
#######################################################
#                                                     #
#                        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        2.67     2.67
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       4_A - 63_A        1.96     2.78
  LCS_AVERAGE:     93.15

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      16_A - 39_A        0.95     3.16
  LCS_AVERAGE:     28.55

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      4    4   63      3    3    4    4    4    4    6    7    9   23   26   30   37   37   43   50   60   63   63   63 
LCS_GDT     H     2_A     H     2_A      4   40   63      3    3    4    4   14   32   43   54   58   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     I     3_A     I     3_A      4   53   63      3    3    4   11   20   31   43   47   56   60   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     D     4_A     D     4_A     15   60   63      7   18   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C     5_A     C     5_A     19   60   63      7   15   33   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     D     6_A     D     6_A     19   60   63      7   12   30   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     K     7_A     K     7_A     19   60   63      7   21   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     E     8_A     E     8_A     19   60   63     10   21   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C     9_A     C     9_A     19   60   63      7   20   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     N    10_A     N    10_A     19   60   63     10   21   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     R    11_A     R    11_A     19   60   63     10   21   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     R    12_A     R    12_A     19   60   63      5   20   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    13_A     C    13_A     19   60   63      7   20   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     S    14_A     S    14_A     22   60   63      8   21   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     K    15_A     K    15_A     22   60   63      3   10   20   37   54   57   57   57   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     A    16_A     A    16_A     24   60   63      4   21   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     S    17_A     S    17_A     24   60   63      8   21   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     A    18_A     A    18_A     24   60   63      4   15   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     H    19_A     H    19_A     24   60   63      4   20   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     D    20_A     D    20_A     24   60   63      5   20   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     R    21_A     R    21_A     24   60   63      8   21   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    22_A     C    22_A     24   60   63     10   21   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     L    23_A     L    23_A     24   60   63     10   21   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     K    24_A     K    24_A     24   60   63      8   21   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     24   60   63      8   21   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    26_A     C    26_A     24   60   63      5   20   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     G    27_A     G    27_A     24   60   63      4   17   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     I    28_A     I    28_A     24   60   63      7   21   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    29_A     C    29_A     24   60   63      7   21   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    30_A     C    30_A     24   60   63      5   18   38   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     E    31_A     E    31_A     24   60   63      4   14   32   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     K    32_A     K    32_A     24   60   63      4   17   34   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    33_A     C    33_A     24   60   63      6   21   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     N    34_A     N    34_A     24   60   63      4   21   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    35_A     C    35_A     24   60   63      8   21   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     V    36_A     V    36_A     24   60   63     10   21   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     P    37_A     P    37_A     24   60   63     10   20   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     P    38_A     P    38_A     24   60   63     10   21   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     G    39_A     G    39_A     24   60   63      8   21   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     T    40_A     T    40_A      8   60   63      3    6   13   29   42   50   56   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     Y    41_A     Y    41_A      8   60   63      3    6   16   22   37   45   56   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     G    42_A     G    42_A     12   60   63      4    4   16   22   37   45   56   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     N    43_A     N    43_A     13   60   63      5   18   36   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     E    44_A     E    44_A     13   60   63      5   20   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     D    45_A     D    45_A     13   60   63      5   20   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     S    46_A     S    46_A     13   60   63      5   17   38   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    47_A     C    47_A     13   60   63     10   20   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     P    48_A     P    48_A     13   60   63     10   20   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    49_A     C    49_A     13   60   63     10   20   37   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     14   60   63      5   20   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     A    51_A     A    51_A     14   60   63     10   20   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     N    52_A     N    52_A     14   60   63     10   20   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     L    53_A     L    53_A     14   60   63      4   20   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     K    54_A     K    54_A     14   60   63      3   13   31   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     N    55_A     N    55_A     14   60   63      5   14   29   49   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     S    56_A     S    56_A     14   60   63      5   10   21   37   47   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     K    57_A     K    57_A     14   60   63      5   13   28   37   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     G    58_A     G    58_A     14   60   63      5   13   28   37   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     G    59_A     G    59_A     14   60   63      5   13   28   50   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     H    60_A     H    60_A     14   60   63      4   13   37   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     K    61_A     K    61_A     14   60   63      4   16   39   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    62_A     C    62_A     14   60   63      6   21   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     P    63_A     P    63_A     14   60   63      8   21   40   51   55   57   57   59   60   61   62   62   62   62   62   62   62   63   63   63 
LCS_AVERAGE  LCS_A:  73.90  (  28.55   93.15  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     10     21     40     51     55     57     57     59     60     61     62     62     62     62     62     62     62     63     63     63 
GDT PERCENT_AT  15.87  33.33  63.49  80.95  87.30  90.48  90.48  93.65  95.24  96.83  98.41  98.41  98.41  98.41  98.41  98.41  98.41 100.00 100.00 100.00
GDT RMS_LOCAL    0.28   0.68   1.10   1.33   1.56   1.66   1.66   1.92   1.96   2.10   2.22   2.22   2.22   2.22   2.22   2.22   2.22   2.67   2.67   2.67
GDT RMS_ALL_AT   3.22   3.27   2.97   2.84   2.79   2.80   2.80   2.78   2.78   2.73   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.67   2.67   2.67

