
#######################################################
#                                                     #
#                        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        0.97     0.97
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.97     0.97
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.97     0.97
  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     10   19   37   62   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     13   42   64   66   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     10   34   52   66   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   34   51   66   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     13   38   64   66   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     13   52   64   66   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     12   38   64   66   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     13   46   64   66   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     22   58   64   66   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     35   58   64   66   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     35   58   64   66   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     35   58   64   66   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     35   58   64   66   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     35   58   64   66   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     35   58   64   66   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     35   58   64   66   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     35   58   64   66   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     35   58   64   66   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   58   64   66   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      4   58   64   66   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     29   58   64   66   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     11   58   64   66   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   58   64   66   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     35   58   64   66   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     35   58   64   66   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     35   58   64   66   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     35   58   64   66   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     35   58   64   66   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     32   58   64   66   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     35   58   64   66   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     35   58   64   66   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     21   58   64   66   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     15   58   64   66   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     20   58   64   66   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     20   58   64   66   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     19   58   64   66   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     19   58   64   66   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     19   58   64   66   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     19   58   64   66   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     29   58   64   66   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     19   58   64   66   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     31   58   64   66   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     31   58   64   66   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     29   58   64   66   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     19   58   64   66   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     32   58   64   66   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     35   58   64   66   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     29   58   64   66   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     35   58   64   66   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     35   58   64   66   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     35   58   64   66   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     35   58   64   66   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     35   58   64   66   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     35   58   64   66   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     35   58   64   66   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     35   58   64   66   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     35   58   64   66   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     35   58   64   66   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     35   58   64   66   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     35   58   64   66   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     35   58   64   66   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     35   58   64   66   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     35   58   64   66   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     14   58   64   66   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     35   58   64   66   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     35   58   64   66   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   49   64   66   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     35     58     64     66     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67 
GDT PERCENT_AT  52.24  86.57  95.52  98.51 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.33   0.56   0.78   0.89   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97
GDT RMS_ALL_AT   1.08   1.14   1.00   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97   0.97

