
#######################################################
#                                                     #
#                        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        2.13     2.13
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    56       1_A - 56_A        1.96     2.15
  LCS_AVERAGE:     88.13

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    32       5_A - 36_A        0.97     3.64
  LCS_AVERAGE:     36.18

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      9   56   63      3   11   29   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     2_A     S     2_A     12   56   63      3   15   30   43   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     3_A     S     3_A     12   56   63      3   13   24   41   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     F     4_A     F     4_A     12   56   63      3   13   30   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     32   56   63      4   19   32   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     32   56   63      4   24   32   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     7_A     S     7_A     32   56   63      5   24   32   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     8_A     K     8_A     32   56   63     11   24   32   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     32   56   63      6   24   32   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    10_A     G    10_A     32   56   63      4   24   32   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    11_A     V    11_A     32   56   63     11   24   32   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     32   56   63     11   24   32   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     32   56   63     11   24   32   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     32   56   63      4   21   32   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     32   56   63      3   17   32   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     32   56   63      4   24   32   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    17_A     G    17_A     32   56   63      4   21   31   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    18_A     Y    18_A     32   56   63      9   24   32   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Q    19_A     Q    19_A     32   56   63      4   19   32   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    20_A     E    20_A     32   56   63      9   24   32   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     32   56   63     10   24   32   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     32   56   63      6   24   32   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     32   56   63     10   24   32   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     32   56   63     11   24   32   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     32   56   63     11   24   32   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     32   56   63     11   24   32   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     32   56   63     11   24   32   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     32   56   63     11   24   32   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     32   56   63     11   24   32   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     32   56   63     11   24   32   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     32   56   63     10   24   32   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     32   56   63     10   24   32   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     32   56   63     10   24   32   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    34_A     H    34_A     32   56   63     10   22   32   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     32   56   63     10   21   32   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     32   56   63     10   21   32   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     24   56   63     10   21   30   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    38_A     S    38_A     24   56   63      9   21   29   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     24   56   63      7   19   32   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A     23   56   63      3   19   32   38   50   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     16   56   63      3   19   23   34   48   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     13   56   63      3    9   18   35   50   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     12   56   63      4   18   29   43   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    44_A     K    44_A     12   56   63      4   15   29   43   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A     12   56   63      4   10   24   35   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    46_A     E    46_A     12   56   63      4   15   29   43   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     12   56   63      5   17   29   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     12   56   63      4    7   16   34   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     12   56   63      4   10   29   43   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     12   56   63      4   10   22   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    51_A     R    51_A     12   56   63      4    9   29   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    52_A     D    52_A     12   56   63      4   16   29   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     12   56   63      5   17   29   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     12   56   63      4   15   25   40   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     11   56   63      4   11   22   32   45   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     11   56   63      6    9   20   30   38   47   59   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     11   55   63      6   10   22   31   40   50   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     11   55   63      6    9   22   33   49   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    59_A     N    59_A     11   55   63      6   15   29   43   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    60_A     P    60_A     11   55   63     10   21   30   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     11   54   63      6    9   29   44   53   57   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     11   50   63      3   17   31   38   47   55   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     11   38   63      4   11   31   37   43   53   59   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  74.77  (  36.18   88.13  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     24     32     44     53     57     60     62     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  17.46  38.10  50.79  69.84  84.13  90.48  95.24  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    0.31   0.65   0.93   1.42   1.65   1.78   1.92   2.08   2.13   2.13   2.13   2.13   2.13   2.13   2.13   2.13   2.13   2.13   2.13   2.13
GDT RMS_ALL_AT   3.75   3.88   3.46   2.51   2.24   2.22   2.16   2.14   2.13   2.13   2.13   2.13   2.13   2.13   2.13   2.13   2.13   2.13   2.13   2.13

