
#######################################################
#                                                     #
#                        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 (  472),  selected   63 , name one
# Molecule2: number of CA atoms   63 (  472),  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        2.17     2.17
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    56       1_A - 56_A        1.98     2.19
  LCS_AVERAGE:     87.10

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    32       5_A - 36_A        0.98     3.74
  LCS_AVERAGE:     36.33

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     G     1_A     G     1_A     11   56   63      3    6   28   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     2_A     S     2_A     13   56   63      3   17   30   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     3_A     S     3_A     13   56   63      3   17   30   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     F     4_A     F     4_A     13   56   63      3   13   30   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     32   56   63      4   20   32   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     32   56   63      4   23   32   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     7_A     S     7_A     32   56   63      4   24   32   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     8_A     K     8_A     32   56   63      9   24   32   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     32   56   63      7   24   32   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    10_A     G    10_A     32   56   63      5   24   32   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    11_A     V    11_A     32   56   63     11   24   32   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     32   56   63     11   24   32   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     32   56   63      9   24   32   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     32   56   63      4   21   32   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     32   56   63      3    9   31   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     32   56   63      4   24   32   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    17_A     G    17_A     32   56   63      4   21   31   43   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    18_A     Y    18_A     32   56   63     12   24   32   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Q    19_A     Q    19_A     32   56   63      4   17   32   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    20_A     E    20_A     32   56   63      7   24   32   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     32   56   63     12   24   32   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     32   56   63      7   24   32   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     32   56   63      9   24   32   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     32   56   63     12   24   32   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     32   56   63     12   24   32   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     32   56   63     11   24   32   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     32   56   63     12   24   32   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     32   56   63     12   24   32   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     32   56   63     12   24   32   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     32   56   63     12   24   32   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     32   56   63     12   24   32   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     32   56   63     12   24   32   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     32   56   63     12   24   32   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    34_A     H    34_A     32   56   63     10   21   32   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     32   56   63     10   21   32   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     32   56   63      9   21   32   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     24   56   63     10   21   30   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    38_A     S    38_A     24   56   63      4   21   28   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     24   56   63     12   19   32   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A     24   56   63      4   19   32   39   51   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     16   56   63      3   12   26   35   49   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     13   56   63      3    8   16   37   51   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     12   56   63      4   16   28   43   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    44_A     K    44_A     12   56   63      3   16   28   43   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A     12   56   63      3    8   24   34   52   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    46_A     E    46_A     12   56   63      3   13   28   41   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     12   56   63      4   16   28   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     12   56   63      5    8   24   33   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     12   56   63      5   10   28   43   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     12   56   63      5   10   20   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    51_A     R    51_A     12   56   63      5    8   27   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    52_A     D    52_A     12   56   63      5   16   28   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     12   56   63      4   16   28   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     12   56   63      4   15   25   41   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     11   56   63      3   10   21   32   44   56   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     11   56   63      4   10   19   29   38   45   58   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     11   49   63      4   10   19   30   39   45   58   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     11   49   63      4   10   19   32   44   56   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    59_A     N    59_A     11   49   63      4   16   25   41   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    60_A     P    60_A     11   49   63     10   21   28   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     11   49   63      4   10   28   45   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     11   41   63      5   24   31   38   49   55   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     11   35   63      3   13   31   38   43   53   59   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  74.48  (  36.33   87.10  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     12     24     32     45     53     57     60     62     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  19.05  38.10  50.79  71.43  84.13  90.48  95.24  98.41 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.64   0.94   1.46   1.66   1.79   1.95   2.13   2.17   2.17   2.17   2.17   2.17   2.17   2.17   2.17   2.17   2.17   2.17   2.17
GDT RMS_ALL_AT   3.23   4.07   3.61   2.55   2.29   2.27   2.20   2.18   2.17   2.17   2.17   2.17   2.17   2.17   2.17   2.17   2.17   2.17   2.17   2.17

