
#######################################################
#                                                     #
#                        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        2.03     2.03
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    62       1_A - 62_A        1.95     2.03
  LONGEST_CONTINUOUS_SEGMENT:    62       2_A - 63_A        1.92     2.03
  LCS_AVERAGE:     98.41

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    32       5_A - 36_A        0.94     3.38
  LCS_AVERAGE:     37.97

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   62   63      0    3   13   21   34   44   56   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     2_A     S     2_A     13   62   63      5   19   31   43   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     3_A     S     3_A     13   62   63      5   14   30   43   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     F     4_A     F     4_A     13   62   63      5   12   29   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     32   62   63      5   22   33   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     32   62   63      6   26   33   45   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     7_A     S     7_A     32   62   63      8   26   33   42   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     8_A     K     8_A     32   62   63     11   26   33   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     32   62   63     12   26   33   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    10_A     G    10_A     32   62   63     12   26   33   45   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    11_A     V    11_A     32   62   63     12   26   33   40   51   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     32   62   63     12   26   33   40   53   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     32   62   63     11   26   33   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     32   62   63      6   26   33   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     32   62   63      3   16   31   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     32   62   63      6   26   33   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    17_A     G    17_A     32   62   63      3   20   31   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    18_A     Y    18_A     32   62   63     11   26   33   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Q    19_A     Q    19_A     32   62   63      3   23   33   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    20_A     E    20_A     32   62   63     12   26   33   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     32   62   63     12   26   33   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     32   62   63     12   26   33   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     32   62   63     12   26   33   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     32   62   63     12   26   33   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     32   62   63     12   26   33   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     32   62   63     12   26   33   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     32   62   63     12   26   33   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     32   62   63     11   26   33   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     32   62   63     11   26   33   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     32   62   63     11   26   33   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     32   62   63     11   26   33   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     32   62   63     11   26   33   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     32   62   63     11   26   33   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    34_A     H    34_A     32   62   63     11   26   33   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     32   62   63      9   23   33   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     32   62   63      5   24   33   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     26   62   63     11   20   31   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    38_A     S    38_A     26   62   63      9   20   31   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     26   62   63      7   20   33   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A     25   62   63      4   26   33   40   51   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     14   62   63      3   10   22   36   49   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     11   62   63      3    6   14   23   49   58   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     11   62   63      4    7   31   44   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    44_A     K    44_A     11   62   63      4   15   31   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A      8   62   63      4    7   15   35   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    46_A     E    46_A     15   62   63      4   15   31   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     16   62   63      3   17   31   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     16   62   63      5   14   25   41   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     16   62   63      5   14   29   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     16   62   63      5   11   24   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    51_A     R    51_A     16   62   63      5   12   31   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    52_A     D    52_A     16   62   63      5   17   31   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     16   62   63      5   16   31   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     16   62   63      4   16   31   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     16   62   63      4   16   31   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     16   62   63      5   16   31   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     16   62   63      5   17   31   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     16   62   63      9   17   31   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    59_A     N    59_A     16   62   63      9   18   31   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    60_A     P    60_A     16   62   63     11   20   31   46   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     16   62   63      4   12   30   42   54   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     16   62   63     11   26   33   40   48   59   61   62   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     12   62   63      4    8   24   30   39   47   56   60   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  78.79  (  37.97   98.41  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     26     33     46     54     59     61     62     62     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  19.05  41.27  52.38  73.02  85.71  93.65  96.83  98.41  98.41 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.28   0.67   0.90   1.42   1.60   1.76   1.83   1.95   1.92   2.03   2.03   2.03   2.03   2.03   2.03   2.03   2.03   2.03   2.03   2.03
GDT RMS_ALL_AT   4.32   3.63   3.29   2.08   2.05   2.04   2.04   2.03   2.03   2.03   2.03   2.03   2.03   2.03   2.03   2.03   2.03   2.03   2.03   2.03

