
#######################################################
#                                                     #
#                        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        1.90     1.90
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.90     1.90
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    34       3_A - 36_A        0.96     3.05
  LONGEST_CONTINUOUS_SEGMENT:    34       4_A - 37_A        0.95     2.97
  LONGEST_CONTINUOUS_SEGMENT:    34       5_A - 38_A        0.99     2.87
  LCS_AVERAGE:     41.24

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   63   63      3    6   28   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     2_A     S     2_A     13   63   63      3   11   30   46   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     3_A     S     3_A     34   63   63      3   18   33   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     F     4_A     F     4_A     34   63   63      3   12   33   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     34   63   63      8   23   34   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     34   63   63      8   28   34   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     7_A     S     7_A     34   63   63      8   28   34   44   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     8_A     K     8_A     34   63   63     10   28   34   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     34   63   63     12   28   34   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    10_A     G    10_A     34   63   63     12   28   34   47   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    11_A     V    11_A     34   63   63     12   28   34   44   55   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     34   63   63     12   23   34   44   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     34   63   63      6   28   34   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     34   63   63      7   28   34   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     34   63   63      5   22   34   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     34   63   63      4   22   34   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    17_A     G    17_A     34   63   63      9   28   34   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    18_A     Y    18_A     34   63   63     10   28   34   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Q    19_A     Q    19_A     34   63   63      5   24   34   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    20_A     E    20_A     34   63   63     12   28   34   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     34   63   63     12   28   34   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     34   63   63     12   28   34   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     34   63   63     12   28   34   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     34   63   63     12   28   34   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     34   63   63     12   28   34   46   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     34   63   63     12   28   34   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     34   63   63     12   28   34   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     34   63   63     10   28   34   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     34   63   63     10   28   34   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     34   63   63     10   28   34   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     34   63   63     10   28   34   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     34   63   63     10   28   34   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     34   63   63     10   28   34   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    34_A     H    34_A     34   63   63     10   28   34   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     34   63   63     10   25   34   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     34   63   63      7   28   34   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     34   63   63     10   22   33   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    38_A     S    38_A     34   63   63      4   22   33   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     28   63   63      8   22   33   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A     28   63   63      7   28   34   44   53   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     10   63   63      4    8   14   29   41   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     10   63   63      3    6   12   15   27   47   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     10   63   63      5    7   32   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    44_A     K    44_A      9   63   63      5    8   32   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A      9   63   63      5    7   19   36   54   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    46_A     E    46_A     14   63   63      5   14   32   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     15   63   63      5   19   33   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     16   63   63      6   14   26   47   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     16   63   63      6   13   30   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     16   63   63      6   10   23   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    51_A     R    51_A     16   63   63      6   12   32   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    52_A     D    52_A     16   63   63      6   19   33   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     16   63   63      6   19   32   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     16   63   63      5   19   32   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     16   63   63      4   19   32   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     16   63   63      5   17   31   45   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     16   63   63      5   19   32   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     16   63   63      5   19   32   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    59_A     N    59_A     16   63   63     10   20   33   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    60_A     P    60_A     16   63   63     10   22   33   48   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     16   63   63      4   13   30   44   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     16   63   63      4   28   34   41   50   58   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     16   63   63      3   13   28   37   41   50   61   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  80.41  (  41.24  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     28     34     48     56     60     61     62     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  19.05  44.44  53.97  76.19  88.89  95.24  96.83  98.41 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.27   6.01   0.81   1.43   1.60   1.73   1.77   1.83   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90
GDT RMS_ALL_AT   4.14   3.41   3.36   1.92   1.91   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90

