
#######################################################
#                                                     #
#                        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  102 (  819),  selected   60 , name one
# Molecule2: number of CA atoms   76 (  627),  selected   60 , 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:    37      40_A - 76_A        4.85    20.63
  LCS_AVERAGE:     41.03

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    21      44_A - 64_A        1.97    20.80
  LONGEST_CONTINUOUS_SEGMENT:    21      45_A - 65_A        1.97    20.72
  LONGEST_CONTINUOUS_SEGMENT:    21      46_A - 66_A        1.92    20.60
  LCS_AVERAGE:     17.50

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13      47_A - 59_A        0.94    19.52
  LCS_AVERAGE:     10.42

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   60
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     A    17_A     A    17_A      8    9   15      4    8    9    9   10   10   10   11   12   13   13   14   14   16   18   18   18   20   20   21 
LCS_GDT     N    18_A     N    18_A      8    9   15      4    8    9    9   10   10   10   11   12   13   13   14   14   16   18   18   18   21   21   23 
LCS_GDT     Q    19_A     Q    19_A      8    9   15      4    8    9    9   10   10   10   11   12   13   13   14   14   16   18   18   18   21   21   23 
LCS_GDT     F    20_A     F    20_A      8    9   15      4    8    9    9   10   10   10   11   12   13   13   14   14   16   18   18   18   20   20   23 
LCS_GDT     A    21_A     A    21_A      8    9   15      4    8    9    9   10   10   10   11   12   13   13   14   14   16   18   18   18   21   21   23 
LCS_GDT     K    22_A     K    22_A      8    9   15      4    8    9    9   10   10   10   11   12   13   13   14   14   16   18   18   18   22   22   24 
LCS_GDT     I    23_A     I    23_A      8    9   15      4    8    9    9   10   10   10   11   12   13   13   14   14   16   18   21   23   24   25   25 
LCS_GDT     L    24_A     L    24_A      8    9   21      4    8    9    9   10   10   10   11   12   13   13   14   15   17   21   22   24   24   25   25 
LCS_GDT     I    25_A     I    25_A      5    9   23      0    3    3    6   10   10   10   11   12   13   13   15   19   20   22   23   24   24   25   25 
LCS_GDT     N    26_A     N    26_A      3    4   23      3    3    3    4    4    5    7    8    8   13   13   14   19   20   22   23   24   24   25   25 
LCS_GDT     K    27_A     K    27_A      3    4   23      3    3    3    4    5    9   11   12   13   15   18   20   21   21   22   23   24   24   25   25 
LCS_GDT     D    28_A     D    28_A      3    5   23      3    3    3    4    7    9   11   12   12   15   18   20   21   21   22   23   24   24   25   25 
LCS_GDT     G    29_A     G    29_A      4    5   23      4    7    9    9   10   10   10   11   15   17   19   20   21   21   22   23   24   25   25   26 
LCS_GDT     S    30_A     S    30_A      4    5   24      4    4    4    5    7    9   11   12   15   17   19   20   21   21   23   23   24   25   27   27 
LCS_GDT     N    31_A     N    31_A      4    5   24      4    4    4    5    7    9   11   12   15   17   19   20   21   22   23   23   24   26   27   27 
LCS_GDT     V    32_A     V    32_A      4    8   24      4    4    4    5    7    9   11   14   15   17   19   20   21   22   23   23   24   26   27   27 
LCS_GDT     D    33_A     D    33_A      8    8   24      3    7    8    8   10   12   13   14   15   17   19   20   21   22   23   23   24   26   27   27 
LCS_GDT     R    34_A     R    34_A      8    8   24      5    7    8    8   10   12   13   15   15   17   19   20   21   22   23   23   24   26   27   28 
LCS_GDT     K    35_A     K    35_A      8    8   24      5    7    8    8   10   12   13   15   15   17   19   20   21   22   23   23   24   26   27   28 
LCS_GDT     T    36_A     T    36_A      8    8   24      5    7    8    8   10   12   13   15   15   17   19   20   21   22   23   23   24   26   27   28 
LCS_GDT     I    37_A     I    37_A      8    8   24      5    7    8    8   10   12   13   15   15   17   19   20   23   24   26   28   31   34   35   36 
LCS_GDT     Q    38_A     Q    38_A      8    8   33      5    7    8    8   10   12   13   15   15   17   19   20   23   24   26   28   31   34   35   36 
LCS_GDT     N    39_A     N    39_A      8    8   36      4    7    8    8   10   12   13   15   15   17   19   20   21   22   25   28   31   33   35   36 
LCS_GDT     W    40_A     W    40_A      8    8   37      3    5    7    8    9   12   14   17   20   23   26   29   31   32   32   33   33   34   35   36 
LCS_GDT     I    41_A     I    41_A      6    6   37      4    5    5   10   16   20   25   27   28   30   31   31   31   32   32   33   33   34   35   36 
LCS_GDT     N    42_A     N    42_A      6    6   37      4    5    5    6    7    9   11   12   15   17   19   20   21   22   27   31   33   34   35   36 
LCS_GDT     R    43_A     R    43_A      6    6   37      4    5    5    6    6    9   11   12   15   17   19   20   21   26   31   33   33   34   35   36 
