
#######################################################
#                                                     #
#                        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        1.92     1.92
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.92     1.92
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       4_A - 36_A        1.00     3.08
  LONGEST_CONTINUOUS_SEGMENT:    33       5_A - 37_A        0.99     3.01
  LCS_AVERAGE:     37.87

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      2   10   28   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     2_A     S     2_A     12   63   63      3   15   31   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     3_A     S     3_A     12   63   63      3   12   30   47   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     F     4_A     F     4_A     33   63   63      3   10   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     33   63   63      5   21   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     33   63   63      5   25   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     7_A     S     7_A     33   63   63      4   25   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     8_A     K     8_A     33   63   63     10   25   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     33   63   63      9   24   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    10_A     G    10_A     33   63   63      4   25   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    11_A     V    11_A     33   63   63      9   25   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     33   63   63     10   25   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     33   63   63      6   25   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     33   63   63      4   19   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     33   63   63      4   17   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     33   63   63      4   20   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    17_A     G    17_A     33   63   63      4   21   29   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    18_A     Y    18_A     33   63   63      8   25   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Q    19_A     Q    19_A     33   63   63      4   14   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    20_A     E    20_A     33   63   63     11   25   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     33   63   63     10   25   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     33   63   63      6   25   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     33   63   63     11   25   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     33   63   63     10   25   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     33   63   63     10   25   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     33   63   63     10   25   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     33   63   63     11   25   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     33   63   63     10   25   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     33   63   63     11   25   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     33   63   63     11   25   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     33   63   63     11   25   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     33   63   63     11   25   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     33   63   63     11   25   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    34_A     H    34_A     33   63   63     11   25   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     33   63   63      9   24   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     33   63   63     11   25   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     33   63   63     11   21   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    38_A     S    38_A     25   63   63      5   21   30   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     25   63   63      4   25   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A     24   63   63      3   20   33   41   53   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     16   63   63      3   20   28   41   51   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     13   63   63      3    9   22   37   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     12   63   63      5   21   30   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    44_A     K    44_A     12   63   63      6   21   30   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A     12   63   63      5   11   28   45   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    46_A     E    46_A     12   63   63      5   21   30   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     12   63   63      5   21   32   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     12   63   63      5    8   22   35   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     12   63   63      5   10   28   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     12   63   63      5   10   23   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    51_A     R    51_A     12   63   63      5    8   30   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    52_A     D    52_A     12   63   63      5   21   32   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     12   63   63      5   18   30   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     12   63   63      4   18   30   47   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     11   63   63      4   12   26   37   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     11   63   63      6   11   26   36   44   58   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     11   63   63      6   13   26   37   51   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     11   63   63      6   11   27   45   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    59_A     N    59_A     11   63   63      9   21   30   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    60_A     P    60_A     11   63   63     11   21   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     11   63   63      6   10   33   47   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     11   63   63      3   10   31   39   49   58   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     11   63   63      3   10   18   37   43   54   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  79.29  (  37.87  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     11     25     33     48     56     59     62     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  17.46  39.68  52.38  76.19  88.89  93.65  98.41 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.34   0.67   0.90   1.44   1.62   1.72   1.87   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92
GDT RMS_ALL_AT   2.42   3.15   3.11   2.03   1.95   1.93   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92