# Checking swapping
#   possible swapping detected:  E    20_A      E    20_A
#   possible swapping detected:  Y    25_A      Y    25_A
#   possible swapping detected:  D    45_A      D    45_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     5.492     0    0.123   0.123     7.922   25.714   25.714
LGA    S     2_A      S     2_A     2.272     0    0.522   0.588     3.479   66.786   61.190
LGA    S     3_A      S     3_A     2.162     0    0.129   0.299     4.027   68.810   61.587
LGA    F     4_A      F     4_A     1.537     0    0.079   0.242     3.652   72.857   62.511
LGA    C     5_A      C     5_A     1.742     0    0.121   0.821     2.574   72.857   70.238
LGA    D     6_A      D     6_A     1.887     0    0.079   1.070     5.905   72.857   55.774
LGA    S     7_A      S     7_A     2.477     0    0.098   0.561     4.735   62.857   56.667
LGA    K     8_A      K     8_A     1.864     0    0.129   0.793     6.592   72.857   59.947
LGA    C     9_A      C     9_A     1.657     0    0.040   0.064     1.999   72.857   75.714
LGA    G    10_A      G    10_A     2.000     0    0.057   0.057     2.236   66.786   66.786
LGA    V    11_A      V    11_A     2.815     0    0.053   0.063     3.373   55.357   54.082
LGA    R    12_A      R    12_A     2.608     0    0.111   1.268     7.306   57.262   48.009
LGA    C    13_A      C    13_A     1.167     0    0.638   0.709     2.811   73.214   75.952
LGA    S    14_A      S    14_A     1.335     0    0.082   0.580     1.831   79.286   78.571
LGA    K    15_A      K    15_A     1.629     0    0.151   0.870     4.526   79.286   62.063
LGA    A    16_A      A    16_A     1.334     0    0.690   0.650     4.252   66.190   69.238
LGA    G    17_A      G    17_A     2.404     0    0.598   0.598     2.404   68.929   68.929
LGA    Y    18_A      Y    18_A     2.116     0    0.300   1.286     7.686   66.786   49.841
LGA    Q    19_A      Q    19_A     1.294     0    0.058   0.942     2.397   83.690   75.926
LGA    E    20_A      E    20_A     1.905     0    0.016   0.749     6.452   68.810   49.577
LGA    R    21_A      R    21_A     2.411     0    0.058   1.216     9.386   64.762   38.528
LGA    C    22_A      C    22_A     1.618     0    0.076   0.123     1.883   72.857   74.286
LGA    L    23_A      L    23_A     1.259     0    0.020   0.271     2.050   81.429   79.345
LGA    K    24_A      K    24_A     1.945     0    0.091   0.957     7.117   68.810   53.069
LGA    Y    25_A      Y    25_A     2.256     0    0.123   0.620     4.033   62.857   58.294
LGA    C    26_A      C    26_A     1.343     0    0.029   0.095     1.459   81.429   81.429
LGA    G    27_A      G    27_A     0.951     0    0.053   0.053     1.221   83.690   83.690
LGA    I    28_A      I    28_A     1.334     0    0.015   0.743     4.108   81.429   71.786
LGA    C    29_A      C    29_A     1.085     0    0.127   0.772     4.071   88.333   78.651
LGA    C    30_A      C    30_A     0.872     0    0.132   0.121     1.112   88.214   90.556
LGA    E    31_A      E    31_A     0.887     0    0.025   0.749     3.713   90.476   80.370
LGA    K    32_A      K    32_A     0.751     0    0.033   1.181     5.766   90.476   70.423
LGA    C    33_A      C    33_A     0.709     0    0.203   0.221     1.510   86.071   89.127
LGA    H    34_A      H    34_A     0.942     0    0.142   1.237     3.443   88.214   75.381
LGA    C    35_A      C    35_A     0.949     0    0.074   0.205     1.762   85.952   83.016
LGA    V    36_A      V    36_A     1.198     0    0.058   0.231     2.465   85.952   79.184
LGA    P    37_A      P    37_A     0.435     0    0.023   0.266     0.939   92.857   94.558
LGA    S    38_A      S    38_A     1.249     0    0.298   0.673     4.681   83.810   73.254
LGA    G    39_A      G    39_A     1.609     0    0.072   0.072     2.882   66.905   66.905
LGA    T    40_A      T    40_A     2.809     0    0.501   0.416     4.254   54.286   54.762
LGA    Y    41_A      Y    41_A     3.016     0    0.177   1.170    11.097   61.190   31.548
LGA    G    42_A      G    42_A     3.336     0    0.596   0.596     5.045   44.048   44.048
LGA    N    43_A      N    43_A     2.464     0    0.401   1.121     4.725   54.524   53.333
LGA    K    44_A      K    44_A     1.605     0    0.129   0.901     6.715   75.000   57.513
LGA    D    45_A      D    45_A     2.820     0    0.165   1.194     7.691   62.857   44.345
LGA    E    46_A      E    46_A     1.956     0    0.125   0.138     3.595   77.381   64.656
LGA    C    47_A      C    47_A     1.277     0    0.084   0.702     2.514   72.976   71.746
LGA    P    48_A      P    48_A     2.428     0    0.174   0.393     2.930   68.810   69.524
LGA    C    49_A      C    49_A     1.852     0    0.077   0.181     2.156   72.976   73.016
LGA    Y    50_A      Y    50_A     1.894     0    0.166   0.747     4.781   72.857   57.024
LGA    R    51_A      R    51_A     1.275     0    0.038   1.225     6.019   83.690   62.468
LGA    D    52_A      D    52_A     0.855     0    0.193   0.775     2.479   83.810   81.667
LGA    L    53_A      L    53_A     1.437     0    0.141   0.869     2.821   73.214   70.179
LGA    K    54_A      K    54_A     1.431     0    0.044   0.903     4.484   79.286   66.085
LGA    N    55_A      N    55_A     1.684     0    0.063   0.222     1.764   72.857   73.929
LGA    S    56_A      S    56_A     2.015     0    0.160   0.487     3.573   68.810   63.889
LGA    K    57_A      K    57_A     1.694     0    0.046   0.764     4.152   75.000   61.534
LGA    G    58_A      G    58_A     0.908     0    0.061   0.061     1.108   88.214   88.214
LGA    N    59_A      N    59_A     0.397     0    0.129   0.302     1.758   95.238   93.036
LGA    P    60_A      P    60_A     1.304     0    0.108   0.332     3.159   79.286   72.109
LGA    K    61_A      K    61_A     2.313     0    0.119   0.972     3.167   61.190   65.873
LGA    C    62_A      C    62_A     3.191     0    0.367   1.122     4.966   45.476   45.079
LGA    P    63_A      P    63_A     4.950     0    0.565   0.557     5.901   38.810   33.605

# 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):     2.029          2.084                  2.898           72.387   65.863

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     62    1.95    78.175    87.852     3.026

LGA_LOCAL      RMSD:   1.949  Number of atoms:   62  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.031  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   2.029  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.043847 * X  +  -0.508934 * Y  +   0.859688 * Z  +   7.961977
  Y_new =  -0.709892 * X  +   0.621349 * Y  +   0.331630 * Z  +   3.049649
  Z_new =  -0.702944 * X  +  -0.595745 * Y  +  -0.388533 * Z  +   2.919107 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.632484  0.779528 -2.148702   [DEG:  -93.5345   44.6637 -123.1116 ]
ZXZ:  1.938963  1.969835 -2.273837   [DEG:  111.0944  112.8632 -130.2813 ]
 
# END of job