# Checking swapping
#   possible swapping detected:  E    20_A      E    20_A
#   possible swapping detected:  Y    25_A      Y    25_A
#   possible swapping detected:  E    31_A      E    31_A
#   possible swapping detected:  D    45_A      D    45_A
#   possible swapping detected:  Y    50_A      Y    50_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     1.849     0    0.127   0.127     2.621   73.214   73.214
LGA    S     2_A      S     2_A     2.071     0    0.206   0.833     3.647   70.833   63.968
LGA    S     3_A      S     3_A     1.759     0    0.100   0.671     4.690   75.000   66.032
LGA    F     4_A      F     4_A     1.390     0    0.097   0.224     3.570   79.286   65.455
LGA    C     5_A      C     5_A     1.588     0    0.113   0.810     2.496   77.143   74.365
LGA    D     6_A      D     6_A     1.753     0    0.071   1.046     5.768   72.857   56.488
LGA    S     7_A      S     7_A     2.315     0    0.094   0.550     4.498   62.857   58.889
LGA    K     8_A      K     8_A     1.777     0    0.130   0.782     6.666   72.857   59.947
LGA    C     9_A      C     9_A     1.505     0    0.043   0.064     1.830   72.857   75.714
LGA    G    10_A      G    10_A     1.846     0    0.057   0.057     2.089   68.810   68.810
LGA    V    11_A      V    11_A     2.662     0    0.054   0.059     3.166   59.048   57.211
LGA    R    12_A      R    12_A     2.540     0    0.060   1.295     7.550   60.952   45.887
LGA    C    13_A      C    13_A     1.222     0    0.638   0.712     2.935   73.214   75.952
LGA    S    14_A      S    14_A     1.335     0    0.116   0.587     1.784   79.286   78.571
LGA    K    15_A      K    15_A     1.089     0    0.095   0.668     4.583   81.429   67.937
LGA    A    16_A      A    16_A     1.171     0    0.094   0.114     1.399   81.429   81.429
LGA    G    17_A      G    17_A     1.157     0    0.209   0.209     1.235   83.690   83.690
LGA    Y    18_A      Y    18_A     1.463     0    0.234   1.267     8.114   79.286   53.611
LGA    Q    19_A      Q    19_A     1.100     0    0.057   1.086     4.149   88.214   73.280
LGA    E    20_A      E    20_A     1.536     0    0.020   0.753     6.109   72.976   54.180
LGA    R    21_A      R    21_A     2.148     0    0.057   1.204     8.540   68.810   43.160
LGA    C    22_A      C    22_A     1.548     0    0.081   0.124     1.896   75.000   75.714
LGA    L    23_A      L    23_A     1.174     0    0.021   0.252     1.745   81.429   82.619
LGA    K    24_A      K    24_A     1.948     0    0.086   0.948     6.884   68.810   54.074
LGA    Y    25_A      Y    25_A     2.245     0    0.084   0.631     4.081   64.762   60.238
LGA    C    26_A      C    26_A     1.341     0    0.024   0.100     1.461   81.429   81.429
LGA    G    27_A      G    27_A     0.969     0    0.044   0.044     1.364   83.690   83.690
LGA    I    28_A      I    28_A     1.647     0    0.022   0.742     4.313   77.143   66.667
LGA    C    29_A      C    29_A     1.566     0    0.110   0.109     2.399   79.405   75.873
LGA    C    30_A      C    30_A     1.105     0    0.134   0.121     1.391   81.429   86.032
LGA    E    31_A      E    31_A     1.063     0    0.016   0.835     4.375   81.429   71.958
LGA    K    32_A      K    32_A     1.008     0    0.025   0.979     2.784   85.952   78.836
LGA    C    33_A      C    33_A     1.035     0    0.204   0.227     1.599   79.286   81.508
LGA    H    34_A      H    34_A     1.113     0    0.154   1.243     3.438   81.548   71.905
LGA    C    35_A      C    35_A     0.916     0    0.073   0.204     1.549   88.214   84.524
LGA    V    36_A      V    36_A     1.155     0    0.067   0.272     2.579   88.214   79.388
LGA    P    37_A      P    37_A     0.533     0    0.017   0.283     1.079   88.214   93.265
LGA    S    38_A      S    38_A     1.339     0    0.547   0.792     4.557   81.548   71.746
LGA    G    39_A      G    39_A     1.420     0    0.029   0.029     1.937   75.000   75.000
LGA    T    40_A      T    40_A     2.894     0    0.561   1.218     4.866   52.857   54.762
LGA    Y    41_A      Y    41_A     3.420     0    0.174   1.234     9.701   57.262   32.183
LGA    G    42_A      G    42_A     3.934     0    0.651   0.651     5.284   39.048   39.048
LGA    N    43_A      N    43_A     2.188     0    0.227   0.901     5.927   68.810   58.571
LGA    K    44_A      K    44_A     1.725     0    0.047   0.916     8.085   68.810   51.270
LGA    D    45_A      D    45_A     2.744     0    0.191   1.171     7.701   64.881   44.702
LGA    E    46_A      E    46_A     1.976     0    0.142   0.142     3.561   75.119   63.651
LGA    C    47_A      C    47_A     1.268     0    0.096   0.708     2.459   72.976   73.016
LGA    P    48_A      P    48_A     2.339     0    0.171   0.392     2.727   68.810   69.524
LGA    C    49_A      C    49_A     1.977     0    0.099   0.191     2.190   72.976   73.016
LGA    Y    50_A      Y    50_A     2.024     0    0.137   0.771     5.125   68.810   54.246
LGA    R    51_A      R    51_A     1.262     0    0.034   1.238     5.994   83.690   62.857
LGA    D    52_A      D    52_A     0.729     0    0.194   0.771     2.580   85.952   80.714
LGA    L    53_A      L    53_A     1.388     0    0.176   0.917     4.674   75.476   67.976
LGA    K    54_A      K    54_A     1.238     0    0.038   0.918     4.086   81.429   68.571
LGA    N    55_A      N    55_A     1.849     0    0.060   0.228     2.039   70.833   70.833
LGA    S    56_A      S    56_A     2.471     0    0.157   0.487     4.190   62.857   57.619
LGA    K    57_A      K    57_A     2.041     0    0.044   0.770     4.400   66.786   56.402
LGA    G    58_A      G    58_A     1.241     0    0.057   0.057     1.405   83.690   83.690
LGA    N    59_A      N    59_A     0.595     0    0.127   0.298     2.005   90.476   88.452
LGA    P    60_A      P    60_A     1.655     0    0.120   0.336     3.603   70.833   64.082
LGA    K    61_A      K    61_A     2.519     0    0.070   1.141     3.652   55.833   61.164
LGA    C    62_A      C    62_A     3.374     0    0.123   0.329     3.967   48.452   50.159
LGA    P    63_A      P    63_A     4.424     0    0.426   0.386     4.853   37.262   37.279

# 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):     1.896          1.918                  2.801           73.341   66.921

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     62    1.83    79.762    89.223     3.214

LGA_LOCAL      RMSD:   1.829  Number of atoms:   62  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.898  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.896  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.558308 * X  +   0.646425 * Y  +  -0.520026 * Z  +   2.749612
  Y_new =   0.269039 * X  +  -0.734010 * Y  +  -0.623576 * Z  +   0.417264
  Z_new =  -0.784799 * X  +   0.208240 * Y  +  -0.583718 * Z  +   6.104991 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.449049  0.902372  2.798919   [DEG:   25.7286   51.7021  160.3662 ]
ZXZ: -0.695097  2.194096 -1.311431   [DEG:  -39.8261  125.7124  -75.1395 ]
 
# END of job