# Checking swapping
#   possible swapping detected:  E    31_A      E    31_A
#   possible swapping detected:  E    44_A      E    44_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    13.101     0    0.041   0.085    15.337    0.000    0.000
LGA    H     2_A      H     2_A     6.446     0    0.118   0.747     8.488   12.262   34.857
LGA    I     3_A      I     3_A     6.677     0    0.600   1.518    12.514   23.810   12.321
LGA    D     4_A      D     4_A     1.026     0    0.550   0.872     5.342   75.357   56.667
LGA    C     5_A      C     5_A     1.888     0    0.089   0.201     2.362   72.857   71.508
LGA    D     6_A      D     6_A     1.552     0    0.030   0.494     3.122   77.143   72.202
LGA    K     7_A      K     7_A     0.673     0    0.080   0.879     3.575   90.476   80.423
LGA    E     8_A      E     8_A     1.038     0    0.060   0.964     2.775   83.690   77.937
LGA    C     9_A      C     9_A     1.299     0    0.033   0.179     1.668   81.429   78.571
LGA    N    10_A      N    10_A     0.528     0    0.116   0.713     2.202   88.214   86.190
LGA    R    11_A      R    11_A     1.188     0    0.019   1.350     6.075   83.690   64.892
LGA    R    12_A      R    12_A     1.427     0    0.039   1.452     6.063   79.286   65.714
LGA    C    13_A      C    13_A     1.147     0    0.281   0.274     3.140   81.548   76.270
LGA    S    14_A      S    14_A     1.048     0    0.025   0.664     3.111   73.452   72.381
LGA    K    15_A      K    15_A     3.492     0    0.314   1.417     8.576   59.167   39.894
LGA    A    16_A      A    16_A     1.953     0    0.048   0.064     2.447   66.786   69.714
LGA    S    17_A      S    17_A     2.385     0    0.065   0.495     4.407   64.762   58.889
LGA    A    18_A      A    18_A     2.398     0    0.162   0.163     2.540   62.857   63.238
LGA    H    19_A      H    19_A     2.072     0    0.148   1.186     3.229   62.857   61.000
LGA    D    20_A      D    20_A     2.076     0    0.147   0.240     2.841   68.810   63.929
LGA    R    21_A      R    21_A     2.110     0    0.092   1.174     5.789   70.952   52.078
LGA    C    22_A      C    22_A     1.379     0    0.112   0.229     1.712   79.286   81.508
LGA    L    23_A      L    23_A     1.148     0    0.096   0.172     2.087   83.690   77.262
LGA    K    24_A      K    24_A     2.223     0    0.060   0.789     4.928   64.762   54.021
LGA    Y    25_A      Y    25_A     2.200     0    0.025   0.681     3.012   64.762   66.310
LGA    C    26_A      C    26_A     1.920     0    0.019   0.543     2.443   70.833   70.159
LGA    G    27_A      G    27_A     1.984     0    0.131   0.131     2.687   66.905   66.905
LGA    I    28_A      I    28_A     1.673     0    0.055   1.510     6.369   75.000   60.774
LGA    C    29_A      C    29_A     1.620     0    0.042   0.660     1.804   77.143   77.143
LGA    C    30_A      C    30_A     1.598     0    0.036   0.093     2.052   75.000   72.937
LGA    E    31_A      E    31_A     1.737     0    0.046   0.325     3.881   70.833   61.958
LGA    K    32_A      K    32_A     1.487     0    0.057   0.367     1.942   79.286   80.476
LGA    C    33_A      C    33_A     0.973     0    0.630   0.545     3.591   74.286   70.000
LGA    N    34_A      N    34_A     0.931     0    0.233   1.244     4.473   90.595   76.250
LGA    C    35_A      C    35_A     1.177     0    0.116   0.896     1.684   85.952   81.587
