
#######################################################
#                                                     #
#                        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   63 (  471),  selected   63 , name one
# Molecule2: number of CA atoms   63 (  471),  selected   63 , 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:    63       1_A - 63_A        2.08     2.08
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    42       1_A - 42_A        1.98     2.29
  LCS_AVERAGE:     60.29

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29       7_A - 35_A        1.00     3.49
  LCS_AVERAGE:     33.46

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   63
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     A     1_A     A     1_A     11   42   63      3    5   20   37   47   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H     2_A     H     2_A     13   42   63      3   14   22   43   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I     3_A     I     3_A     13   42   63      6   19   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     4_A     D     4_A     14   42   63      7   16   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     21   42   63      7   18   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     21   42   63      7   14   25   43   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     7_A     K     7_A     29   42   63      7   20   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E     8_A     E     8_A     29   42   63      7   22   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     29   42   63      7   18   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    10_A     N    10_A     29   42   63      7   22   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    11_A     R    11_A     29   42   63      4   19   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     29   42   63      5   19   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     29   42   63      4   18   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     29   42   63      9   22   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     29   42   63      3   19   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     29   42   63      6   22   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    17_A     S    17_A     29   42   63      9   22   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    18_A     A    18_A     29   42   63      4   22   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    19_A     H    19_A     29   42   63      4   22   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    20_A     D    20_A     29   42   63      4   22   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     29   42   63      9   22   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     29   42   63      8   22   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     29   42   63      6   22   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     29   42   63      5   22   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     29   42   63      9   22   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     29   42   63      3   22   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     29   42   63      5   22   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     29   42   63      9   22   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     29   42   63      9   22   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     29   42   63      4   20   33   47   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     29   42   63      4   10   33   47   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     29   42   63      4   19   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     29   42   63      9   22   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    34_A     N    34_A     29   42   63      6   22   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     29   42   63      8   22   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     25   42   63      6   19   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     24   42   63      6   14   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    38_A     P    38_A     21   42   63      6   14   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     13   42   63      6   14   31   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A     13   42   63      4   10   22   31   42   55   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     13   42   63      4   10   20   30   38   48   58   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     13   42   63      3   10   21   31   39   49   59   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     13   31   63      4   10   22   31   43   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    44_A     E    44_A     13   31   63      4    9   22   36   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A      9   31   63      4   14   24   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    46_A     S    46_A      9   31   63      4    7   22   34   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A      9   31   63      6   14   27   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A      9   31   63      4   19   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     14   31   63      5   13   27   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     14   31   63      5   10   17   43   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    51_A     A    51_A     14   31   63      5   12   16   27   32   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    52_A     N    52_A     14   31   63      5   12   17   30   54   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     14   31   63      5   13   27   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     14   31   63      5   13   27   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     14   31   63      4   12   21   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     14   31   63      4   12   17   29   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     14   31   63      5   12   25   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     14   31   63      5   13   27   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    59_A     G    59_A     14   31   63      5   13   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    60_A     H    60_A     14   30   63      5   19   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     14   30   63      6   19   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     14   21   63      9   22   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     14   21   63      9   22   33   48   55   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  64.58  (  33.46   60.29  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      9     22     33     48     55     57     61     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  14.29  34.92  52.38  76.19  87.30  90.48  96.83 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.38   0.68   0.98   1.48   1.64   1.71   1.93   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08
GDT RMS_ALL_AT   3.18   3.34   3.20   2.21   2.15   2.13   2.10   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08