# Checking swapping
#   possible swapping detected:  Y    41_A      Y    41_A
#   possible swapping detected:  D    45_A      D    45_A
#   possible swapping detected:  D    52_A      D    52_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G     1_A      G     1_A     2.128     0    0.092   0.092     2.681   71.190   71.190
LGA    S     2_A      S     2_A     2.352     0    0.153   0.774     3.489   68.810   62.540
LGA    S     3_A      S     3_A     2.400     0    0.118   0.472     3.145   64.762   61.032
LGA    F     4_A      F     4_A     1.907     0    0.089   0.359     3.226   70.833   62.900
LGA    C     5_A      C     5_A     2.129     0    0.089   0.810     2.975   66.786   64.841
LGA    D     6_A      D     6_A     2.206     0    0.108   0.266     3.195   64.762   60.060
LGA    S     7_A      S     7_A     2.676     0    0.122   0.557     4.886   60.952   55.397
LGA    K     8_A      K     8_A     1.692     0    0.120   0.532     3.484   72.857   76.138
LGA    C     9_A      C     9_A     1.564     0    0.067   0.089     1.733   72.857   75.714
LGA    G    10_A      G    10_A     1.598     0    0.080   0.080     1.640   75.000   75.000
LGA    V    11_A      V    11_A     2.267     0    0.026   0.105     2.696   64.762   62.585
LGA    R    12_A      R    12_A     2.060     0    0.033   1.374     7.764   66.786   51.775
LGA    C    13_A      C    13_A     1.209     0    0.662   0.745     2.360   79.524   78.730
LGA    S    14_A      S    14_A     1.597     0    0.057   0.606     1.972   75.000   74.286
LGA    K    15_A      K    15_A     1.874     0    0.257   0.867     3.858   72.857   63.598
LGA    A    16_A      A    16_A     1.593     0    0.620   0.560     3.215   67.143   70.000
LGA    G    17_A      G    17_A     2.433     0    0.057   0.057     2.661   60.952   60.952
LGA    Y    18_A      Y    18_A     2.550     0    0.342   0.258     2.858   61.071   58.452
LGA    Q    19_A      Q    19_A     1.419     0    0.078   1.385     5.497   81.429   64.127
LGA    E    20_A      E    20_A     2.408     0    0.029   1.262     7.096   62.976   41.640
LGA    R    21_A      R    21_A     3.003     0    0.064   1.351    12.737   55.357   27.749
LGA    C    22_A      C    22_A     1.849     0    0.083   0.189     2.074   68.810   70.159
LGA    L    23_A      L    23_A     1.427     0    0.036   1.016     4.707   77.143   65.893
LGA    K    24_A      K    24_A     2.235     0    0.045   1.178    10.681   66.786   41.323
LGA    Y    25_A      Y    25_A     2.443     0    0.113   0.462     3.619   62.857   57.421
LGA    C    26_A      C    26_A     1.354     0    0.022   0.178     1.552   79.286   80.000
LGA    G    27_A      G    27_A     1.109     0    0.020   0.020     1.475   81.429   81.429
LGA    I    28_A      I    28_A     1.908     0    0.023   0.752     5.295   75.000   60.476
LGA    C    29_A      C    29_A     1.521     0    0.094   0.103     2.267   79.405   75.873
LGA    C    30_A      C    30_A     0.927     0    0.085   0.096     1.231   88.214   90.556
LGA    E    31_A      E    31_A     0.939     0    0.047   0.944     3.263   85.952   76.296
LGA    K    32_A      K    32_A     1.247     0    0.046   1.421     5.140   81.429   68.254
LGA    C    33_A      C    33_A     1.305     0    0.107   0.241     1.982   77.143   78.571
LGA    H    34_A      H    34_A     1.503     0    0.101   1.137     4.938   75.000   62.286
LGA    C    35_A      C    35_A     1.366     0    0.023   0.157     1.951   81.429   78.571
