
#######################################################
#                                                     #
#                        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        2.72     2.72
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    42       4_A - 45_A        1.99     3.02
  LCS_AVERAGE:     55.35

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       5_A - 37_A        0.98     3.58
  LCS_AVERAGE:     35.50

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    5   63      0    5    7   13   20   26   32   40   51   58   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     S     2_A     S     2_A      4   40   63      0    5    9   15   22   36   48   55   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     S     3_A     S     3_A      4   41   63      3    3    5   11   24   36   50   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     F     4_A     F     4_A     11   42   63      4   14   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     33   42   63     10   23   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     33   42   63     11   23   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     S     7_A     S     7_A     33   42   63     12   23   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     K     8_A     K     8_A     33   42   63      6   18   30   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     33   42   63      5   20   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     G    10_A     G    10_A     33   42   63      8   20   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     V    11_A     V    11_A     33   42   63      8   22   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     33   42   63      8   17   30   40   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     33   42   63      6   23   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     33   42   63     12   23   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     33   42   63      3   21   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     33   42   63     10   23   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     G    17_A     G    17_A     33   42   63      3   14   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     Y    18_A     Y    18_A     33   42   63      3   19   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     Q    19_A     Q    19_A     33   42   63      3   13   30   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     E    20_A     E    20_A     33   42   63     12   23   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     33   42   63     12   23   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     33   42   63     11   23   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     33   42   63     12   23   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     33   42   63     12   23   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     33   42   63     10   23   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     33   42   63      8   23   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     33   42   63     12   23   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     33   42   63     12   23   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     33   42   63     12   23   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     33   42   63     12   23   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     33   42   63     12   23   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     33   42   63     12   23   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     33   42   63     11   23   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     H    34_A     H    34_A     33   42   63      8   23   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     33   42   63     11   23   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     33   42   63     10   23   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     33   42   63      4   23   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     S    38_A     S    38_A     29   42   63      8   16   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     27   42   63      7   20   31   37   44   49   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A     23   42   63      5   16   29   36   41   47   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     17   42   63      0    6   13   30   39   44   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A      4   42   63      0    3    7   14   19   27   42   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A      5   42   63      3    5    9   18   33   48   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     K    44_A     K    44_A      5   42   63      3    5   10   18   43   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A      5   42   63      3    5   10   18   41   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     E    46_A     E    46_A      5   22   63      3    7   19   36   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A      8   22   63      5   19   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     10   19   63      3    5   25   32   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     11   19   63      4   14   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     11   19   63      4   14   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     R    51_A     R    51_A     11   19   63      4   19   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     D    52_A     D    52_A     11   19   63      4   15   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     11   19   63      4   15   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     11   19   63      4   10   24   40   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     11   19   63      4    9   16   25   43   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     11   19   63      5    9   16   22   31   45   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     11   19   63      5    9   14   22   32   45   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     11   19   63      5    9   16   27   44   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     N    59_A     N    59_A     11   19   63      5   12   28   40   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     P    60_A     P    60_A     11   19   63      9   22   31   41   45   50   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     11   19   63      3    9   18   34   44   49   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     11   19   63      4   13   22   35   41   47   54   57   59   61   61   62   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A      6   18   63      0    0    5   11   14   20   40   48   53   59   60   62   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  63.62  (  35.50   55.35  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     23     31     41     45     50     54     57     59     61     61     62     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  19.05  36.51  49.21  65.08  71.43  79.37  85.71  90.48  93.65  96.83  96.83  98.41 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.37   0.59   0.90   1.25   1.42   1.73   1.91   2.12   2.28   2.45   2.45   2.55   2.72   2.72   2.72   2.72   2.72   2.72   2.72   2.72
GDT RMS_ALL_AT   3.66   3.47   3.62   3.03   2.93   2.82   2.81   2.78   2.78   2.73   2.73   2.73   2.72   2.72   2.72   2.72   2.72   2.72   2.72   2.72

