
#######################################################
#                                                     #
#                        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        2.15     2.15
  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     2.17
  LCS_AVERAGE:     87.81

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    32       5_A - 36_A        0.96     3.71
  LCS_AVERAGE:     35.85

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      8   56   63      3    8   29   45   52   57   60   63   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   27   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     3_A     S     3_A     12   56   63      3    8   22   39   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     F     4_A     F     4_A     12   56   63      3    8   27   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     32   56   63      4   20   32   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     32   56   63      4   23   32   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     7_A     S     7_A     32   56   63      4   23   32   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     8_A     K     8_A     32   56   63      8   23   32   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     32   56   63      6   23   32   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    10_A     G    10_A     32   56   63      4   23   32   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    11_A     V    11_A     32   56   63      8   23   32   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     32   56   63      8   23   32   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     32   56   63      8   23   32   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     32   56   63      4   18   32   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     32   56   63      3   10   32   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     32   56   63      3   16   32   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    17_A     G    17_A     32   56   63      5   23   32   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    18_A     Y    18_A     32   56   63      8   23   32   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Q    19_A     Q    19_A     32   56   63      3   17   32   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    20_A     E    20_A     32   56   63      8   23   32   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     32   56   63      5   23   32   44   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     32   56   63      6   23   32   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     32   56   63      8   23   32   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     32   56   63      8   23   32   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     32   56   63      8   23   32   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     32   56   63      8   23   32   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     32   56   63     10   23   32   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     32   56   63      8   23   32   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     32   56   63     10   23   32   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     32   56   63     10   23   32   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     32   56   63     10   23   32   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     32   56   63     10   23   32   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     32   56   63     10   23   32   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    34_A     H    34_A     32   56   63     10   21   32   45   52   57   60   63   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   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     32   56   63      8   21   32   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     25   56   63     10   21   28   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    38_A     S    38_A     25   56   63      8   21   28   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     25   56   63      8   19   32   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A     24   56   63      4   18   31   40   51   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     16   56   63      3   17   22   33   48   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     13   56   63      3    8   19   34   51   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     11   56   63      4   19   27   43   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    44_A     K    44_A     11   56   63      4   16   27   43   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A      8   56   63      4    8   22   37   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    46_A     E    46_A     10   56   63      4   16   27   41   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     11   56   63      4   16   27   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     11   56   63      5    8   19   35   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     11   56   63      5   11   27   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     11   56   63      5   11   26   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    51_A     R    51_A     11   56   63      5    8   28   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    52_A     D    52_A     11   56   63      5   19   28   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     11   56   63      4   16   27   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     11   56   63      4   14   25   40   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     11   56   63      4   10   22   33   44   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     11   56   63      4   11   20   31   39   48   59   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     11   54   63      5   11   20   31   39   48   59   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     11   54   63      5    9   21   34   45   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    59_A     N    59_A     11   54   63      5   16   26   41   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    60_A     P    60_A     11   54   63     10   21   28   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     11   54   63      5    9   29   45   52   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     11   41   63      5   23   31   38   48   55   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     11   38   63      3   16   30   38   43   52   59   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  74.55  (  35.85   87.81  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     10     23     32     45     52     57     60     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  15.87  36.51  50.79  71.43  82.54  90.48  95.24 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.31   0.63   0.95   1.46   1.63   1.79   1.94   2.15   2.15   2.15   2.15   2.15   2.15   2.15   2.15   2.15   2.15   2.15   2.15   2.15
GDT RMS_ALL_AT   2.54   3.96   3.58   2.47   2.30   2.24   2.18   2.15   2.15   2.15   2.15   2.15   2.15   2.15   2.15   2.15   2.15   2.15   2.15   2.15