# Checking swapping
#   possible swapping detected:  F     4_A      F     4_A
#   possible swapping detected:  Y    18_A      Y    18_A
#   possible swapping detected:  E    46_A      E    46_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     1.888     0    0.051   0.051     2.840   77.738   77.738
LGA    S     2_A      S     2_A     2.259     0    0.204   0.788     3.842   68.810   61.429
LGA    S     3_A      S     3_A     2.248     0    0.147   0.682     5.665   68.810   58.968
LGA    F     4_A      F     4_A     1.729     0    0.079   0.231     3.670   72.857   61.082
LGA    C     5_A      C     5_A     1.895     0    0.113   0.795     2.642   72.857   70.238
LGA    D     6_A      D     6_A     1.879     0    0.109   1.098     5.975   72.857   55.774
LGA    S     7_A      S     7_A     2.227     0    0.131   0.234     2.572   62.857   63.492
LGA    K     8_A      K     8_A     1.442     0    0.107   0.743     5.499   79.286   68.360
LGA    C     9_A      C     9_A     1.504     0    0.051   0.065     1.763   75.000   77.143
LGA    G    10_A      G    10_A     1.530     0    0.118   0.118     1.565   75.000   75.000
LGA    V    11_A      V    11_A     1.947     0    0.061   0.077     2.263   70.833   68.231
LGA    R    12_A      R    12_A     1.703     0    0.051   1.365     8.257   72.857   51.991
LGA    C    13_A      C    13_A     1.028     0    0.641   0.718     2.454   79.524   81.667
LGA    S    14_A      S    14_A     1.452     0    0.098   0.623     2.063   77.143   74.365
LGA    K    15_A      K    15_A     1.301     0    0.102   0.653     4.265   81.429   68.571
LGA    A    16_A      A    16_A     1.262     0    0.620   0.557     2.829   75.357   76.571
LGA    G    17_A      G    17_A     2.265     0    0.034   0.034     2.637   64.881   64.881
LGA    Y    18_A      Y    18_A     1.955     0    0.290   1.370     7.540   72.976   51.389
LGA    Q    19_A      Q    19_A     1.440     0    0.125   1.170     4.262   83.690   72.011
LGA    E    20_A      E    20_A     1.860     0    0.030   0.769     4.730   72.976   58.413
LGA    R    21_A      R    21_A     2.401     0    0.047   1.155    10.377   66.786   35.584
LGA    C    22_A      C    22_A     1.542     0    0.062   0.078     1.763   75.000   75.714
LGA    L    23_A      L    23_A     1.131     0    0.055   0.280     2.269   81.429   78.274
LGA    K    24_A      K    24_A     1.997     0    0.066   1.132    10.122   68.810   44.339
LGA    Y    25_A      Y    25_A     2.190     0    0.117   0.677     3.685   62.857   63.333
LGA    C    26_A      C    26_A     1.132     0    0.049   0.108     1.361   83.690   84.444
LGA    G    27_A      G    27_A     0.915     0    0.057   0.057     1.456   85.952   85.952
LGA    I    28_A      I    28_A     1.765     0    0.046   0.753     4.832   75.000   63.869
LGA    C    29_A      C    29_A     1.398     0    0.102   0.124     1.876   83.690   80.079
LGA    C    30_A      C    30_A     0.864     0    0.130   0.140     1.191   88.214   90.556
LGA    E    31_A      E    31_A     0.722     0    0.021   0.881     3.984   90.476   77.672
LGA    K    32_A      K    32_A     1.096     0    0.060   0.890     1.916   83.690   78.624
LGA    C    33_A      C    33_A     1.158     0    0.222   0.232     2.073   77.262   80.159
LGA    H    34_A      H    34_A     1.411     0    0.098   1.231     3.051   79.286   70.952
LGA    C    35_A      C    35_A     1.344     0    0.079   0.605     2.463   81.429   77.222
LGA    V    36_A      V    36_A     1.207     0    0.068   0.278     2.266   81.429   76.599
LGA    P    37_A      P    37_A     1.031     0    0.040   0.324     1.318   83.690   85.306
LGA    S    38_A      S    38_A     1.457     0    0.230   0.660     5.214   81.548   68.254
LGA    G    39_A      G    39_A     1.796     0    0.068   0.068     2.444   68.810   68.810
LGA    T    40_A      T    40_A     2.923     0    0.467   0.378     4.007   52.262   53.401
LGA    Y    41_A      Y    41_A     3.095     0    0.156   0.304     3.942   57.381   50.238
LGA    G    42_A      G    42_A     2.361     0    0.638   0.638     4.578   54.524   54.524
LGA    N    43_A      N    43_A     1.250     0    0.195   0.846     4.292   83.690   67.560
LGA    K    44_A      K    44_A     1.307     0    0.052   1.044     8.018   77.143   57.407
LGA    D    45_A      D    45_A     2.126     0    0.090   1.038     3.743   70.833   62.262
LGA    E    46_A      E    46_A     1.508     0    0.125   0.165     2.705   79.405   70.476
LGA    C    47_A      C    47_A     0.850     0    0.103   0.236     2.401   81.548   78.730
LGA    P    48_A      P    48_A     2.260     0    0.246   0.437     2.808   68.810   69.524
LGA    C    49_A      C    49_A     1.846     0    0.104   0.224     2.167   72.976   73.016
LGA    Y    50_A      Y    50_A     1.923     0    0.079   0.776     5.172   72.857   55.595
LGA    R    51_A      R    51_A     1.219     0    0.038   1.225     5.723   83.690   63.939
LGA    D    52_A      D    52_A     0.311     0    0.087   0.772     3.293   92.857   81.190
LGA    L    53_A      L    53_A     1.136     0    0.032   0.755     4.260   83.690   72.798
LGA    K    54_A      K    54_A     1.538     0    0.036   1.270     5.991   70.952   59.841
LGA    N    55_A      N    55_A     2.738     0    0.091   0.281     3.110   55.476   58.214
LGA    S    56_A      S    56_A     3.991     0    0.162   0.567     6.230   38.810   33.968
LGA    K    57_A      K    57_A     3.475     0    0.037   0.771     6.153   50.000   38.466
LGA    G    58_A      G    58_A     2.252     0    0.039   0.039     2.523   66.905   66.905
LGA    N    59_A      N    59_A     0.719     0    0.039   0.302     2.308   92.976   87.440
LGA    P    60_A      P    60_A     1.656     0    0.078   0.322     2.891   75.000   69.524
LGA    K    61_A      K    61_A     2.434     0    0.038   0.967     3.191   59.167   59.153
LGA    C    62_A      C    62_A     3.328     0    0.107   0.538     4.284   48.452   46.825
LGA    P    63_A      P    63_A     3.854     0    0.303   0.284     4.315   41.786   43.401

# 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):     1.917          1.937                  2.793           73.142   66.626

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    1.92    78.968    88.805     3.123

LGA_LOCAL      RMSD:   1.917  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.917  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.917  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.673115 * X  +  -0.055321 * Y  +   0.737466 * Z  +  -4.021151
  Y_new =   0.527818 * X  +   0.734412 * Y  +  -0.426669 * Z  +   1.431428
  Z_new =  -0.518000 * X  +   0.676445 * Y  +   0.523543 * Z  +  -9.553346 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.664997  0.544511  0.912135   [DEG:   38.1015   31.1982   52.2615 ]
ZXZ:  1.046290  1.019792 -0.653517   [DEG:   59.9480   58.4298  -37.4437 ]
 
# END of job
