
#######################################################
#                                                     #
#                        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        1.80     1.80
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.80     1.80
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    26      13_A - 38_A        0.99     2.23
  LONGEST_CONTINUOUS_SEGMENT:    26      14_A - 39_A        1.00     2.32
  LCS_AVERAGE:     30.69

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     13   63   63      5   12   28   51   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H     2_A     H     2_A     13   63   63      5   16   34   53   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I     3_A     I     3_A     15   63   63      6   25   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     4_A     D     4_A     21   63   63      7   21   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     21   63   63      7   16   39   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     21   63   63      7   12   40   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     7_A     K     7_A     22   63   63      7   25   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E     8_A     E     8_A     22   63   63     12   25   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     22   63   63      7   20   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    10_A     N    10_A     22   63   63     12   25   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    11_A     R    11_A     22   63   63      5   20   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     22   63   63      5   20   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     26   63   63      4   20   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     26   63   63      5   25   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     26   63   63      3    6   23   48   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     26   63   63      5   23   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    17_A     S    17_A     26   63   63      5   25   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    18_A     A    18_A     26   63   63      4   11   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    19_A     H    19_A     26   63   63      4   23   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    20_A     D    20_A     26   63   63     12   25   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     26   63   63     12   25   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     26   63   63     12   25   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     26   63   63     12   25   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     26   63   63      6   25   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     26   63   63      6   25   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     26   63   63      5   25   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     26   63   63      4   25   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     26   63   63      7   25   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     26   63   63      6   25   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     26   63   63      5   21   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     26   63   63      5   15   44   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     26   63   63      4   23   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     26   63   63      7   25   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    34_A     N    34_A     26   63   63      4   25   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     26   63   63      6   25   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     26   63   63     12   24   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     26   63   63     12   25   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    38_A     P    38_A     26   63   63      5   25   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     26   63   63      3   22   44   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A      8   63   63      3    6   13   30   47   55   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A      8   63   63      3    6   15   28   45   53   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     12   63   63      3    5   15   29   45   54   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     12   63   63      6   20   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    44_A     E    44_A     12   63   63     12   21   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A     12   63   63      7   25   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    46_A     S    46_A     12   63   63      6   14   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     12   63   63      6   20   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     12   63   63     12   25   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     12   63   63      4   14   37   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     12   63   63     12   21   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    51_A     A    51_A     12   63   63     12   20   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    52_A     N    52_A     12   63   63      4   20   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     12   63   63      4   20   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     12   63   63      5   14   44   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     12   63   63      5   16   33   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     12   63   63      5    7   21   35   56   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     12   63   63      5   16   33   48   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     12   63   63      5   16   31   51   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    59_A     G    59_A     12   63   63      5   15   42   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    60_A     H    60_A     12   63   63      5   19   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     12   63   63      5   21   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     12   63   63      7   25   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     12   63   63      7   25   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  76.90  (  30.69  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     12     25     46     54     57     60     61     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  19.05  39.68  73.02  85.71  90.48  95.24  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    0.39   0.79   1.07   1.27   1.38   1.53   1.69   1.80   1.80   1.80   1.80   1.80   1.80   1.80   1.80   1.80   1.80   1.80   1.80   1.80
GDT RMS_ALL_AT   2.22   2.16   1.96   1.87   1.83   1.83   1.80   1.80   1.80   1.80   1.80   1.80   1.80   1.80   1.80   1.80   1.80   1.80   1.80   1.80