# Checking swapping
#   possible swapping detected:  E    20_A      E    20_A
#   possible swapping detected:  Y    41_A      Y    41_A
#   possible swapping detected:  D    45_A      D    45_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     2.079     0    0.114   0.114     2.679   71.190   71.190
LGA    S     2_A      S     2_A     2.354     0    0.134   0.760     3.542   68.810   61.429
LGA    S     3_A      S     3_A     2.665     0    0.167   0.461     4.131   60.952   54.048
LGA    F     4_A      F     4_A     1.973     0    0.074   0.286     4.254   68.810   56.537
LGA    C     5_A      C     5_A     2.250     0    0.127   0.651     2.981   66.786   64.841
LGA    D     6_A      D     6_A     2.154     0    0.094   1.036     5.884   64.762   50.774
LGA    S     7_A      S     7_A     2.638     0    0.112   0.234     2.919   60.952   59.683
LGA    K     8_A      K     8_A     1.704     0    0.090   1.199     6.277   72.857   64.709
LGA    C     9_A      C     9_A     1.639     0    0.063   0.087     1.804   72.857   74.286
LGA    G    10_A      G    10_A     1.652     0    0.081   0.081     1.670   75.000   75.000
LGA    V    11_A      V    11_A     2.259     0    0.015   0.124     2.680   64.762   63.673
LGA    R    12_A      R    12_A     2.001     0    0.041   1.325     8.259   68.810   51.515
LGA    C    13_A      C    13_A     1.067     0    0.533   0.609     2.314   79.524   80.159
LGA    S    14_A      S    14_A     1.480     0    0.049   0.666     2.407   79.286   75.794
LGA    K    15_A      K    15_A     1.657     0    0.210   0.847     2.481   77.143   78.836
LGA    A    16_A      A    16_A     1.514     0    0.119   0.111     2.139   72.976   74.667
LGA    G    17_A      G    17_A     1.820     0    0.114   0.114     2.515   69.048   69.048
LGA    Y    18_A      Y    18_A     2.458     0    0.308   0.291     2.947   64.881   59.722
LGA    Q    19_A      Q    19_A     1.472     0    0.079   1.396     3.667   81.429   72.593
LGA    E    20_A      E    20_A     2.644     0    0.024   0.780     7.714   59.048   39.312
LGA    R    21_A      R    21_A     3.071     0    0.065   1.485    14.018   55.357   27.143
LGA    C    22_A      C    22_A     1.839     0    0.093   0.163     2.082   68.810   70.159
LGA    L    23_A      L    23_A     1.522     0    0.032   1.016     4.779   75.000   64.821
LGA    K    24_A      K    24_A     2.268     0    0.051   1.411    10.753   64.762   40.899
LGA    Y    25_A      Y    25_A     2.431     0    0.116   0.458     4.208   62.857   52.817
LGA    C    26_A      C    26_A     1.282     0    0.020   0.174     1.476   81.429   81.429
LGA    G    27_A      G    27_A     1.064     0    0.019   0.019     1.420   83.690   83.690
LGA    I    28_A      I    28_A     1.797     0    0.018   1.306     6.610   75.000   59.048
LGA    C    29_A      C    29_A     1.467     0    0.106   0.657     4.134   81.548   72.698
LGA    C    30_A      C    30_A     0.951     0    0.071   0.734     2.397   88.214   84.683
LGA    E    31_A      E    31_A     0.943     0    0.055   0.970     3.508   85.952   74.709
LGA    K    32_A      K    32_A     1.182     0    0.056   1.266     6.478   81.429   65.291
LGA    C    33_A      C    33_A     1.226     0    0.135   0.164     1.965   79.286   81.508
LGA    H    34_A      H    34_A     1.488     0    0.100   1.011     4.176   77.143   65.619
LGA    C    35_A      C    35_A     1.357     0    0.020   0.211     1.874   81.429   78.571
LGA    V    36_A      V    36_A     1.299     0    0.070   0.280     2.448   81.429   76.599
LGA    P    37_A      P    37_A     0.883     0    0.032   0.348     1.039   88.214   91.905
LGA    S    38_A      S    38_A     1.207     0    0.266   0.681     4.799   81.548   70.397
LGA    G    39_A      G    39_A     1.781     0    0.037   0.037     2.576   66.905   66.905
LGA    T    40_A      T    40_A     3.124     0    0.540   0.434     4.173   48.571   52.517
LGA    Y    41_A      Y    41_A     3.234     0    0.202   1.354    10.627   55.476   30.992
LGA    G    42_A      G    42_A     2.594     0    0.666   0.666     4.544   50.714   50.714
LGA    N    43_A      N    43_A     1.211     0    0.189   0.938     4.548   83.690   66.845
LGA    K    44_A      K    44_A     1.286     0    0.022   0.941     7.533   77.143   56.878
LGA    D    45_A      D    45_A     2.340     0    0.135   0.864     3.794   68.810   63.274
LGA    E    46_A      E    46_A     1.908     0    0.069   0.129     3.014   72.976   66.825
LGA    C    47_A      C    47_A     1.262     0    0.052   0.614     2.579   72.976   71.746
LGA    P    48_A      P    48_A     2.220     0    0.158   0.428     2.577   70.833   70.680
LGA    C    49_A      C    49_A     1.646     0    0.102   0.234     1.908   77.143   78.651
LGA    Y    50_A      Y    50_A     1.707     0    0.120   0.848     5.352   72.857   55.159
LGA    R    51_A      R    51_A     1.053     0    0.027   1.002     5.969   83.690   59.827
LGA    D    52_A      D    52_A     0.173     0    0.044   0.766     3.267  100.000   85.774
LGA    L    53_A      L    53_A     0.893     0    0.108   0.930     4.820   88.333   75.476
LGA    K    54_A      K    54_A     1.689     0    0.048   0.969     4.509   70.952   60.794
LGA    N    55_A      N    55_A     3.073     0    0.067   0.098     3.525   50.119   52.738
LGA    S    56_A      S    56_A     4.597     0    0.045   0.738     7.773   32.857   27.460
LGA    K    57_A      K    57_A     4.767     0    0.191   0.519     5.457   32.857   32.751
LGA    G    58_A      G    58_A     3.199     0    0.036   0.036     3.569   53.810   53.810
LGA    N    59_A      N    59_A     1.281     0    0.027   0.198     2.902   86.548   76.964
LGA    P    60_A      P    60_A     1.530     0    0.088   0.176     2.619   75.000   69.524
LGA    K    61_A      K    61_A     2.611     0    0.066   0.941     3.595   55.833   59.259
LGA    C    62_A      C    62_A     3.630     0    0.144   0.560     4.524   43.452   41.429
LGA    P    63_A      P    63_A     4.006     0    0.447   0.397     4.240   38.690   38.912

# 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):     2.152          2.146                  3.166           70.210   63.583

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    2.15    76.984    84.260     2.798

LGA_LOCAL      RMSD:   2.152  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.152  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   2.152  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.875023 * X  +  -0.329782 * Y  +  -0.354370 * Z  +   3.178582
  Y_new =  -0.281456 * X  +  -0.248999 * Y  +   0.926705 * Z  +  -0.922956
  Z_new =  -0.393849 * X  +   0.910628 * Y  +   0.125061 * Z  +  -1.752459 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.830388  0.404815  1.434315   [DEG: -162.1693   23.1942   82.1802 ]
ZXZ: -2.776352  1.445407 -0.408208   [DEG: -159.0732   82.8157  -23.3886 ]
 
# END of job