LGA    V    36_A      V    36_A     0.475     0    0.160   0.202     1.580   97.619   92.041
LGA    P    37_A      P    37_A     0.349     0    0.025   0.339     0.957   95.238   94.558
LGA    P    38_A      P    38_A     1.241     0    0.055   0.344     2.257   83.690   79.116
LGA    G    39_A      G    39_A     1.974     0    0.205   0.205     2.545   65.000   65.000
LGA    T    40_A      T    40_A     4.505     0    0.605   0.543     5.553   34.762   33.605
LGA    Y    41_A      Y    41_A     4.670     0    0.087   1.292     5.481   34.286   32.024
LGA    G    42_A      G    42_A     4.439     0    0.631   0.631     5.493   32.976   32.976
LGA    N    43_A      N    43_A     1.321     0    0.285   0.346     1.944   77.143   80.417
LGA    E    44_A      E    44_A     0.637     0    0.100   0.731     3.498   90.476   82.381
LGA    D    45_A      D    45_A     0.993     0    0.134   0.356     1.366   88.214   84.821
LGA    S    46_A      S    46_A     1.147     0    0.062   0.230     1.647   85.952   81.587
LGA    C    47_A      C    47_A     0.535     0    0.101   0.425     2.727   90.476   83.413
LGA    P    48_A      P    48_A     0.668     0    0.059   0.357     1.356   90.595   91.905
LGA    C    49_A      C    49_A     1.714     0    0.046   0.288     3.302   72.976   67.778
LGA    Y    50_A      Y    50_A     1.080     0    0.089   0.304     2.062   81.429   78.611
LGA    A    51_A      A    51_A     1.020     0    0.099   0.125     1.361   81.429   81.429
LGA    N    52_A      N    52_A     0.965     0    0.054   0.522     2.000   88.214   83.869
LGA    L    53_A      L    53_A     1.077     0    0.142   0.711     2.407   81.548   80.536
LGA    K    54_A      K    54_A     1.363     0    0.075   0.850     2.539   81.429   76.878
LGA    N    55_A      N    55_A     1.965     0    0.033   0.440     2.783   67.143   65.000
LGA    S    56_A      S    56_A     3.811     0    0.026   0.390     5.755   43.452   38.730
LGA    K    57_A      K    57_A     3.263     0    0.032   0.774     4.230   48.333   49.418
LGA    G    58_A      G    58_A     3.046     0    0.075   0.075     3.046   53.571   53.571
LGA    G    59_A      G    59_A     1.906     0    0.102   0.102     2.275   75.119   75.119
LGA    H    60_A      H    60_A     1.279     0    0.129   1.289     6.863   85.952   54.429
LGA    K    61_A      K    61_A     1.450     0    0.046   0.873     2.155   79.405   75.926
LGA    C    62_A      C    62_A     2.150     0    0.103   0.167     2.484   66.786   66.111
LGA    P    63_A      P    63_A     1.979     0    0.375   0.431     2.428   68.810   70.544

# 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):     2.673          2.674                  3.001           71.107   66.790

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     59    1.92    76.587    86.006     2.919

LGA_LOCAL      RMSD:   1.921  Number of atoms:   59  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.783  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   2.673  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.991749 * X  +  -0.125568 * Y  +   0.025812 * Z  +   2.825622
  Y_new =  -0.116591 * X  +   0.967225 * Y  +   0.225572 * Z  +  -4.628480
  Z_new =  -0.053291 * X  +   0.220701 * Y  +  -0.973885 * Z  +  -2.024518 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -3.024568  0.053316  2.918737   [DEG: -173.2950    3.0548  167.2313 ]
ZXZ:  3.027657  2.912552 -0.236927   [DEG:  173.4720  166.8769  -13.5749 ]
 
# END of job