# 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    52_A      D    52_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G     1_A      G     1_A     2.055     0    0.090   0.090     2.666   71.190   71.190
LGA    S     2_A      S     2_A     2.391     0    0.199   0.830     3.582   68.810   61.429
LGA    S     3_A      S     3_A     2.517     0    0.120   0.330     4.765   64.881   56.825
LGA    F     4_A      F     4_A     1.772     0    0.093   0.383     3.306   70.833   62.900
LGA    C     5_A      C     5_A     2.090     0    0.133   0.795     2.777   68.810   66.190
LGA    D     6_A      D     6_A     2.184     0    0.110   1.130     6.284   64.762   49.524
LGA    S     7_A      S     7_A     2.633     0    0.115   0.251     2.851   60.952   59.683
LGA    K     8_A      K     8_A     1.682     0    0.120   0.871     6.128   72.857   63.757
LGA    C     9_A      C     9_A     1.595     0    0.065   0.097     1.817   72.857   75.714
LGA    G    10_A      G    10_A     1.683     0    0.101   0.101     1.778   75.000   75.000
LGA    V    11_A      V    11_A     2.267     0    0.028   0.061     2.670   64.762   62.585
LGA    R    12_A      R    12_A     2.001     0    0.052   1.376     8.338   66.786   50.346
LGA    C    13_A      C    13_A     1.075     0    0.583   0.674     2.327   79.524   81.667
LGA    S    14_A      S    14_A     1.617     0    0.137   0.564     2.062   72.857   71.508
LGA    K    15_A      K    15_A     1.630     0    0.041   0.678     4.934   72.857   60.794
LGA    A    16_A      A    16_A     1.546     0    0.623   0.561     2.854   71.071   73.143
LGA    G    17_A      G    17_A     2.622     0    0.032   0.032     3.083   57.262   57.262
LGA    Y    18_A      Y    18_A     2.722     0    0.272   1.364     7.375   59.048   45.079
LGA    Q    19_A      Q    19_A     1.492     0    0.098   1.171     3.825   81.429   74.550
LGA    E    20_A      E    20_A     2.188     0    0.033   0.768     4.796   64.881   53.968
LGA    R    21_A      R    21_A     2.759     0    0.064   1.161     9.491   60.952   35.065
LGA    C    22_A      C    22_A     1.834     0    0.081   0.101     2.070   68.810   70.159
LGA    L    23_A      L    23_A     1.327     0    0.045   0.286     2.463   79.286   77.202
LGA    K    24_A      K    24_A     2.061     0    0.067   1.223    10.830   66.786   41.323
LGA    Y    25_A      Y    25_A     2.330     0    0.125   0.516     3.027   62.857   64.960
LGA    C    26_A      C    26_A     1.360     0    0.026   0.111     1.584   79.286   80.000
LGA    G    27_A      G    27_A     1.004     0    0.048   0.048     1.397   83.690   83.690
LGA    I    28_A      I    28_A     1.806     0    0.038   0.752     4.766   75.000   63.036
LGA    C    29_A      C    29_A     1.537     0    0.118   0.124     2.244   79.405   75.873
LGA    C    30_A      C    30_A     0.949     0    0.124   0.128     1.316   88.214   90.556
LGA    E    31_A      E    31_A     0.823     0    0.041   0.783     3.400   90.476   78.307
LGA    K    32_A      K    32_A     1.161     0    0.044   1.309     5.152   83.690   69.365
LGA    C    33_A      C    33_A     1.161     0    0.213   0.218     2.211   75.119   78.730
LGA    H    34_A      H    34_A     1.519     0    0.103   1.221     3.830   77.143   67.095
LGA    C    35_A      C    35_A     1.311     0    0.009   0.173     1.749   81.429   78.571
LGA    V    36_A      V    36_A     1.290     0    0.076   0.252     2.413   81.429   76.599
LGA    P    37_A      P    37_A     0.872     0    0.036   0.273     1.179   85.952   89.252
LGA    S    38_A      S    38_A     1.490     0    0.228   0.633     5.078   81.548   69.524
LGA    G    39_A      G    39_A     1.977     0    0.081   0.081     2.810   66.905   66.905
LGA    T    40_A      T    40_A     3.136     0    0.465   0.392     4.157   50.476   51.429
LGA    Y    41_A      Y    41_A     3.262     0    0.224   1.313    10.812   53.571   30.357
LGA    G    42_A      G    42_A     2.532     0    0.628   0.628     4.505   52.619   52.619
LGA    N    43_A      N    43_A     1.136     0    0.131   0.945     4.395   83.690   67.560
LGA    K    44_A      K    44_A     1.163     0    0.035   0.965     8.033   77.143   55.926
LGA    D    45_A      D    45_A     2.218     0    0.146   1.123     7.011   70.833   50.774
LGA    E    46_A      E    46_A     1.725     0    0.077   0.191     2.692   77.143   69.471
LGA    C    47_A      C    47_A     1.226     0    0.016   0.576     2.412   75.119   74.444
LGA    P    48_A      P    48_A     2.358     0    0.211   0.457     2.845   70.833   70.680
LGA    C    49_A      C    49_A     1.648     0    0.086   0.176     2.006   77.381   77.302
LGA    Y    50_A      Y    50_A     1.665     0    0.083   0.824     5.370   77.143   56.111
LGA    R    51_A      R    51_A     1.073     0    0.041   1.272     6.126   83.690   63.074
LGA    D    52_A      D    52_A     0.351     0    0.103   0.784     3.744  100.000   80.833
LGA    L    53_A      L    53_A     0.839     0    0.066   0.879     3.167   88.333   77.917
LGA    K    54_A      K    54_A     1.703     0    0.037   1.276     5.645   69.048   59.683
LGA    N    55_A      N    55_A     3.039     0    0.062   0.221     3.587   48.452   52.798
LGA    S    56_A      S    56_A     4.723     0    0.079   0.537     6.702   31.548   27.619
LGA    K    57_A      K    57_A     4.271     0    0.024   0.755     6.742   38.690   30.000
LGA    G    58_A      G    58_A     2.942     0    0.042   0.042     3.268   59.167   59.167
LGA    N    59_A      N    59_A     1.175     0    0.049   0.258     2.749   86.190   78.750
LGA    P    60_A      P    60_A     1.664     0    0.074   0.320     3.245   75.000   68.503
LGA    K    61_A      K    61_A     2.702     0    0.066   0.989     3.598   53.810   58.413
LGA    C    62_A      C    62_A     3.733     0    0.142   0.495     4.452   41.905   41.349
LGA    P    63_A      P    63_A     4.220     0    0.390   0.383     4.590   35.714   38.980

# 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):     2.134          2.148                  3.061           70.268   63.858

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     62    2.08    76.587    84.377     2.838

LGA_LOCAL      RMSD:   2.084  Number of atoms:   62  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.135  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   2.134  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.954444 * X  +  -0.153601 * Y  +  -0.255820 * Z  +   3.381551
  Y_new =  -0.149125 * X  +  -0.497047 * Y  +   0.854813 * Z  +  -2.219511
  Z_new =  -0.258455 * X  +   0.854021 * Y  +   0.451497 * Z  +  -9.373203 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.986603  0.261422  1.084475   [DEG: -171.1197   14.9784   62.1358 ]
ZXZ: -2.850806  1.102353 -0.293870   [DEG: -163.3391   63.1602  -16.8375 ]
 
# END of job
