
#######################################################
#                                                     #
#                        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        3.20     3.20
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49       3_A - 51_A        1.99     3.57
  LCS_AVERAGE:     69.31

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       5_A - 37_A        1.00     4.19
  LCS_AVERAGE:     39.05

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    4   63      3    3    4    4    4    4    4   10   11   13   15   16   17   26   43   50   54   58   62   63 
LCS_GDT     S     2_A     S     2_A      3   46   63      3    3    4    8   20   28   42   48   54   56   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     S     3_A     S     3_A     12   49   63      4   11   28   37   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     F     4_A     F     4_A     12   49   63      4   11   28   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     C     5_A     C     5_A     33   49   63      5   26   34   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     D     6_A     D     6_A     33   49   63      7   26   34   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     S     7_A     S     7_A     33   49   63     11   26   34   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     K     8_A     K     8_A     33   49   63     12   26   34   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     C     9_A     C     9_A     33   49   63     13   26   34   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     G    10_A     G    10_A     33   49   63     13   26   34   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     V    11_A     V    11_A     33   49   63     13   26   34   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     R    12_A     R    12_A     33   49   63     13   26   34   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     C    13_A     C    13_A     33   49   63     13   26   34   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     S    14_A     S    14_A     33   49   63      4   24   34   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     K    15_A     K    15_A     33   49   63      4   24   34   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     A    16_A     A    16_A     33   49   63      3   23   34   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     G    17_A     G    17_A     33   49   63      3   16   18   34   39   44   48   52   55   57   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     Y    18_A     Y    18_A     33   49   63     13   25   34   38   42   46   50   54   56   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     Q    19_A     Q    19_A     33   49   63      3   26   34   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     E    20_A     E    20_A     33   49   63     13   26   34   38   42   46   51   54   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     R    21_A     R    21_A     33   49   63     13   26   34   38   42   46   51   54   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     C    22_A     C    22_A     33   49   63     13   26   34   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     L    23_A     L    23_A     33   49   63     13   26   34   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     K    24_A     K    24_A     33   49   63     13   26   34   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     Y    25_A     Y    25_A     33   49   63     13   26   34   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     C    26_A     C    26_A     33   49   63     13   26   34   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     G    27_A     G    27_A     33   49   63     13   26   34   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     I    28_A     I    28_A     33   49   63     10   26   34   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     C    29_A     C    29_A     33   49   63     10   26   34   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     C    30_A     C    30_A     33   49   63     13   26   34   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     E    31_A     E    31_A     33   49   63      8   25   34   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     K    32_A     K    32_A     33   49   63      8   25   34   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     C    33_A     C    33_A     33   49   63     10   25   34   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     H    34_A     H    34_A     33   49   63      6   26   34   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     C    35_A     C    35_A     33   49   63      8   26   34   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     V    36_A     V    36_A     33   49   63      6   25   34   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     P    37_A     P    37_A     33   49   63      6   17   33   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     S    38_A     S    38_A     25   49   63      4   21   33   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     G    39_A     G    39_A     24   49   63      4   26   34   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     T    40_A     T    40_A     24   49   63      4   26   34   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     Y    41_A     Y    41_A     24   49   63      4   26   34   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     G    42_A     G    42_A     17   49   63      3    8   32   38   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     N    43_A     N    43_A      7   49   63      3    9   29   37   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     K    44_A     K    44_A      7   49   63      6   10   23   37   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     D    45_A     D    45_A      7   49   63      3    6    9   21   33   41   48   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     E    46_A     E    46_A      7   49   63      3    6   14   25   37   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     C    47_A     C    47_A     17   49   63      3    8   16   26   41   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     P    48_A     P    48_A     17   49   63      7   12   16   19   35   41   48   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     C    49_A     C    49_A     17   49   63      6   12   16   25   35   45   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     Y    50_A     Y    50_A     17   49   63      6   12   21   36   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     R    51_A     R    51_A     17   49   63      6   12   23   37   42   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     D    52_A     D    52_A     17   29   63      7   12   16   32   40   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     L    53_A     L    53_A     17   29   63      5   12   16   28   40   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     K    54_A     K    54_A     17   29   63      7   12   16   26   37   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     N    55_A     N    55_A     17   25   63      7   12   16   25   32   41   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     S    56_A     S    56_A     17   25   63      7   12   16   25   32   41   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     K    57_A     K    57_A     17   25   63      7   12   16   25   37   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     G    58_A     G    58_A     17   25   63      5   13   18   30   40   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     N    59_A     N    59_A     17   25   63      7   12   16   34   40   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     P    60_A     P    60_A     17   25   63      5   12   25   34   40   47   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     K    61_A     K    61_A     17   21   63      4    8   16   19   25   38   51   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     C    62_A     C    62_A     17   21   63      7   12   16   19   24   30   44   56   58   59   60   61   62   62   62   62   62   62   62   63 
LCS_GDT     P    63_A     P    63_A     17   21   63      3    8   16   19   20   25   33   41   44   55   58   61   62   62   62   62   62   62   62   63 
LCS_AVERAGE  LCS_A:  69.45  (  39.05   69.31  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     13     26     34     38     42     47     51     56     58     59     60     61     62     62     62     62     62     62     62     63 
GDT PERCENT_AT  20.63  41.27  53.97  60.32  66.67  74.60  80.95  88.89  92.06  93.65  95.24  96.83  98.41  98.41  98.41  98.41  98.41  98.41  98.41 100.00
GDT RMS_LOCAL    0.31   0.66   0.89   1.09   1.42   1.87   2.04   2.44   2.51   2.55   2.64   2.73   2.83   2.83   2.83   2.83   2.83   2.83   2.83   3.20
GDT RMS_ALL_AT   4.62   4.18   4.19   3.94   3.62   3.29   3.29   3.27   3.26   3.25   3.25   3.25   3.22   3.22   3.22   3.22   3.22   3.22   3.22   3.20

