
#######################################################
#                                                     #
#                        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        2.14     2.14
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    50       1_A - 50_A        1.97     2.21
  LCS_AVERAGE:     77.32

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29       7_A - 35_A        1.00     3.29
  LCS_AVERAGE:     32.48

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   50   63      3    6   23   36   51   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H     2_A     H     2_A     13   50   63      6   15   23   43   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I     3_A     I     3_A     13   50   63      6   15   33   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     4_A     D     4_A     13   50   63      7   15   33   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     21   50   63      7   15   30   42   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     21   50   63      7   15   23   36   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     7_A     K     7_A     29   50   63      7   17   33   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E     8_A     E     8_A     29   50   63      7   19   33   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     29   50   63      9   15   30   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    10_A     N    10_A     29   50   63      7   19   30   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    11_A     R    11_A     29   50   63      5   18   30   41   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     29   50   63      9   18   30   42   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     29   50   63      5   15   30   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     29   50   63      9   19   33   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     29   50   63      8   17   33   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     29   50   63      9   19   33   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    17_A     S    17_A     29   50   63      9   19   32   42   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    18_A     A    18_A     29   50   63      4   19   33   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    19_A     H    19_A     29   50   63      4   19   33   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    20_A     D    20_A     29   50   63      9   19   33   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     29   50   63      9   19   33   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     29   50   63      9   19   33   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     29   50   63      9   19   33   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     29   50   63      6   19   33   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     29   50   63      8   19   33   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     29   50   63      3   19   33   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     29   50   63      8   18   33   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     29   50   63      8   19   33   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     29   50   63      8   19   33   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     29   50   63      4   17   33   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     29   50   63      4   15   28   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     29   50   63      4   16   33   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     29   50   63      8   19   33   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    34_A     N    34_A     29   50   63      8   19   33   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     29   50   63      8   19   33   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     25   50   63      6   15   33   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     23   50   63      6   15   33   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    38_A     P    38_A     12   50   63      6   15   27   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     12   50   63      5   14   23   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A     12   50   63      3   15   23   30   39   53   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     12   50   63      3   15   22   29   37   50   58   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     12   50   63      3   15   23   30   41   53   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     12   50   63      4   15   23   30   46   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    44_A     E    44_A      9   50   63      4    8   22   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A      9   50   63      4   15   32   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    46_A     S    46_A      9   50   63      4   13   23   35   53   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A      9   50   63      6   15   33   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A      9   50   63      3   16   33   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     11   50   63      5   13   33   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     11   50   63      5    7   17   37   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    51_A     A    51_A     13   46   63      5   10   17   24   39   53   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    52_A     N    52_A     13   46   63      5   11   18   30   47   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     13   46   63      6   12   21   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     13   46   63      5   12   21   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     13   46   63      6   12   32   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     13   46   63      6   12   23   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     13   46   63      6   12   33   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     13   46   63      6   13   33   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    59_A     G    59_A     13   46   63      6   16   33   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    60_A     H    60_A     13   45   63      5   13   27   42   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     13   45   63      3   16   33   44   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     13   45   63      3   12   29   40   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     13   20   63      3    6   14   20   28   37   49   59   61   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  69.93  (  32.48   77.32  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     19     33     44     54     57     59     61     62     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  14.29  30.16  52.38  69.84  85.71  90.48  93.65  96.83  98.41 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.36   0.70   1.16   1.44   1.63   1.73   1.84   1.98   2.06   2.14   2.14   2.14   2.14   2.14   2.14   2.14   2.14   2.14   2.14   2.14
GDT RMS_ALL_AT   3.86   3.24   2.29   2.18   2.19   2.17   2.16   2.14   2.14   2.14   2.14   2.14   2.14   2.14   2.14   2.14   2.14   2.14   2.14   2.14

