
#######################################################
#                                                     #
#                        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        2.50     2.50
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    45       3_A - 47_A        1.97     2.69
  LCS_AVERAGE:     64.17

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       5_A - 37_A        0.99     3.43
  LONGEST_CONTINUOUS_SEGMENT:    33       6_A - 38_A        1.00     3.40
  LONGEST_CONTINUOUS_SEGMENT:    33       7_A - 39_A        0.98     3.46
  LCS_AVERAGE:     37.89

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   42   63      0    3    3   11   16   24   28   35   54   60   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     2_A     S     2_A     12   44   63      5   12   14   26   34   51   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     3_A     S     3_A     12   45   63      5   12   23   38   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     F     4_A     F     4_A     12   45   63      5   15   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     33   45   63      5   22   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     33   45   63      5   19   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     7_A     S     7_A     33   45   63     11   25   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     8_A     K     8_A     33   45   63      7   20   31   38   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     33   45   63      8   25   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    10_A     G    10_A     33   45   63      8   25   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    11_A     V    11_A     33   45   63      7   18   30   37   44   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     33   45   63      7   18   30   38   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     33   45   63     11   25   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     33   45   63     12   25   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     33   45   63     10   24   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     33   45   63     10   25   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    17_A     G    17_A     33   45   63      4    9   29   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    18_A     Y    18_A     33   45   63     11   25   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     Q    19_A     Q    19_A     33   45   63      4   19   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    20_A     E    20_A     33   45   63     12   25   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     33   45   63     12   25   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     33   45   63     11   25   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     33   45   63     12   25   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     33   45   63     12   25   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     33   45   63     11   25   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     33   45   63     11   25   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     33   45   63     12   25   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     33   45   63     12   25   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     33   45   63     12   25   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     33   45   63     12   25   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     33   45   63     12   25   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     33   45   63     12   25   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     33   45   63     10   25   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    34_A     H    34_A     33   45   63     10   25   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     33   45   63     10   25   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     33   45   63     12   25   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     33   45   63      5   25   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    38_A     S    38_A     33   45   63      5   12   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     33   45   63      9   24   31   38   44   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A     29   45   63      5   18   27   37   41   49   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     24   45   63      7   18   27   37   41   45   53   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A      4   45   63      3    4    5   11   23   36   55   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A      5   45   63      3    5   12   25   42   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    44_A     K    44_A      5   45   63      3    5   12   25   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A      5   45   63      3    7   12   18   34   52   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    46_A     E    46_A      5   45   63      3    8   18   37   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     11   45   63      3   17   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     14   30   63      3    6   20   26   43   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     14   30   63      8   11   28   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     14   30   63      8   11   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    51_A     R    51_A     14   30   63      8   15   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    52_A     D    52_A     14   30   63      8   14   30   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     14   30   63      8   14   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     14   30   63      8   13   26   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     14   30   63      8   11   19   33   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     14   30   63      8   11   19   25   41   50   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     14   30   63      5   11   19   29   41   52   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     14   30   63      5   10   23   37   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    59_A     N    59_A     14   30   63      6   16   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    60_A     P    60_A     14   19   63     10   24   31   39   45   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     14   19   63      3   11   15   32   44   53   57   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     14   19   63      4   11   27   37   41   46   52   59   61   61   62   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     12   19   63      3    3   14   19   32   38   46   50   55   60   62   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  67.36  (  37.89   64.17  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     25     31     39     45     53     57     59     61     61     62     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  19.05  39.68  49.21  61.90  71.43  84.13  90.48  93.65  96.83  96.83  98.41 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.40   0.69   0.87   1.24   1.50   1.81   1.98   2.10   2.23   2.23   2.35   2.50   2.50   2.50   2.50   2.50   2.50   2.50   2.50   2.50
GDT RMS_ALL_AT   3.40   3.37   3.28   2.65   2.58   2.55   2.54   2.53   2.51   2.51   2.51   2.50   2.50   2.50   2.50   2.50   2.50   2.50   2.50   2.50