# Checking swapping
#   possible swapping detected:  Y    18_A      Y    18_A
#   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    12.592     0    0.064   0.064    13.756    0.833    0.833
LGA    S     2_A      S     2_A     6.388     0    0.209   0.299     9.803   19.643   14.365
LGA    S     3_A      S     3_A     1.270     0    0.676   0.869     4.709   77.262   65.079
LGA    F     4_A      F     4_A     2.018     0    0.044   0.271     4.447   70.952   53.550
LGA    C     5_A      C     5_A     0.668     0    0.092   0.766     2.374   88.214   86.270
LGA    D     6_A      D     6_A     1.068     0    0.084   1.029     5.106   83.690   67.798
LGA    S     7_A      S     7_A     1.684     0    0.088   0.680     2.327   72.976   72.937
LGA    K     8_A      K     8_A     1.535     0    0.105   0.736     7.163   79.286   58.624
LGA    C     9_A      C     9_A     0.846     0    0.069   0.076     1.485   83.690   87.540
LGA    G    10_A      G    10_A     1.570     0    0.074   0.074     1.781   75.000   75.000
LGA    V    11_A      V    11_A     1.545     0    0.023   1.347     3.703   77.143   68.844
LGA    R    12_A      R    12_A     0.556     0    0.042   1.336     8.086   95.238   64.545
LGA    C    13_A      C    13_A     1.407     0    0.616   0.701     4.026   68.452   72.778
LGA    S    14_A      S    14_A     1.411     0    0.071   0.595     2.941   75.119   73.175
LGA    K    15_A      K    15_A     2.648     0    0.082   0.676     3.567   57.262   55.714
LGA    A    16_A      A    16_A     3.106     0    0.647   0.590     3.457   55.476   55.810
LGA    G    17_A      G    17_A     6.468     0    0.040   0.040     6.468   18.214   18.214
LGA    Y    18_A      Y    18_A     4.967     0    0.380   1.398     7.182   32.976   27.659
LGA    Q    19_A      Q    19_A     2.604     0    0.037   1.063     3.486   57.262   61.640
LGA    E    20_A      E    20_A     4.123     0    0.020   0.752     7.888   38.690   25.556
LGA    R    21_A      R    21_A     4.145     0    0.049   1.172    12.600   41.905   19.784
LGA    C    22_A      C    22_A     2.560     0    0.099   0.116     3.130   59.167   62.381
LGA    L    23_A      L    23_A     2.114     0    0.019   1.168     3.510   66.786   62.143
LGA    K    24_A      K    24_A     2.912     0    0.053   1.223    11.744   57.143   33.439
LGA    Y    25_A      Y    25_A     2.958     0    0.130   0.468     4.680   57.143   45.952
LGA    C    26_A      C    26_A     1.545     0    0.019   0.120     1.929   77.143   80.079
LGA    G    27_A      G    27_A     1.287     0    0.021   0.021     1.371   81.429   81.429
LGA    I    28_A      I    28_A     1.775     0    0.025   0.748     3.904   70.833   63.274
LGA    C    29_A      C    29_A     2.608     0    0.068   0.075     3.571   60.952   57.381
LGA    C    30_A      C    30_A     1.896     0    0.106   0.120     2.107   66.786   70.238
LGA    E    31_A      E    31_A     2.482     0    0.025   0.874     5.897   59.167   51.323
LGA    K    32_A      K    32_A     3.120     0    0.032   1.285     4.899   51.786   46.720
LGA    C    33_A      C    33_A     2.960     0    0.140   0.189     3.204   53.571   56.032
LGA    H    34_A      H    34_A     2.999     0    0.091   1.249     3.495   57.143   63.667
LGA    C    35_A      C    35_A     1.949     0    0.018   0.131     2.283   75.119   75.794
LGA    V    36_A      V    36_A     0.724     0    0.021   0.629     3.154   85.952   82.109
