.055   0.071     0.537  100.000   98.095
LGA    K    54_A      K    54_A     0.109     0    0.021   0.568     1.790  100.000   93.810
LGA    V    55_A      V    55_A     0.118     0    0.017   0.038     0.227  100.000  100.000
LGA    N    56_A      N    56_A     0.199     0    0.040   0.057     0.293  100.000  100.000
LGA    E    57_A      E    57_A     0.299     0    0.015   0.155     0.659  100.000   98.942
LGA    A    58_A      A    58_A     0.226     0    0.021   0.020     0.277  100.000  100.000
LGA    L    59_A      L    59_A     0.181     0    0.017   1.271     2.725  100.000   87.917
LGA    E    60_A      E    60_A     0.425     0    0.118   1.117     4.922   97.619   77.725
LGA    V    61_A      V    61_A     0.361     0    0.024   0.068     0.543   97.619   98.639
LGA    L    62_A      L    62_A     0.520     0    0.033   0.152     1.064   92.857   90.536
LGA    K    63_A      K    63_A     0.638     0    0.011   0.221     1.159   90.476   88.466
LGA    E    64_A      E    64_A     0.399     0    0.026   0.919     3.013   97.619   79.101
LGA    Y    65_A      Y    65_A     0.586     0    0.064   1.127     6.018   92.857   68.135
LGA    Q    66_A      Q    66_A     1.076     0    0.015   0.258     3.146   88.214   75.344
LGA    Q    67_A      Q    67_A     0.780     0    0.340   0.623     3.648   88.214   74.815
LGA    N    68_A      N    68_A     2.521     0    0.096   1.095     6.123   43.333   41.071

# 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):     0.703          0.805                  1.351           94.319   89.468

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   68   67    4.0     67    0.70    97.761    99.070     8.339

LGA_LOCAL      RMSD:   0.703  Number of atoms:   67  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.703  Number of assigned atoms:   67 
Std_ASGN_ATOMS RMSD:   0.703  Standard rmsd on all 67 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.424141 * X  +  -0.458086 * Y  +   0.781192 * Z  +   7.206853
  Y_new =  -0.766053 * X  +   0.641549 * Y  +  -0.039720 * Z  +   4.005661
  Z_new =  -0.482978 * X  +  -0.615282 * Y  +  -0.623025 * Z  +   6.606409 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.076453  0.504053 -2.362448   [DEG: -118.9720   28.8801 -135.3583 ]
ZXZ:  1.519994  2.243401 -2.476083   [DEG:   87.0893  128.5374 -141.8691 ]
 
# END of job