# Checking swapping
#   possible swapping detected:  E    31_A      E    31_A
#   possible swapping detected:  D    45_A      D    45_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     1_A      A     1_A     3.605     0    0.078   0.117     4.194   45.119   44.762
LGA    H     2_A      H     2_A     2.175     0    0.049   1.100     5.810   70.952   52.857
LGA    I     3_A      I     3_A     0.880     0    0.048   0.977     2.500   79.405   77.500
LGA    D     4_A      D     4_A     1.591     0    0.061   1.069     4.162   75.000   66.488
LGA    C     5_A      C     5_A     2.143     0    0.081   0.202     2.465   66.786   67.460
LGA    D     6_A      D     6_A     2.103     0    0.015   1.097     5.412   68.810   58.274
LGA    K     7_A      K     7_A     1.130     0    0.082   0.517     1.936   79.286   80.582
LGA    E     8_A      E     8_A     1.163     0    0.075   0.359     1.588   81.429   80.529
LGA    C     9_A      C     9_A     1.605     0    0.044   0.055     1.783   75.000   74.286
LGA    N    10_A      N    10_A     1.299     0    0.092   0.257     1.993   79.286   76.071
LGA    R    11_A      R    11_A     2.253     0    0.016   1.507     5.373   64.762   54.026
LGA    R    12_A      R    12_A     2.022     0    0.049   1.204     4.212   68.810   66.926
LGA    C    13_A      C    13_A     1.364     0    0.210   0.232     3.369   83.810   76.349
LGA    S    14_A      S    14_A     0.285     0    0.030   0.662     1.931   90.595   87.619
LGA    K    15_A      K    15_A     2.321     0    0.154   1.050     4.186   68.929   61.058
LGA    A    16_A      A    16_A     1.696     0    0.013   0.021     1.960   72.857   74.571
LGA    S    17_A      S    17_A     2.461     0    0.018   0.660     4.237   62.857   57.619
LGA    A    18_A      A    18_A     2.460     0    0.065   0.064     2.664   64.762   63.238
LGA    H    19_A      H    19_A     1.810     0    0.127   1.160     3.182   68.810   65.000
LGA    D    20_A      D    20_A     1.938     0    0.177   0.198     2.652   72.857   65.952
LGA    R    21_A      R    21_A     2.206     0    0.062   1.345     9.753   68.810   39.481
LGA    C    22_A      C    22_A     1.385     0    0.127   0.168     1.717   81.548   81.508
LGA    L    23_A      L    23_A     0.770     0    0.104   1.274     3.977   92.857   81.310
LGA    K    24_A      K    24_A     2.182     0    0.062   0.470     6.036   68.810   52.381
LGA    Y    25_A      Y    25_A     2.229     0    0.040   0.508     2.957   64.762   61.587
LGA    C    26_A      C    26_A     1.724     0    0.051   0.196     1.860   72.857   74.286
LGA    G    27_A      G    27_A     1.669     0    0.124   0.124     2.430   70.833   70.833
LGA    I    28_A      I    28_A     1.773     0    0.040   0.684     4.798   75.000   64.762
LGA    C    29_A      C    29_A     1.878     0    0.050   0.728     1.983   72.857   74.286
LGA    C    30_A      C    30_A     1.718     0    0.029   0.079     2.235   72.857   71.508
LGA    E    31_A      E    31_A     1.872     0    0.020   0.490     4.209   72.857   60.529
LGA    K    32_A      K    32_A     1.647     0    0.054   0.713     3.589   72.857   69.577
LGA    C    33_A      C    33_A     1.201     0    0.610   0.527     3.756   69.762   70.873
LGA    N    34_A      N    34_A     1.254     0    0.219   0.723     3.678   81.548   70.655
LGA    C    35_A      C    35_A     1.685     0    0.092   0.835     2.397   79.286   77.222
LGA    V    36_A      V    36_A     0.632     0    0.091   1.344     2.628   88.214   79.660
LGA    P    37_A      P    37_A     0.627     0    0.009   0.109     0.740   90.476   90.476
LGA    P    38_A      P    38_A     0.928     0    0.031   0.112     1.085   88.214   87.891
LGA    G    39_A      G    39_A     1.038     0    0.169   0.169     1.839   79.405   79.405
LGA    T    40_A      T    40_A     3.820     0    0.595   0.566     6.152   37.262   40.816
LGA    Y    41_A      Y    41_A     4.847     0    0.168   0.743    12.937   37.262   14.921
LGA    G    42_A      G    42_A     4.525     0    0.157   0.157     4.945   37.381   37.381
LGA    N    43_A      N    43_A     3.504     0    0.301   0.454     4.081   45.119   52.083
LGA    E    44_A      E    44_A     2.348     0    0.095   1.025     3.949   66.905   60.000
LGA    D    45_A      D    45_A     1.344     0    0.166   1.209     5.730   77.143   60.417
LGA    S    46_A      S    46_A     2.421     0    0.134   0.720     2.919   66.786   63.571
LGA    C    47_A      C    47_A     1.086     0    0.079   0.436     2.077   83.690   78.730
LGA    P    48_A      P    48_A     1.269     0    0.065   0.337     1.879   81.548   81.565
LGA    C    49_A      C    49_A     1.381     0    0.068   0.210     2.761   77.381   73.254
LGA    Y    50_A      Y    50_A     2.198     0    0.026   1.114     4.782   66.786   61.270
LGA    A    51_A      A    51_A     3.505     0    0.198   0.212     4.006   48.452   46.190
LGA    N    52_A      N    52_A     2.794     0    0.143   0.244     3.305   59.048   55.417
LGA    L    53_A      L    53_A     1.472     0    0.015   1.008     2.501   79.286   76.369
LGA    K    54_A      K    54_A     1.213     0    0.095   1.218     3.379   79.286   76.085
LGA    N    55_A      N    55_A     1.955     0    0.040   0.218     2.253   70.952   69.881
LGA    S    56_A      S    56_A     3.103     0    0.127   0.669     6.495   53.571   45.794
LGA    K    57_A      K    57_A     1.491     0    0.135   0.657     2.025   83.810   79.683
LGA    G    58_A      G    58_A     0.685     0    0.100   0.100     1.017   88.214   88.214
LGA    G    59_A      G    59_A     1.044     0    0.059   0.059     1.426   83.690   83.690
LGA    H    60_A      H    60_A     1.797     0    0.110   1.398     8.769   72.857   42.571
LGA    K    61_A      K    61_A     1.867     0    0.024   0.743     2.228   68.810   78.942
LGA    C    62_A      C    62_A     2.361     0    0.108   0.150     2.581   62.857   63.492
LGA    P    63_A      P    63_A     2.052     0    0.250   0.412     2.152   66.786   69.388

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       63     252    252  100.00     471    471  100.00                63
SUMMARY(RMSD_GDC):     2.085          2.074                  2.839           71.410   66.811

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    2.08    77.778    78.113     2.884

LGA_LOCAL      RMSD:   2.085  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.085  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   2.085  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.681249 * X  +  -0.002864 * Y  +   0.732046 * Z  + -13.084723
  Y_new =  -0.352565 * X  +  -0.877661 * Y  +   0.324667 * Z  +   1.603287
  Z_new =   0.641559 * X  +  -0.479273 * Y  +  -0.598916 * Z  +  -9.516096 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.477571 -0.696528 -2.466709   [DEG:  -27.3628  -39.9081 -141.3320 ]
ZXZ:  1.988237  2.212943  2.212403   [DEG:  113.9176  126.7923  126.7614 ]
 
# END of job