# Checking swapping
#   possible swapping detected:  E    31_A      E    31_A
#   possible swapping detected:  Y    41_A      Y    41_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     2.949     0    0.069   0.103     3.469   55.357   55.714
LGA    H     2_A      H     2_A     2.066     0    0.053   1.177     5.441   70.952   59.667
LGA    I     3_A      I     3_A     0.842     0    0.040   0.956     2.799   81.548   77.440
LGA    D     4_A      D     4_A     1.590     0    0.057   1.081     3.672   77.262   70.357
LGA    C     5_A      C     5_A     2.257     0    0.066   0.216     2.605   64.762   64.841
LGA    D     6_A      D     6_A     2.473     0    0.010   0.627     4.043   64.762   59.405
LGA    K     7_A      K     7_A     1.366     0    0.071   0.428     2.145   79.286   78.677
LGA    E     8_A      E     8_A     1.201     0    0.075   0.508     2.024   81.429   80.582
LGA    C     9_A      C     9_A     1.896     0    0.050   0.053     2.237   72.857   70.159
LGA    N    10_A      N    10_A     1.605     0    0.080   0.288     1.978   75.000   73.929
LGA    R    11_A      R    11_A     2.569     0    0.018   1.535     4.831   59.048   48.788
LGA    R    12_A      R    12_A     2.253     0    0.054   0.884     2.681   64.762   66.407
LGA    C    13_A      C    13_A     1.803     0    0.220   0.231     3.564   77.381   69.603
LGA    S    14_A      S    14_A     1.093     0    0.025   0.668     1.477   85.952   84.444
LGA    K    15_A      K    15_A     1.835     0    0.131   1.102     4.260   75.000   64.550
LGA    A    16_A      A    16_A     1.568     0    0.019   0.029     2.012   70.833   72.952
LGA    S    17_A      S    17_A     2.638     0    0.007   0.672     4.479   60.952   55.159
LGA    A    18_A      A    18_A     2.117     0    0.076   0.076     2.236   68.810   68.000
LGA    H    19_A      H    19_A     1.255     0    0.131   0.299     1.699   79.286   80.571
LGA    D    20_A      D    20_A     1.416     0    0.190   0.173     2.090   81.429   76.131
LGA    R    21_A      R    21_A     1.611     0    0.058   0.931     7.431   77.143   48.009
LGA    C    22_A      C    22_A     1.195     0    0.123   0.192     1.709   83.690   81.508
LGA    L    23_A      L    23_A     0.826     0    0.109   1.282     4.203   90.476   80.417
LGA    K    24_A      K    24_A     1.549     0    0.054   0.861     6.313   79.286   60.265
LGA    Y    25_A      Y    25_A     1.669     0    0.035   0.612     2.310   72.857   73.651
LGA    C    26_A      C    26_A     1.614     0    0.054   0.169     1.758   72.857   74.286
LGA    G    27_A      G    27_A     1.397     0    0.116   0.116     2.085   75.119   75.119
LGA    I    28_A      I    28_A     1.432     0    0.043   0.689     4.549   81.429   69.940
LGA    C    29_A      C    29_A     1.410     0    0.040   0.702     1.542   81.429   80.000
LGA    C    30_A      C    30_A     1.531     0    0.044   0.067     2.156   72.857   71.508
LGA    E    31_A      E    31_A     1.851     0    0.037   0.618     4.407   72.857   60.529
LGA    K    32_A      K    32_A     1.389     0    0.033   1.397     7.339   81.429   59.206
LGA    C    33_A      C    33_A     0.790     0    0.593   0.504     3.283   75.833   74.921
LGA    N    34_A      N    34_A     0.858     0    0.193   0.721     3.488   88.214   77.857
LGA    C    35_A      C    35_A     1.135     0    0.028   0.461     2.128   85.952   81.667
LGA    V    36_A      V    36_A     0.955     0    0.075   1.336     2.792   85.952   77.075
LGA    P    37_A      P    37_A     1.037     0    0.014   0.108     1.169   81.429   82.721
LGA    P    38_A      P    38_A     1.559     0    0.022   0.117     1.798   75.000   75.306
LGA    G    39_A      G    39_A     1.981     0    0.177   0.177     2.396   68.810   68.810
LGA    T    40_A      T    40_A     4.159     0    0.545   0.503     6.602   31.667   36.667
LGA    Y    41_A      Y    41_A     5.001     0    0.122   1.280     7.294   35.952   24.841
LGA    G    42_A      G    42_A     4.323     0    0.252   0.252     4.758   37.262   37.262
LGA    N    43_A      N    43_A     3.460     0    0.284   0.476     3.934   50.119   50.060
LGA    E    44_A      E    44_A     2.066     0    0.107   1.033     2.914   70.952   67.566
LGA    D    45_A      D    45_A     1.054     0    0.162   1.075     6.077   81.548   61.667
LGA    S    46_A      S    46_A     2.506     0    0.152   0.722     3.042   60.952   58.492
LGA    C    47_A      C    47_A     1.065     0    0.067   0.408     2.501   83.690   77.460
LGA    P    48_A      P    48_A     1.177     0    0.047   0.326     1.937   81.548   79.048
LGA    C    49_A      C    49_A     1.163     0    0.077   0.266     2.677   79.405   74.603
LGA    Y    50_A      Y    50_A     2.319     0    0.036   1.101     4.148   62.976   62.341
LGA    A    51_A      A    51_A     3.745     0    0.190   0.207     4.249   43.452   42.190
LGA    N    52_A      N    52_A     3.030     0    0.098   0.400     3.889   53.571   51.845
LGA    L    53_A      L    53_A     1.877     0    0.039   0.968     2.938   70.833   70.952
LGA    K    54_A      K    54_A     2.063     0    0.121   0.997     2.685   68.810   70.317
LGA    N    55_A      N    55_A     1.417     0    0.022   0.251     1.719   77.143   79.286
LGA    S    56_A      S    56_A     1.979     0    0.131   0.662     4.912   70.833   63.254
LGA    K    57_A      K    57_A     1.480     0    0.120   0.678     3.826   81.429   67.407
LGA    G    58_A      G    58_A     1.257     0    0.118   0.118     1.759   79.286   79.286
LGA    G    59_A      G    59_A     1.613     0    0.046   0.046     2.045   72.976   72.976
LGA    H    60_A      H    60_A     2.234     0    0.120   1.284     9.515   66.786   38.095
LGA    K    61_A      K    61_A     1.846     0    0.069   1.016     4.610   68.810   60.635
LGA    C    62_A      C    62_A     2.618     0    0.403   0.456     4.243   52.262   60.714
LGA    P    63_A      P    63_A     5.095     0    0.266   0.412     6.692   47.024   34.966

# 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):     2.142          2.117                  2.701           71.088   66.224

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     61    1.98    74.206    81.020     2.937

LGA_LOCAL      RMSD:   1.977  Number of atoms:   61  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.143  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   2.142  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.814759 * X  +  -0.410294 * Y  +   0.409666 * Z  + -10.867143
  Y_new =  -0.162940 * X  +  -0.840121 * Y  +  -0.517346 * Z  +   1.584983
  Z_new =   0.556433 * X  +   0.354761 * Y  +  -0.751350 * Z  + -13.819420 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.197382 -0.590087  2.700460   [DEG:  -11.3092  -33.8095  154.7250 ]
ZXZ:  0.669759  2.420902  1.003214   [DEG:   38.3743  138.7075   57.4799 ]
 
# END of job
