
#######################################################
#                                                     #
#                        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        3.14     3.14
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    40       2_A - 41_A        1.99     3.73
  LONGEST_CONTINUOUS_SEGMENT:    40       3_A - 42_A        1.92     3.72
  LONGEST_CONTINUOUS_SEGMENT:    40       4_A - 43_A        1.96     3.74
  LONGEST_CONTINUOUS_SEGMENT:    40       5_A - 44_A        1.99     3.72
  LCS_AVERAGE:     58.38

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29       7_A - 35_A        1.00     4.93
  LCS_AVERAGE:     35.17

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      3   39   63      3    3    7   14   26   36   47   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     2_A     S     2_A     12   40   63      5    9   14   20   26   31   39   42   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     3_A     S     3_A     12   40   63      5    9   15   22   32   44   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     F     4_A     F     4_A     12   40   63      5   10   17   30   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     12   40   63      5   10   22   31   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     12   40   63      5   10   21   31   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     7_A     S     7_A     29   40   63      4   17   28   31   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     8_A     K     8_A     29   40   63      7   20   28   31   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     29   40   63     11   21   28   31   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    10_A     G    10_A     29   40   63      8   21   28   31   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    11_A     V    11_A     29   40   63     11   21   28   31   34   40   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     29   40   63     10   21   28   31   34   43   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     29   40   63      7   21   28   31   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     29   40   63      3   17   28   31   35   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     29   40   63      3   21   28   31   37   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     29   40   63      3    9   28   31   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    17_A     G    17_A     29   40   63      7   19   24   30   38   45   49   54   56   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    18_A     Y    18_A     29   40   63     10   21   28   31   38   45   49   54   56   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Q    19_A     Q    19_A     29   40   63      3   15   28   31   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    20_A     E    20_A     29   40   63      4   21   28   31   38   45   49   54   56   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     29   40   63     11   21   28   31   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     29   40   63     10   21   28   31   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     29   40   63     11   21   28   31   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     29   40   63     11   21   28   31   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     29   40   63     11   21   28   31   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     29   40   63     11   21   28   31   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     29   40   63     11   21   28   31   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     29   40   63     11   21   28   31   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     29   40   63     11   21   28   31   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     29   40   63     11   21   28   31   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     29   40   63      7   21   28   31   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     29   40   63      8   21   28   31   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     29   40   63      8   21   28   31   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    34_A     H    34_A     29   40   63     10   21   28   31   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     29   40   63      8   20   28   31   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     22   40   63      8   16   27   31   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     22   40   63      8   16   24   30   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    38_A     S    38_A     22   40   63      6   16   24   30   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     22   40   63      8   16   24   30   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A     22   40   63      8   16   24   30   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     22   40   63      3   16   24   30   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     22   40   63      6   16   24   30   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     20   40   63      3    8   18   30   37   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    44_A     K    44_A     11   40   63      3    8   18   30   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A      9   36   63      3    8   15   20   26   34   45   51   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    46_A     E    46_A      9   36   63      3    8   15   22   31   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     17   36   63      3    8   16   22   37   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     17   36   63      6   13   16   19   26   30   41   51   56   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     17   36   63      6   13   16   21   28   42   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     17   36   63      8   13   18   30   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    51_A     R    51_A     17   36   63      8   13   18   30   38   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    52_A     D    52_A     17   36   63      8   13   17   22   35   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     17   29   63      4   13   16   22   32   45   49   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     17   29   63      8   13   16   21   27   39   48   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     17   24   63      8   13   16   21   27   34   41   49   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     17   24   63      3   13   16   21   27   34   41   49   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     17   24   63      8   13   16   21   27   34   44   51   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     17   24   63      4   13   16   21   30   39   48   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    59_A     N    59_A     17   24   63      8   13   16   24   32   37   47   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    60_A     P    60_A     17   23   63      6   13   19   27   32   39   48   54   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     17   23   63      4    8   16   19   27   34   41   51   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     17   23   63      8   13   16   21   27   34   41   49   57   60   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     17   23   63      3    3   16   19   25   30   34   42   51   60   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  64.52  (  35.17   58.38  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     11     21     28     31     38     45     49     54     57     60     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  17.46  33.33  44.44  49.21  60.32  71.43  77.78  85.71  90.48  95.24 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.62   0.93   1.24   1.75   2.11   2.25   2.58   2.89   2.94   3.14   3.14   3.14   3.14   3.14   3.14   3.14   3.14   3.14   3.14
GDT RMS_ALL_AT   5.55   5.35   4.87   4.47   3.84   3.58   3.51   3.26   3.17   3.17   3.14   3.14   3.14   3.14   3.14   3.14   3.14   3.14   3.14   3.14