LGA    P    37_A      P    37_A     0.777     0    0.014   0.275     1.078   92.857   91.905
LGA    S    38_A      S    38_A     1.102     0    0.225   0.501     2.536   73.214   74.524
LGA    G    39_A      G    39_A     1.871     0    0.091   0.091     1.871   75.000   75.000
LGA    T    40_A      T    40_A     1.531     0    0.441   0.355     2.433   72.976   75.374
LGA    Y    41_A      Y    41_A     1.609     0    0.157   1.241    12.401   72.976   36.032
LGA    G    42_A      G    42_A     1.250     0    0.674   0.674     3.990   72.024   72.024
LGA    N    43_A      N    43_A     1.708     0    0.142   1.006     5.669   77.143   60.417
LGA    K    44_A      K    44_A     1.541     0    0.025   0.690     4.791   65.357   62.222
LGA    D    45_A      D    45_A     4.236     0    0.253   1.260     9.145   43.452   27.500
LGA    E    46_A      E    46_A     2.912     0    0.198   0.175     3.811   57.262   54.921
LGA    C    47_A      C    47_A     2.544     0    0.028   0.612     4.017   53.571   52.698
LGA    P    48_A      P    48_A     4.407     0    0.195   0.396     5.693   41.786   37.619
LGA    C    49_A      C    49_A     3.440     0    0.095   0.176     3.854   53.810   50.317
LGA    Y    50_A      Y    50_A     2.131     0    0.120   0.735     3.401   64.881   63.056
LGA    R    51_A      R    51_A     2.313     0    0.027   1.262     9.014   64.762   40.476
LGA    D    52_A      D    52_A     2.552     0    0.148   0.759     2.746   59.048   62.976
LGA    L    53_A      L    53_A     2.235     0    0.033   0.867     3.587   64.762   61.131
LGA    K    54_A      K    54_A     2.397     0    0.026   0.908     4.739   55.714   50.688
LGA    N    55_A      N    55_A     4.082     0    0.058   0.214     5.100   43.452   39.702
LGA    S    56_A      S    56_A     4.164     0    0.143   0.499     5.908   40.238   36.587
LGA    K    57_A      K    57_A     2.964     0    0.051   1.001     4.320   61.190   54.444
LGA    G    58_A      G    58_A     1.617     0    0.060   0.060     2.235   72.976   72.976
LGA    N    59_A      N    59_A     2.648     0    0.045   0.265     4.067   59.048   50.417
LGA    P    60_A      P    60_A     2.488     0    0.131   0.333     3.711   55.476   53.197
LGA    K    61_A      K    61_A     3.918     0    0.033   1.286     4.912   40.476   40.794
LGA    C    62_A      C    62_A     4.582     0    0.032   0.371     4.852   32.857   35.317
LGA    P    63_A      P    63_A     6.245     0    0.467   0.599     7.288   19.286   16.327

# 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):     3.204          3.120                  3.829           60.873   55.656

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     56    2.44    72.222    74.896     2.206

LGA_LOCAL      RMSD:   2.438  Number of atoms:   56  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   3.266  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   3.204  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.065201 * X  +   0.908399 * Y  +  -0.412988 * Z  +  -6.904751
  Y_new =  -0.949881 * X  +   0.070305 * Y  +   0.304604 * Z  +   1.330879
  Z_new =   0.305737 * X  +   0.412150 * Y  +   0.858287 * Z  +  -7.327401 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.639330 -0.310713  0.447683   [DEG:  -93.9267  -17.8025   25.6504 ]
ZXZ: -2.206289  0.538874  0.638239   [DEG: -126.4110   30.8752   36.5684 ]
 
# END of job
