
#######################################################
#                                                     #
#                        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     2.14
  LCS_AVERAGE:     88.21

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    32       5_A - 36_A        0.94     3.69
  LCS_AVERAGE:     36.71

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     11   56   63      3    5   28   43   53   58   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   16   29   44   53   58   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   13   27   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     F     4_A     F     4_A     31   56   63      3   13   29   44   53   58   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      5   20   32   44   53   58   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   24   32   44   53   58   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   24   32   44   53   58   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     14   24   32   44   53   58   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      8   24   32   44   53   58   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   24   32   44   53   58   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     14   24   32   44   53   58   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     14   24   32   44   53   58   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   24   32   44   53   58   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      7   15   32   44   53   58   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   12   32   44   53   58   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   18   32   44   53   58   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      7   24   32   44   53   58   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   24   32   44   53   58   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   12   31   44   53   58   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      7   24   32   44   53   58   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     14   24   32   44   53   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     14   24   32   44   53   58   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     14   24   32   44   53   58   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     14   24   32   44   53   58   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     14   24   32   44   53   58   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     14   24   32   44   53   58   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     14   24   32   44   53   58   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     14   24   32   44   53   58   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     14   24   32   44   53   58   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     14   24   32   44   53   58   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     11   24   32   44   53   58   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     12   24   32   44   53   58   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     14   24   32   44   53   58   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     11   21   32   44   53   58   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     11   21   32   44   53   58   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      9   21   32   44   53   58   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   29   44   53   58   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     11   21   28   44   53   58   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      9   20   32   44   53   58   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   19   29   41   51   58   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   19   23   35   49   58   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   17   32   51   58   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      5   19   28   43   53   58   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   15   28   43   53   58   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   21   33   51   58   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   14   27   39   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     12   56   63      5   16   28   44   53   58   60   63   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   20   33   53   58   60   63   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   28   43   53   58   60   63   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   21   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    51_A     R    51_A     12   56   63      4    7   28   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    52_A     D    52_A     12   56   63      5   19   28   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     12   56   63      5   16   28   43   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     12   56   63      4   13   25   39   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     12   56   63      4   10   22   32   49   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     12   56   63      4   10   20   32   39   48   58   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     12   55   63      4   10   21   32   41   51   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     12   55   63      4   10   22   33   49   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    59_A     N    59_A     11   55   63      5   15   27   43   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    60_A     P    60_A     11   55   63     11   21   29   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     11   55   63      4   10   24   44   53   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     11   51   63      6   24   32   39   49   55   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     11   39   63      3   12   26   39   45   53   59   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  74.97  (  36.71   88.21  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     14     24     32     44     53     58     60     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  22.22  38.10  50.79  69.84  84.13  92.06  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    0.33   0.61   0.94   1.42   1.66   1.87   1.92   2.13   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   3.88   3.95   3.56   2.58   2.23   2.14   2.15   2.13   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:  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    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     2.103     0    0.160   0.160     2.694   71.190   71.190