# Checking swapping
#   possible swapping detected:  Y    18_A      Y    18_A
#   possible swapping detected:  E    20_A      E    20_A
#   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
#   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     3.846     0    0.023   0.023     5.626   32.024   32.024
LGA    S     2_A      S     2_A     4.925     0    0.301   0.959     6.614   40.357   32.698
LGA    S     3_A      S     3_A     2.771     0    0.121   0.677     5.568   63.690   54.365
LGA    F     4_A      F     4_A     2.221     0    0.045   0.125     5.894   68.810   44.848
LGA    C     5_A      C     5_A     1.472     0    0.102   0.785     3.638   81.548   73.730
LGA    D     6_A      D     6_A     1.879     0    0.064   1.063     6.935   72.857   51.190
LGA    S     7_A      S     7_A     2.009     0    0.059   0.635     2.952   67.024   66.270
LGA    K     8_A      K     8_A     2.070     0    0.121   0.730     8.473   70.952   50.370
LGA    C     9_A      C     9_A     1.602     0    0.032   0.038     2.216   70.833   74.365
LGA    G    10_A      G    10_A     2.176     0    0.077   0.077     2.483   66.786   66.786
LGA    V    11_A      V    11_A     3.201     0    0.028   1.344     5.661   51.786   47.959
LGA    R    12_A      R    12_A     2.786     0    0.042   1.150     7.175   57.143   44.502
LGA    C    13_A      C    13_A     1.969     0    0.631   0.711     3.535   61.429   65.317
LGA    S    14_A      S    14_A     2.311     0    0.088   0.584     2.845   64.762   67.778
LGA    K    15_A      K    15_A     1.908     0    0.088   0.722     4.722   70.833   60.688
LGA    A    16_A      A    16_A     1.121     0    0.647   0.590     2.180   79.524   79.905
LGA    G    17_A      G    17_A     3.223     0    0.027   0.027     3.722   52.024   52.024
LGA    Y    18_A      Y    18_A     2.748     0    0.337   1.342     7.391   62.976   45.794
LGA    Q    19_A      Q    19_A     1.798     0    0.063   1.079     4.301   75.000   62.910
LGA    E    20_A      E    20_A     3.097     0    0.030   0.866     8.152   53.571   34.921
LGA    R    21_A      R    21_A     2.966     0    0.043   1.122    11.084   59.048   29.740
LGA    C    22_A      C    22_A     1.330     0    0.097   0.120     1.808   77.143   80.079
LGA    L    23_A      L    23_A     1.468     0    0.018   1.178     4.418   77.143   68.512
LGA    K    24_A      K    24_A     2.509     0    0.059   1.199    11.902   62.857   36.720
LGA    Y    25_A      Y    25_A     2.388     0    0.134   0.560     3.241   62.857   58.492
LGA    C    26_A      C    26_A     1.158     0    0.020   0.080     1.506   83.690   83.016
LGA    G    27_A      G    27_A     0.722     0    0.054   0.054     0.878   90.476   90.476
LGA    I    28_A      I    28_A     1.614     0    0.016   0.735     5.014   79.286   62.619
LGA    C    29_A      C    29_A     2.266     0    0.088   0.092     3.578   68.810   62.619
LGA    C    30_A      C    30_A     1.654     0    0.128   0.133     2.169   75.000   74.365
LGA    E    31_A      E    31_A     1.187     0    0.027   0.786     3.135   77.143   75.132
LGA    K    32_A      K    32_A     2.056     0    0.033   0.944     2.850   64.881   66.825
LGA    C    33_A      C    33_A     2.608     0    0.171   0.222     3.215   57.262   59.762
LGA    H    34_A      H    34_A     2.674     0    0.079   1.228     3.409   60.952   64.571
LGA    C    35_A      C    35_A     2.136     0    0.025   0.170     2.428   68.810   67.460