LGA    V    36_A      V    36_A     1.277     0    0.064   0.264     2.424   81.429   76.599
LGA    P    37_A      P    37_A     0.892     0    0.030   0.347     1.091   88.214   90.544
LGA    S    38_A      S    38_A     1.350     0    0.269   0.519     3.803   81.548   72.381
LGA    G    39_A      G    39_A     1.836     0    0.042   0.042     2.654   66.905   66.905
LGA    T    40_A      T    40_A     3.175     0    0.515   0.413     4.104   48.571   50.340
LGA    Y    41_A      Y    41_A     3.272     0    0.204   1.430    10.689   55.476   30.992
LGA    G    42_A      G    42_A     2.551     0    0.659   0.659     4.504   52.619   52.619
LGA    N    43_A      N    43_A     1.164     0    0.173   0.957     4.531   83.690   66.845
LGA    K    44_A      K    44_A     1.279     0    0.016   0.920     7.182   77.143   59.259
LGA    D    45_A      D    45_A     2.285     0    0.146   0.802     3.470   68.810   62.143
LGA    E    46_A      E    46_A     1.892     0    0.060   0.223     2.900   75.000   67.672
LGA    C    47_A      C    47_A     1.366     0    0.075   0.812     2.840   77.143   74.524
LGA    P    48_A      P    48_A     2.184     0    0.164   0.426     2.510   70.833   70.680
LGA    C    49_A      C    49_A     1.739     0    0.061   0.750     2.217   77.143   75.794
LGA    Y    50_A      Y    50_A     1.745     0    0.116   0.826     5.286   72.857   55.159
LGA    R    51_A      R    51_A     1.121     0    0.042   1.287     5.412   83.690   67.619
LGA    D    52_A      D    52_A     0.210     0    0.051   0.694     3.123  100.000   85.774
LGA    L    53_A      L    53_A     0.864     0    0.100   0.936     4.758   90.595   77.679
LGA    K    54_A      K    54_A     1.570     0    0.038   1.239     6.049   70.952   59.365
LGA    N    55_A      N    55_A     3.057     0    0.070   0.120     3.600   50.357   53.750
LGA    S    56_A      S    56_A     4.815     0    0.027   0.528     6.814   31.548   27.619
LGA    K    57_A      K    57_A     4.727     0    0.198   1.084     8.598   32.857   24.021
LGA    G    58_A      G    58_A     3.235     0    0.030   0.030     3.578   53.810   53.810
LGA    N    59_A      N    59_A     1.202     0    0.040   0.261     2.723   86.190   79.762
LGA    P    60_A      P    60_A     1.554     0    0.082   0.171     2.645   75.000   69.524
LGA    K    61_A      K    61_A     2.677     0    0.059   0.966     3.750   53.810   55.873
LGA    C    62_A      C    62_A     3.716     0    0.148   0.545     4.532   41.905   40.397
LGA    P    63_A      P    63_A     4.113     0    0.457   0.405     4.362   38.690   38.912

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       63     252    252  100.00     472    472  100.00                63
SUMMARY(RMSD_GDC):     2.174          2.179                  3.099           69.894   63.688

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     62    2.13    76.984    84.230     2.780

LGA_LOCAL      RMSD:   2.130  Number of atoms:   62  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.176  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   2.174  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.847747 * X  +  -0.345209 * Y  +  -0.402685 * Z  +   3.161734
  Y_new =  -0.323712 * X  +  -0.264671 * Y  +   0.908383 * Z  +  -0.313155
  Z_new =  -0.420161 * X  +   0.900433 * Y  +   0.112626 * Z  +  -1.381729 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.776830  0.433623  1.446363   [DEG: -159.1007   24.8448   82.8705 ]
ZXZ: -2.724325  1.457931 -0.436590   [DEG: -156.0923   83.5333  -25.0147 ]
 
# END of job