LCS_GDT     D    44_A     D    44_A      6   21   37      4    5    5    8   16   24   26   28   29   30   31   31   31   32   32   33   33   34   35   36 
LCS_GDT     Q    45_A     Q    45_A      5   21   37      3    4    5    7   16   24   26   28   29   30   31   31   31   32   32   33   33   34   35   36 
LCS_GDT     D    46_A     D    46_A      5   21   37      3    4    9   17   21   24   26   28   29   30   31   31   31   32   32   33   33   34   35   36 
LCS_GDT     L    47_A     L    47_A     13   21   37      4   11   12   17   19   24   26   28   29   30   31   31   31   32   32   33   33   34   35   36 
LCS_GDT     N    48_A     N    48_A     13   21   37      8   11   13   17   21   24   26   28   29   30   31   31   31   32   32   33   33   34   35   36 
LCS_GDT     D    49_A     D    49_A     13   21   37      5   11   13   17   21   24   26   28   29   30   31   31   31   32   32   33   33   34   35   36 
LCS_GDT     W    50_A     W    50_A     13   21   37      8   11   13   17   21   24   26   28   29   30   31   31   31   32   32   33   33   34   35   36 
LCS_GDT     V    51_A     V    51_A     13   21   37      8   11   13   17   21   24   26   28   29   30   31   31   31   32   32   33   33   34   35   36 
LCS_GDT     I    52_A     I    52_A     13   21   37      8   11   13   17   21   24   26   28   29   30   31   31   31   32   32   33   33   34   35   36 
LCS_GDT     V    53_A     V    53_A     13   21   37      8   11   13   17   21   24   26   28   29   30   31   31   31   32   32   33   33   34   35   36 
LCS_GDT     Q    54_A     Q    54_A     13   21   37      8   11   13   17   21   24   26   28   29   30   31   31   31   32   32   33   33   34   35   36 
LCS_GDT     L    55_A     L    55_A     13   21   37      8   11   13   17   21   24   26   28   29   30   31   31   31   32   32   33   33   34   35   36 
LCS_GDT     K    56_A     K    56_A     13   21   37      8   11   13   17   21   24   26   28   29   30   31   31   31   32   32   33   33   34   35   36 
LCS_GDT     E    57_A     E    57_A     13   21   37      5   11   13   17   21   24   26   28   29   30   31   31   31   32   32   33   33   34   35   36 
LCS_GDT     E    58_A     E    58_A     13   21   37      4    6   13   17   21   24   26   28   29   30   31   31   31   32   32   33   33   34   35   36 
LCS_GDT     L    59_A     L    59_A     13   21   37      4    8   13   17   21   24   26   28   29   30   31   31   31   32   32   33   33   34   35   36 
LCS_GDT     L    60_A     L    60_A      9   21   37      3    8   11   17   21   24   26   28   29   30   31   31   31   32   32   33   33   34   35   36 
LCS_GDT     K    61_A     K    61_A      9   21   37      3    8   10   17   21   24   26   28   29   30   31   31   31   32   32   33   33   34   35   36 
LCS_GDT     R    62_A     R    62_A      9   21   37      4    8   12   16   21   24   26   28   29   30   31   31   31   32   32   33   33   34   35   36 
LCS_GDT     E    63_A     E    63_A      9   21   37      4    8   12   17   21   24   26   28   29   30   31   31   31   32   32   33   33   34   35   36 
LCS_GDT     V    64_A     V    64_A      9   21   37      4    8   10   17   21   24   26   28   29   30   31   31   31   32   32   33   33   34   35   36 
LCS_GDT     I    65_A     I    65_A      9   21   37      4    8   12   13   21   24   26   28   29   30   31   31   31   32   32   33   33   34   35   36 
LCS_GDT     L    66_A     L    66_A      9   21   37      3    8   12   15   21   24   26   28   29   30   31   31   31   32   32   33   33   34   35   36 
LCS_GDT     K    67_A     K    67_A      9   20   37      3    7   10   17   20   24   26   28   29   30   31   31   31   32   32   33   33   34   35   36 
LCS_GDT     N    68_A     N    68_A      8   14   37      3    5    9   12   16   22   25   28   29   30   31   31   31   32   32   33   33   34   35   36 
LCS_GDT     L    69_A     L    69_A      5   14   37      4    5    5    7   16   18   23   25   28   30   31   31   31   32   32   33   33   34   35   36 
LCS_GDT     L    70_A     L    70_A      5   14   37      4    8   13   17   21   24   26   28   29   30   31   31   31   32   32   33   33   34   35   36 
LCS_GDT     T    71_A     T    71_A      5   14   37      4    5    5    6   12   18   22   27   29   30   31   31   31   32   32   33   33   34   35   36 
LCS_GDT     N    72_A     N    72_A      5   14   37      7   11   12   17   19   23   26   28   29   30   31   31   31   32   32   33   33   34   35   36 
LCS_GDT     L    73_A     L    73_A      5    7   37      4    5    5    6   13   17   26   28   29   30   31   31   31   32   32   33   33   34   35   36 
LCS_GDT     S    74_A     S    74_A      3    7   37      3    3    4    6    6    7    8   14   19   25   28   30   31   31   32   33   33   34   35   35 
LCS_GDT     Q    75_A     Q    75_A      3    7   37      3    3    3    4    5    7    7    7    8   10   17   20   20   23   26   29   32   34   34   35 
LCS_GDT     A    76_A     A    76_A      3    5   37      0    2    3    4    4    4    5    5    6    8    9   18   18   21   25   32   33   34   34   35 
LCS_AVERAGE  LCS_A:  22.98  (  10.42   17.50   41.03 )