# Checking swapping
#   possible swapping detected:  E    20_A      E    20_A
#   possible swapping detected:  Y    25_A      Y    25_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:  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     7.414     0    0.526   0.526     9.174    9.643    9.643
LGA    S     2_A      S     2_A     3.535     0    0.503   0.570     4.045   50.595   51.587
LGA    S     3_A      S     3_A     2.251     0    0.149   0.319     4.325   69.048   61.746
LGA    F     4_A      F     4_A     1.471     0    0.078   0.250     4.831   79.286   56.147
LGA    C     5_A      C     5_A     0.994     0    0.134   0.777     2.280   88.214   84.683
LGA    D     6_A      D     6_A     1.796     0    0.062   1.058     6.435   75.000   53.988
LGA    S     7_A      S     7_A     2.453     0    0.102   0.565     4.628   63.095   56.825
LGA    K     8_A      K     8_A     2.384     0    0.129   1.014     9.036   66.786   46.825
LGA    C     9_A      C     9_A     1.428     0    0.013   0.042     1.659   75.000   77.143
LGA    G    10_A      G    10_A     1.950     0    0.055   0.055     2.189   68.810   68.810
LGA    V    11_A      V    11_A     2.932     0    0.055   0.064     3.760   57.143   53.129
LGA    R    12_A      R    12_A     2.566     0    0.063   0.856     4.419   60.952   52.987
LGA    C    13_A      C    13_A     0.614     0    0.646   0.728     3.309   75.833   80.714
LGA    S    14_A      S    14_A     0.622     0    0.097   0.594     1.366   92.857   90.556
LGA    K    15_A      K    15_A     1.039     0    0.165   0.643     4.128   90.595   69.206
LGA    A    16_A      A    16_A     0.811     0    0.653   0.592     1.989   86.071   86.952
LGA    G    17_A      G    17_A     2.973     0    0.027   0.027     2.973   57.143   57.143
LGA    Y    18_A      Y    18_A     2.237     0    0.276   1.332     7.404   66.786   50.873
LGA    Q    19_A      Q    19_A     1.090     0    0.042   0.932     2.261   83.690   76.878
LGA    E    20_A      E    20_A     1.769     0    0.019   0.753     5.780   70.952   52.857
LGA    R    21_A      R    21_A     2.408     0    0.060   1.201     8.993   64.762   39.004
LGA    C    22_A      C    22_A     1.768     0    0.080   0.132     2.044   70.833   71.508
LGA    L    23_A      L    23_A     1.290     0    0.043   1.385     3.667   77.143   69.405
LGA    K    24_A      K    24_A     1.863     0    0.092   0.948     6.308   68.810   55.820
LGA    Y    25_A      Y    25_A     2.298     0    0.111   0.621     3.785   62.857   60.000
LGA    C    26_A      C    26_A     1.435     0    0.020   0.073     1.557   79.286   80.000
LGA    G    27_A      G    27_A     1.019     0    0.051   0.051     1.483   81.429   81.429
LGA    I    28_A      I    28_A     1.819     0    0.022   0.751     4.606   72.857   61.964
LGA    C    29_A      C    29_A     1.716     0    0.129   0.134     2.668   79.405   73.254
LGA    C    30_A      C    30_A     0.988     0    0.123   0.151     1.371   85.952   85.952
LGA    E    31_A      E    31_A     0.705     0    0.021   0.903     3.754   90.476   80.317
LGA    K    32_A      K    32_A     0.900     0    0.020   0.760     2.145   90.476   80.741
LGA    C    33_A      C    33_A     1.033     0    0.204   0.225     1.338   83.690   84.444
LGA    H    34_A      H    34_A     0.884     0    0.154   1.250     4.264   88.214   70.429
LGA    C    35_A      C    35_A     0.397     0    0.037   0.179     1.341   92.976   90.635
LGA    V    36_A      V    36_A     1.294     0    0.039   1.220     4.718   88.214   71.293
LGA    P    37_A      P    37_A     1.243     0    0.027   0.313     2.329   75.119   72.993
LGA    S    38_A      S    38_A     1.954     0    0.564   0.801     3.873   63.690   61.825
LGA    G    39_A      G    39_A     3.067     0    0.126   0.126     3.145   55.476   55.476
LGA    T    40_A      T    40_A     4.086     0    0.440   0.363     4.673   40.238   37.279
LGA    Y    41_A      Y    41_A     5.101     0    0.499   0.852    16.526   45.119   16.389
LGA    G    42_A      G    42_A     4.232     0    0.637   0.637     7.154   28.929   28.929
LGA    N    43_A      N    43_A     2.656     0    0.531   1.268     5.251   55.357   50.119
LGA    K    44_A      K    44_A     2.640     0    0.046   0.487     3.708   55.357   54.815
LGA    D    45_A      D    45_A     3.024     0    0.227   1.288     8.343   59.167   39.107
LGA    E    46_A      E    46_A     2.129     0    0.039   0.779     2.885   70.952   71.323
LGA    C    47_A      C    47_A     0.535     0    0.047   0.634     2.447   77.381   75.952
LGA    P    48_A      P    48_A     3.086     0    0.074   0.133     3.971   55.833   53.537
LGA    C    49_A      C    49_A     1.950     0    0.049   0.179     2.179   70.833   72.937
LGA    Y    50_A      Y    50_A     1.824     0    0.078   1.204     9.075   70.833   44.167
LGA    R    51_A      R    51_A     1.705     0    0.099   1.127     8.704   77.143   45.931
LGA    D    52_A      D    52_A     1.379     0    0.203   0.714     2.073   77.262   81.607
LGA    L    53_A      L    53_A     1.104     0    0.099   0.943     4.346   81.548   73.869
LGA    K    54_A      K    54_A     1.421     0    0.027   0.942     4.420   77.143   64.180
LGA    N    55_A      N    55_A     2.590     0    0.067   0.275     3.378   59.048   57.202
LGA    S    56_A      S    56_A     3.585     0    0.161   0.487     5.799   43.452   38.730
LGA    K    57_A      K    57_A     3.119     0    0.038   0.766     5.591   53.571   41.164
LGA    G    58_A      G    58_A     1.916     0    0.044   0.044     2.218   75.119   75.119
LGA    N    59_A      N    59_A     0.334     0    0.031   0.249     1.537   92.857   90.655
LGA    P    60_A      P    60_A     1.528     0    0.143   0.151     2.151   72.976   70.612
LGA    K    61_A      K    61_A     3.245     0    0.034   1.440     4.412   48.810   50.317
LGA    C    62_A      C    62_A     4.407     0    0.450   0.575     6.031   30.952   36.190
LGA    P    63_A      P    63_A     6.427     0    0.496   0.481     7.767   27.024   20.952

# 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):     2.505          2.502                  3.469           68.350   61.528

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     59    2.10    73.810    75.734     2.683

LGA_LOCAL      RMSD:   2.099  Number of atoms:   59  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.525  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   2.505  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.988079 * X  +  -0.010758 * Y  +   0.153572 * Z  +   7.170771
  Y_new =   0.125141 * X  +   0.524886 * Y  +   0.841923 * Z  +  -2.623083
  Z_new =  -0.089665 * X  +   0.851105 * Y  +  -0.517282 * Z  +  -6.373098 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  3.015613  0.089786  2.116915   [DEG:  172.7819    5.1443  121.2903 ]
ZXZ:  2.961170  2.114469 -0.104964   [DEG:  169.6625  121.1501   -6.0140 ]
 
# END of job