# Checking swapping
#   possible swapping detected:  E     5_A      E     5_A
#   possible swapping detected:  E    12_A      E    12_A
#   possible swapping detected:  E    24_A      E    24_A
#   possible swapping detected:  E    35_A      E    35_A
#   possible swapping detected:  E    46_A      E    46_A
#   possible swapping detected:  E    64_A      E    64_A
#   possible swapping detected:  Y    65_A      Y    65_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     2_A      S     2_A     3.170     0    0.065   0.067     3.645   55.714   51.587
LGA    P     3_A      P     3_A     1.359     0    0.046   0.257     2.095   81.548   79.116
LGA    E     4_A      E     4_A     2.246     0    0.047   0.627     5.412   66.786   54.868
LGA    E     5_A      E     5_A     2.294     0    0.059   0.743     6.670   70.952   46.243
LGA    Q     6_A      Q     6_A     1.411     0    0.040   0.868     2.061   81.548   80.635
LGA    K     7_A      K     7_A     0.916     0    0.037   0.795     2.925   88.214   74.497
LGA    Q     8_A      Q     8_A     1.525     0    0.037   0.857     2.929   79.286   71.270
LGA    M     9_A      M     9_A     1.212     0    0.027   0.912     1.975   85.952   81.548
LGA    L    10_A      L    10_A     0.387     0    0.057   0.150     0.572   97.619   97.619
LGA    G    11_A      G    11_A     0.325     0    0.032   0.032     0.535   97.619   97.619
LGA    E    12_A      E    12_A     0.355     0    0.061   0.956     3.416   95.238   78.095
LGA    A    13_A      A    13_A     0.510     0    0.064   0.062     0.842   92.857   92.381
LGA    I    14_A      I    14_A     0.508     0    0.020   1.217     3.196   92.857   78.274
LGA    Y    15_A      Y    15_A     0.457     0    0.038   0.244     1.120  100.000   92.143
LGA    P    16_A      P    16_A     0.479     0    0.024   0.046     0.521   95.238   97.279
LGA    K    17_A      K    17_A     0.477     0    0.026   0.785     3.212   97.619   86.190
LGA    V    18_A      V    18_A     0.262     0    0.042   0.094     0.418  100.000  100.000
LGA    A    19_A      A    19_A     0.247     0    0.070   0.070     0.446  100.000  100.000
LGA    A    20_A      A    20_A     0.414     0    0.109   0.110     0.990   95.238   96.190
LGA    S    21_A      S    21_A     0.950     0    0.172   0.658     1.535   90.476   86.032
LGA    Q    22_A      Q    22_A     0.502     0    0.116   0.239     1.073   90.476   89.471
LGA    P    23_A      P    23_A     0.719     0    0.051   0.145     0.906   90.476   90.476
LGA    E    24_A      E    24_A     0.623     0    0.037   1.209     3.902   92.857   77.778
LGA    L    25_A      L    25_A     0.546     0    0.060   0.921     3.258   95.238   85.536
LGA    A    26_A      A    26_A     0.354     0    0.021   0.037     0.424  100.000  100.000
LGA    G    27_A      G    27_A     0.376     0    0.025   0.025     0.423  100.000  100.000
LGA    K    28_A      K    28_A     0.339     0    0.027   0.099     1.114  100.000   92.698
LGA    L    29_A      L    29_A     0.237     0    0.033   0.117     0.788  100.000   98.810
LGA    T    30_A      T    30_A     0.536     0    0.049   0.097     0.740   92.857   91.837
LGA    G    31_A      G    31_A     0.498     0    0.036   0.036     0.509   97.619   97.619
LGA    M    32_A      M    32_A     0.092     0    0.024   1.040     2.384  100.000   90.000
LGA    I    33_A      I    33_A     0.590     0    0.023   0.875     3.094   92.857   79.226
LGA    L    34_A      L    34_A     0.746     0    0.090   0.142     1.242   90.476   87.083
LGA    E    35_A      E    35_A     0.927     0    0.023   0.664     3.416   88.214   72.063
LGA    L    36_A      L    36_A     1.059     0    0.046   0.786     2.851   83.690   81.786
LGA    P    37_A      P    37_A     1.228     0    0.037   0.112     1.621   81.429   80.204
LGA    V    38_A      V    38_A     1.395     0    0.034   0.201     2.110   81.429   76.599
LGA    T    39_A      T    39_A     1.414     0    0.027   1.032     3.797   81.429   73.605
LGA    E    40_A      E    40_A     1.184     0    0.028   0.382     2.549   83.690   78.783
LGA    L    41_A      L    41_A     1.008     0    0.032   0.103     1.058   81.429   85.952
LGA    L    42_A      L    42_A     1.192     0    0.027   1.386     3.133   81.429   75.417
LGA    H    43_A      H    43_A     0.741     0    0.034   0.291     0.916   90.476   91.429
LGA    L    44_A      L    44_A     0.721     0    0.061   0.119     0.791   90.476   91.667
LGA    L    45_A      L    45_A     1.000     0    0.045   0.168     1.399   85.952   84.821
LGA    E    46_A      E    46_A     1.186     0    0.108   0.693     3.726   81.429   65.979
LGA    E    47_A      E    47_A     0.826     0    0.086   0.863     2.849   90.476   83.810
LGA    S    48_A      S    48_A     0.619     0    0.039   0.637     2.539   92.857   86.508
LGA    E    49_A      E    49_A     0.842     0    0.120   1.447     5.420   90.476   69.894
LGA    A    50_A      A    50_A     0.208     0    0.034   0.046     0.452  100.000  100.000
LGA    L    51_A      L    51_A     0.233     0    0.042   0.155     0.412  100.000  100.000
LGA    D    52_A      D    52_A     0.425     0    0.039   0.938     3.182   95.238   83.571
LGA    A    53_A      A    53_A     0.615     0    0.038   0.040     0.825   90.476   92.381
LGA    K    54_A      K    54_A     0.561     0    0.028   0.555     2.023   90.476   86.667
LGA    V    55_A      V    55_A     0.266     0    0.029   1.130     2.394  100.000   89.932
LGA    N    56_A      N    56_A     0.751     0    0.031   0.853     2.674   90.476   80.893
LGA    E    57_A      E    57_A     0.849     0    0.052   0.251     1.191   90.476   89.471
LGA    A    58_A      A    58_A     0.782     0    0.043   0.047     0.862   90.476   90.476
LGA    L    59_A      L    59_A     0.564     0    0.028   0.773     1.993   92.857   87.262
LGA    E    60_A      E    60_A     0.882     0    0.040   1.206     6.072   90.476   67.619
LGA    V    61_A      V    61_A     0.923     0    0.024   0.887     2.403   90.476   84.286
LGA    L    62_A      L    62_A     0.760     0    0.036   0.969     3.315   90.476   84.286
LGA    K    63_A      K    63_A     0.839     0    0.039   1.851     6.846   90.476   66.138
LGA    E    64_A      E    64_A     1.009     0    0.039   0.667     3.355   83.690   68.466
LGA    Y    65_A      Y    65_A     1.292     0    0.083   1.325     8.309   79.286   51.270
LGA    Q    66_A      Q    66_A     0.880     0    0.136   1.133     5.409   88.214   72.328
LGA    Q    67_A      Q    67_A     0.750     0    0.153   0.837     4.714   90.595   67.249
LGA    N    68_A      N    68_A     1.044     0    0.304   1.084     5.687   66.310   53.512

# 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):     0.968          0.976                  1.836           89.597   82.633

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   68   67    4.0     67    0.97    96.269    98.501     6.275

LGA_LOCAL      RMSD:   0.968  Number of atoms:   67  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.968  Number of assigned atoms:   67 
Std_ASGN_ATOMS RMSD:   0.968  Standard rmsd on all 67 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.510946 * X  +  -0.005679 * Y  +   0.859594 * Z  + -12.807505
  Y_new =   0.751447 * X  +  -0.482659 * Y  +  -0.449852 * Z  +  27.301744
  Z_new =   0.417446 * X  +   0.875790 * Y  +  -0.242345 * Z  + -20.928555 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.973655 -0.430633  1.840757   [DEG:   55.7863  -24.6735  105.4676 ]
ZXZ:  1.088659  1.815579  0.444795   [DEG:   62.3756  104.0250   25.4848 ]
 
# END of job