LGA    S     2_A      S     2_A     2.410     0    0.171   0.230     3.360   68.810   62.540
LGA    S     3_A      S     3_A     2.473     0    0.133   0.315     4.367   64.762   58.889
LGA    F     4_A      F     4_A     1.858     0    0.071   0.256     3.609   70.833   60.952
LGA    C     5_A      C     5_A     2.169     0    0.087   0.792     3.039   66.786   63.651
LGA    D     6_A      D     6_A     2.185     0    0.099   0.469     3.775   64.762   58.333
LGA    S     7_A      S     7_A     2.652     0    0.084   0.651     3.859   60.952   57.381
LGA    K     8_A      K     8_A     1.748     0    0.101   0.847     5.053   72.857   66.085
LGA    C     9_A      C     9_A     1.721     0    0.053   0.206     1.820   72.857   72.857
LGA    G    10_A      G    10_A     1.646     0    0.087   0.087     1.676   75.000   75.000
LGA    V    11_A      V    11_A     2.222     0    0.021   0.987     2.990   64.762   64.830
LGA    R    12_A      R    12_A     1.989     0    0.026   1.169     6.819   70.833   53.377
LGA    C    13_A      C    13_A     1.172     0    0.537   0.725     2.258   79.524   78.730
LGA    S    14_A      S    14_A     1.570     0    0.051   0.612     2.145   77.143   74.365
LGA    K    15_A      K    15_A     1.560     0    0.209   0.965     6.163   77.143   60.317
LGA    A    16_A      A    16_A     1.508     0    0.114   0.107     2.080   75.119   76.381
LGA    G    17_A      G    17_A     1.624     0    0.091   0.091     2.392   73.214   73.214
LGA    Y    18_A      Y    18_A     2.483     0    0.304   1.236     6.570   64.881   48.651
LGA    Q    19_A      Q    19_A     1.519     0    0.112   1.529     4.015   79.286   67.354
LGA    E    20_A      E    20_A     2.298     0    0.051   1.120     3.874   64.881   57.460
LGA    R    21_A      R    21_A     2.841     0    0.080   1.478    13.800   60.952   29.784
LGA    C    22_A      C    22_A     1.811     0    0.127   0.634     2.856   68.810   67.540
LGA    L    23_A      L    23_A     1.503     0    0.020   0.242     1.905   75.000   76.071
LGA    K    24_A      K    24_A     2.253     0    0.034   1.393    11.416   66.786   41.164
LGA    Y    25_A      Y    25_A     2.394     0    0.103   0.429     3.607   62.857   57.976
LGA    C    26_A      C    26_A     1.286     0    0.066   0.654     2.403   79.286   77.222
LGA    G    27_A      G    27_A     1.112     0    0.028   0.028     1.427   81.429   81.429
LGA    I    28_A      I    28_A     1.766     0    0.019   1.305     6.628   75.000   59.048
LGA    C    29_A      C    29_A     1.472     0    0.104   0.634     4.083   81.548   72.698
LGA    C    30_A      C    30_A     0.896     0    0.109   0.120     1.186   88.214   92.143
LGA    E    31_A      E    31_A     0.988     0    0.028   0.633     2.018   85.952   81.640
LGA    K    32_A      K    32_A     1.253     0    0.059   1.241     6.379   81.429   66.720
LGA    C    33_A      C    33_A     1.304     0    0.124   0.244     2.004   75.119   77.222
LGA    H    34_A      H    34_A     1.574     0    0.093   1.021     3.474   75.000   68.238
LGA    C    35_A      C    35_A     1.399     0    0.026   0.205     1.900   81.429   78.571
LGA    V    36_A      V    36_A     1.292     0    0.063   0.248     2.227   81.429   76.599
LGA    P    37_A      P    37_A     0.895     0    0.036   0.349     1.055   88.214   90.544
LGA    S    38_A      S    38_A     1.250     0    0.271   0.681     4.869   81.548   70.397
LGA    G    39_A      G    39_A     1.718     0    0.040   0.040     2.541   66.905   66.905
LGA    T    40_A      T    40_A     3.062     0    0.493   0.391     4.082   50.476   53.401
LGA    Y    41_A      Y    41_A     3.207     0    0.183   1.426    11.686   55.476   29.048
LGA    G    42_A      G    42_A     2.618     0    0.653   0.653     4.544   50.714   50.714
LGA    N    43_A      N    43_A     1.344     0    0.191   0.926     4.699   81.429   64.167
LGA    K    44_A      K    44_A     1.371     0    0.021   0.915     6.570   77.143   57.566
LGA    D    45_A      D    45_A     2.521     0    0.139   0.956     4.222   62.857   59.643
LGA    E    46_A      E    46_A     2.062     0    0.050   0.274     3.283   68.810   64.074
LGA    C    47_A      C    47_A     1.268     0    0.056   0.595     2.467   72.976   73.016
LGA    P    48_A      P    48_A     2.251     0    0.191   0.434     2.638   70.833   70.680
LGA    C    49_A      C    49_A     1.766     0    0.049   0.753     2.290   77.143   75.794
LGA    Y    50_A      Y    50_A     1.785     0    0.120   0.770     5.425   72.857   54.087
LGA    R    51_A      R    51_A     1.131     0    0.031   1.562     6.653   83.690   65.498
LGA    D    52_A      D    52_A     0.103     0    0.044   0.822     3.213  100.000   88.036
LGA    L    53_A      L    53_A     1.005     0    0.102   1.360     5.042   83.690   68.571
LGA    K    54_A      K    54_A     1.712     0    0.037   1.034     4.103   70.952   68.148
LGA    N    55_A      N    55_A     3.057     0    0.054   0.262     3.578   48.452   50.119
LGA    S    56_A      S    56_A     4.665     0    0.023   0.494     6.340   32.857   29.127
LGA    K    57_A      K    57_A     4.366     0    0.203   1.117     7.336   35.714   27.884
LGA    G    58_A      G    58_A     3.021     0    0.038   0.038     3.364   57.381   57.381
LGA    N    59_A      N    59_A     1.050     0    0.035   0.296     2.386   88.571   82.976
LGA    P    60_A      P    60_A     1.560     0    0.092   0.108     2.311   75.000   71.769
LGA    K    61_A      K    61_A     2.566     0    0.053   0.846     4.092   55.833   54.339
LGA    C    62_A      C    62_A     3.574     0    0.128   0.556     4.418   43.452   42.381
LGA    P    63_A      P    63_A     4.013     0    0.442   0.596     4.252   38.690   44.626

# 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):     2.128          2.128                  3.158           70.278   64.072

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    2.13    76.984    84.577     2.828

LGA_LOCAL      RMSD:   2.128  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.128  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   2.128  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.841861 * X  +  -0.449668 * Y  +  -0.298444 * Z  +   2.301971
  Y_new =  -0.207453 * X  +  -0.240878 * Y  +   0.948125 * Z  +  -1.762221
  Z_new =  -0.498230 * X  +   0.860103 * Y  +   0.109501 * Z  +  -0.430269 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.899984  0.521556  1.444166   [DEG: -166.1569   29.8830   82.7446 ]
ZXZ: -2.836639  1.461075 -0.525036   [DEG: -162.5274   83.7134  -30.0823 ]
 
# END of job