LGA    V    36_A      V    36_A     1.014     0    0.048   0.859     3.825   83.690   77.279
LGA    P    37_A      P    37_A     0.882     0    0.036   0.108     1.362   85.952   87.891
LGA    S    38_A      S    38_A     2.143     0    0.265   0.684     5.650   63.095   55.159
LGA    G    39_A      G    39_A     2.204     0    0.070   0.070     2.234   70.952   70.952
LGA    T    40_A      T    40_A     2.166     0    0.448   0.364     3.373   61.071   58.367
LGA    Y    41_A      Y    41_A     2.443     0    0.186   1.254     9.609   59.167   36.270
LGA    G    42_A      G    42_A     2.974     0    0.063   0.063     3.813   51.905   51.905
LGA    N    43_A      N    43_A     3.550     0    0.161   1.031     6.565   48.333   38.452
LGA    K    44_A      K    44_A     2.684     0    0.028   0.741     3.575   51.905   54.868
LGA    D    45_A      D    45_A     5.127     0    0.192   1.230     9.289   31.548   21.012
LGA    E    46_A      E    46_A     3.720     0    0.181   0.168     4.847   46.905   43.704
LGA    C    47_A      C    47_A     2.946     0    0.034   0.615     4.385   50.119   50.397
LGA    P    48_A      P    48_A     5.051     0    0.190   0.408     6.614   34.405   29.116
LGA    C    49_A      C    49_A     3.833     0    0.111   0.182     4.981   50.595   45.159
LGA    Y    50_A      Y    50_A     1.360     0    0.116   0.485     3.323   79.524   70.635
LGA    R    51_A      R    51_A     2.005     0    0.023   1.299    10.063   70.833   39.524
LGA    D    52_A      D    52_A     2.973     0    0.123   0.761     3.451   55.357   56.429
LGA    L    53_A      L    53_A     2.847     0    0.038   0.881     3.358   53.571   56.429
LGA    K    54_A      K    54_A     4.302     0    0.028   1.093     8.459   32.024   26.190
LGA    N    55_A      N    55_A     6.673     0    0.064   0.225     7.823   16.310   13.214
LGA    S    56_A      S    56_A     7.305     0    0.127   0.508     9.392   11.667    9.206
LGA    K    57_A      K    57_A     6.190     0    0.027   0.846     7.590   20.714   15.608
LGA    G    58_A      G    58_A     4.562     0    0.080   0.080     5.278   34.524   34.524
LGA    N    59_A      N    59_A     4.718     0    0.047   1.055     6.967   31.429   27.976
LGA    P    60_A      P    60_A     3.925     0    0.113   0.326     4.851   35.833   37.279
LGA    K    61_A      K    61_A     5.407     0    0.030   1.419     6.201   24.048   27.778
LGA    C    62_A      C    62_A     5.264     0    0.284   0.633     6.190   25.000   24.762
LGA    P    63_A      P    63_A     6.312     0    0.478   0.594     7.352   19.286   16.327

# 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):     3.144          3.111                  3.984           57.604   51.829

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     54    2.58    67.063    69.572     2.012

LGA_LOCAL      RMSD:   2.583  Number of atoms:   54  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   3.260  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   3.144  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.621036 * X  +   0.734659 * Y  +   0.273113 * Z  + -10.492074
  Y_new =  -0.438726 * X  +   0.037091 * Y  +   0.897855 * Z  +   0.657745
  Z_new =   0.649487 * X  +  -0.677422 * Y  +   0.345349 * Z  +  -5.760506 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.615037 -0.706910 -1.099340   [DEG:  -35.2390  -40.5030  -62.9875 ]
ZXZ:  2.846302  1.218186  2.377243   [DEG:  163.0811   69.7969  136.2060 ]
 
# END of job