# Checking swapping
#   possible swapping detected:  E     8_A      E     8_A
#   possible swapping detected:  Y    41_A      Y    41_A
#   possible swapping detected:  E    44_A      E    44_A
#   possible swapping detected:  D    45_A      D    45_A
#   possible swapping detected:  Y    50_A      Y    50_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     1_A      A     1_A     2.513     0    0.090   0.133     3.437   71.071   66.857
LGA    H     2_A      H     2_A     1.808     0    0.012   0.710     4.447   75.119   60.476
LGA    I     3_A      I     3_A     0.239     0    0.083   0.890     2.863   90.595   85.238
LGA    D     4_A      D     4_A     1.062     0    0.056   1.068     3.542   83.690   71.786
LGA    C     5_A      C     5_A     1.911     0    0.084   0.227     2.531   72.857   68.889
LGA    D     6_A      D     6_A     1.582     0    0.020   0.553     3.664   79.405   71.429
LGA    K     7_A      K     7_A     0.445     0    0.085   0.536     3.230   95.238   79.683
LGA    E     8_A      E     8_A     0.988     0    0.054   0.431     1.598   83.810   86.508
LGA    C     9_A      C     9_A     1.341     0    0.082   0.089     1.840   81.429   78.571
LGA    N    10_A      N    10_A     0.511     0    0.123   0.378     1.353   88.214   88.214
LGA    R    11_A      R    11_A     1.351     0    0.030   1.485     5.752   79.286   62.771
LGA    R    12_A      R    12_A     1.393     0    0.039   1.540     6.727   79.286   62.251
LGA    C    13_A      C    13_A     1.124     0    0.260   0.270     3.025   81.548   76.270
LGA    S    14_A      S    14_A     1.119     0    0.071   0.667     3.328   73.452   72.381
LGA    K    15_A      K    15_A     3.113     0    0.155   1.022     4.792   57.262   51.323
LGA    A    16_A      A    16_A     1.790     0    0.064   0.075     2.199   70.833   72.952
LGA    S    17_A      S    17_A     1.943     0    0.028   0.688     3.769   70.833   65.238
LGA    A    18_A      A    18_A     1.993     0    0.053   0.058     2.169   70.833   69.619
LGA    H    19_A      H    19_A     1.725     0    0.203   1.176     3.382   68.929   65.905
LGA    D    20_A      D    20_A     1.323     0    0.197   0.224     1.923   81.429   78.214
LGA    R    21_A      R    21_A     1.440     0    0.070   0.933     4.397   83.690   65.195
LGA    C    22_A      C    22_A     0.990     0    0.081   0.121     1.286   88.214   88.968
LGA    L    23_A      L    23_A     1.004     0    0.066   0.168     1.748   85.952   82.619
LGA    K    24_A      K    24_A     2.107     0    0.092   0.434     4.948   68.810   55.820
LGA    Y    25_A      Y    25_A     1.947     0    0.018   0.700     2.994   72.857   69.563
LGA    C    26_A      C    26_A     1.497     0    0.099   0.208     1.757   75.000   75.714
LGA    G    27_A      G    27_A     1.611     0    0.189   0.189     2.619   71.071   71.071
LGA    I    28_A      I    28_A     1.615     0    0.105   0.710     4.466   75.000   67.440
LGA    C    29_A      C    29_A     1.484     0    0.050   0.658     1.484   81.429   81.429
LGA    C    30_A      C    30_A     1.356     0    0.033   0.068     1.936   81.429   78.571
LGA    E    31_A      E    31_A     1.374     0    0.047   0.706     4.056   81.429   67.831
LGA    K    32_A      K    32_A     0.985     0    0.046   1.077     6.228   90.476   65.714
LGA    C    33_A      C    33_A     0.701     0    0.601   0.522     3.421   78.095   75.159
LGA    N    34_A      N    34_A     0.967     0    0.228   0.374     3.232   90.595   75.119
LGA    C    35_A      C    35_A     0.953     0    0.020   0.383     1.631   88.214   84.524
LGA    V    36_A      V    36_A     0.787     0    0.150   0.173     1.760   90.476   85.374
LGA    P    37_A      P    37_A     0.432     0    0.074   0.331     0.724   92.857   94.558
LGA    P    38_A      P    38_A     1.514     0    0.041   0.096     1.819   77.143   77.755
LGA    G    39_A      G    39_A     2.196     0    0.132   0.132     2.968   62.976   62.976
LGA    T    40_A      T    40_A     4.428     0    0.558   0.572     5.532   38.929   33.537
LGA    Y    41_A      Y    41_A     4.374     0    0.145   1.306     4.976   35.714   43.770
LGA    G    42_A      G    42_A     4.208     0    0.595   0.595     5.342   35.952   35.952
LGA    N    43_A      N    43_A     1.177     0    0.292   0.364     1.920   77.143   77.143
LGA    E    44_A      E    44_A     0.313     0    0.098   0.633     2.399  100.000   84.339
LGA    D    45_A      D    45_A     1.171     0    0.103   1.100     5.814   83.690   64.762
LGA    S    46_A      S    46_A     1.505     0    0.153   0.159     1.967   77.143   77.143
LGA    C    47_A      C    47_A     0.853     0    0.091   0.341     1.690   90.476   86.032
LGA    P    48_A      P    48_A     0.380     0    0.073   0.334     1.301   92.976   93.265
LGA    C    49_A      C    49_A     1.890     0    0.029   0.242     3.334   72.976   67.778
LGA    Y    50_A      Y    50_A     0.939     0    0.104   0.289     2.285   83.690   81.627
LGA    A    51_A      A    51_A     1.006     0    0.108   0.109     1.526   81.548   83.333
LGA    N    52_A      N    52_A     1.308     0    0.086   0.168     2.649   83.690   74.286
LGA    L    53_A      L    53_A     1.043     0    0.080   0.949     3.372   81.429   78.750
LGA    K    54_A      K    54_A     1.397     0    0.105   1.288     5.164   81.429   69.153
LGA    N    55_A      N    55_A     1.827     0    0.049   0.109     2.673   67.143   70.060
LGA    S    56_A      S    56_A     3.793     0    0.165   0.677     6.340   42.024   37.063
LGA    K    57_A      K    57_A     2.795     0    0.173   0.559     5.253   57.143   51.534
LGA    G    58_A      G    58_A     2.535     0    0.135   0.135     2.535   60.952   60.952
LGA    G    59_A      G    59_A     1.493     0    0.035   0.035     1.785   81.548   81.548
LGA    H    60_A      H    60_A     1.260     0    0.167   1.028     5.854   83.690   59.381
LGA    K    61_A      K    61_A     1.311     0    0.036   0.733     1.802   83.690   84.497
LGA    C    62_A      C    62_A     1.682     0    0.028   0.077     2.171   77.143   74.365
LGA    P    63_A      P    63_A     1.269     0    0.310   0.443     1.814   79.286   78.980

# 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):     1.796          1.826                  2.282           76.829   71.575

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    1.80    81.349    91.124     3.322

LGA_LOCAL      RMSD:   1.796  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.796  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.796  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.352261 * X  +   0.935305 * Y  +   0.033418 * Z  +  -8.223206
  Y_new =  -0.928073 * X  +  -0.344483 * Y  +  -0.141464 * Z  +  -3.173760
  Z_new =  -0.120799 * X  +  -0.080847 * Y  +   0.989379 * Z  + -11.522552 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.933560  0.121095 -0.081533   [DEG: -110.7848    6.9382   -4.6715 ]
ZXZ:  0.231980  0.145874 -2.160595   [DEG:   13.2915    8.3580 -123.7930 ]
 
# END of job