# Checking swapping
#   possible swapping detected:  F     4_A      F     4_A
#   possible swapping detected:  Y    25_A      Y    25_A
#   possible swapping detected:  E    46_A      E    46_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     8.627     0    0.155   0.155    10.809    2.857    2.857
LGA    S     2_A      S     2_A     5.922     0    0.677   0.901     6.108   22.857   27.937
LGA    S     3_A      S     3_A     5.849     0    0.639   0.677     8.938   22.857   17.381
LGA    F     4_A      F     4_A     1.275     0    0.177   1.279     5.065   75.119   57.273
LGA    C     5_A      C     5_A     1.026     0    0.173   0.189     1.549   83.690   83.016
LGA    D     6_A      D     6_A     1.531     0    0.040   1.056     5.950   77.143   57.917
LGA    S     7_A      S     7_A     2.001     0    0.104   0.553     3.998   64.881   61.270
LGA    K     8_A      K     8_A     1.959     0    0.160   0.841     8.619   75.000   53.333
LGA    C     9_A      C     9_A     1.586     0    0.012   0.064     1.716   72.857   72.857
LGA    G    10_A      G    10_A     1.774     0    0.055   0.055     1.804   72.857   72.857
LGA    V    11_A      V    11_A     2.150     0    0.074   0.070     2.404   64.762   64.762
LGA    R    12_A      R    12_A     2.051     0    0.033   1.134     4.291   70.833   61.082
LGA    C    13_A      C    13_A     0.886     0    0.650   0.723     3.211   75.833   79.206
LGA    S    14_A      S    14_A     0.630     0    0.161   0.574     1.251   88.214   85.952
LGA    K    15_A      K    15_A     1.438     0    0.144   0.895     4.010   83.690   65.344
LGA    A    16_A      A    16_A     0.924     0    0.622   0.560     2.251   81.786   83.524
LGA    G    17_A      G    17_A     2.750     0    0.189   0.189     3.975   53.810   53.810
LGA    Y    18_A      Y    18_A     2.896     0    0.079   1.294     5.673   65.000   50.635
LGA    Q    19_A      Q    19_A     1.624     0    0.680   1.027     5.008   59.405   64.550
LGA    E    20_A      E    20_A     1.352     0    0.255   0.847     2.599   72.976   70.265
LGA    R    21_A      R    21_A     1.898     0    0.043   1.316    11.733   72.857   38.009
LGA    C    22_A      C    22_A     1.292     0    0.136   0.175     1.793   79.286   81.508
LGA    L    23_A      L    23_A     1.099     0    0.010   0.211     2.146   81.429   79.345
LGA    K    24_A      K    24_A     1.998     0    0.044   1.172    10.400   68.810   43.492
LGA    Y    25_A      Y    25_A     2.239     0    0.103   0.614     3.448   66.786   59.206
LGA    C    26_A      C    26_A     0.958     0    0.034   0.092     1.447   88.214   87.460
LGA    G    27_A      G    27_A     1.070     0    0.005   0.005     1.622   81.548   81.548
LGA    I    28_A      I    28_A     2.078     0    0.020   0.738     5.036   70.833   58.393
LGA    C    29_A      C    29_A     1.784     0    0.113   0.127     2.799   77.143   71.746
LGA    C    30_A      C    30_A     0.946     0    0.115   0.769     1.478   83.690   84.444
LGA    E    31_A      E    31_A     1.385     0    0.025   0.707     2.614   77.143   72.116
LGA    K    32_A      K    32_A     1.666     0    0.051   1.157     5.733   72.857   62.381
LGA    C    33_A      C    33_A     1.341     0    0.184   0.211     1.581   79.286   80.000
LGA    H    34_A      H    34_A     1.298     0    0.154   1.288     5.450   79.286   61.524
LGA    C    35_A      C    35_A     0.442     0    0.036   0.154     1.225   90.595   89.048
LGA    V    36_A      V    36_A     1.241     0    0.045   1.191     4.722   88.214   74.558
LGA    P    37_A      P    37_A     1.437     0    0.034   0.316     2.591   73.214   69.660
LGA    S    38_A      S    38_A     2.423     0    0.583   0.801     4.510   54.762   55.635
LGA    G    39_A      G    39_A     3.486     0    0.186   0.186     4.220   46.905   46.905
LGA    T    40_A      T    40_A     4.158     0    0.381   1.300     4.648   38.690   37.279
LGA    Y    41_A      Y    41_A     4.940     0    0.390   1.056    15.163   42.738   17.103
LGA    G    42_A      G    42_A     5.261     0    0.657   0.657     8.330   18.571   18.571
LGA    N    43_A      N    43_A     3.278     0    0.503   1.348     4.368   46.786   52.262
LGA    K    44_A      K    44_A     2.744     0    0.056   0.485     3.129   55.357   55.556
LGA    D    45_A      D    45_A     2.989     0    0.083   0.953     7.844   59.048   39.643
LGA    E    46_A      E    46_A     2.252     0    0.010   0.811     2.770   68.810   72.275
LGA    C    47_A      C    47_A     0.408     0    0.052   0.655     2.278   83.929   81.825
LGA    P    48_A      P    48_A     2.798     0    0.245   0.300     4.701   52.857   54.898
LGA    C    49_A      C    49_A     1.727     0    0.121   0.199     1.935   72.857   74.286
LGA    Y    50_A      Y    50_A     1.605     0    0.098   1.282     9.224   72.857   44.841
LGA    R    51_A      R    51_A     1.546     0    0.091   1.114     8.714   77.143   45.455
LGA    D    52_A      D    52_A     0.886     0    0.210   0.734     2.355   81.548   78.333
LGA    L    53_A      L    53_A     0.929     0    0.141   0.942     4.410   90.476   78.333
LGA    K    54_A      K    54_A     1.456     0    0.028   0.914     3.403   75.119   68.677
LGA    N    55_A      N    55_A     2.873     0    0.101   0.999     6.510   55.476   43.155
LGA    S    56_A      S    56_A     4.149     0    0.123   0.471     6.504   37.262   32.302
LGA    K    57_A      K    57_A     4.429     0    0.054   0.760     7.810   38.690   25.291
LGA    G    58_A      G    58_A     2.841     0    0.041   0.041     3.178   59.167   59.167
LGA    N    59_A      N    59_A     0.915     0    0.029   1.240     5.368   88.452   67.024
LGA    P    60_A      P    60_A     1.663     0    0.421   0.425     4.117   66.310   66.939
LGA    K    61_A      K    61_A     3.108     0    0.408   1.609     5.035   46.071   45.397
LGA    C    62_A      C    62_A     3.662     0    0.565   0.588     4.031   43.452   44.524
LGA    P    63_A      P    63_A     5.972     0    0.496   0.432     8.569   20.595   14.762

# 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):     2.721          2.825                  3.725           65.263   58.741

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     57    2.12    73.016    72.499     2.564

LGA_LOCAL      RMSD:   2.123  Number of atoms:   57  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.784  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   2.721  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.217213 * X  +  -0.752641 * Y  +   0.621570 * Z  +   6.148801
  Y_new =   0.974579 * X  +  -0.203032 * Y  +   0.094729 * Z  +  -4.422282
  Z_new =   0.054902 * X  +   0.626346 * Y  +   0.777610 * Z  +  -6.664989 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.790090 -0.054930  0.678071   [DEG:  102.5646   -3.1472   38.8506 ]
ZXZ:  1.722035  0.679941  0.087431   [DEG:   98.6653   38.9578    5.0094 ]
 
# END of job