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      8     11     13     17     21     24     26     28     29     30     31     31     31     32     32     33     33     34     35     36 
GDT PERCENT_AT  10.53  14.47  17.11  22.37  27.63  31.58  34.21  36.84  38.16  39.47  40.79  40.79  40.79  42.11  42.11  43.42  43.42  44.74  46.05  47.37
GDT RMS_LOCAL    0.24   0.44   1.07   1.37   1.89   2.06   2.21   2.40   2.53   2.66   2.80   2.80   2.80   3.21   3.21   3.57   3.57   3.90   4.20   5.22
GDT RMS_ALL_AT  18.59  18.68  19.75  20.09  20.82  20.77  20.78  20.83  20.87  20.72  20.65  20.65  20.65  20.35  20.82  20.20  20.20  20.37  20.31  19.25

# Checking swapping
#   possible swapping detected:  F    20_A      F    20_A
#   possible swapping detected:  D    28_A      D    28_A
#   possible swapping detected:  D    33_A      D    33_A
#   possible swapping detected:  D    44_A      D    44_A
#   possible swapping detected:  E    58_A      E    58_A
#   possible swapping detected:  E    63_A      E    63_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    17_A      A    17_A    44.336     0    0.036   0.020    46.015    0.000    0.000
LGA    N    18_A      N    18_A    45.937     0    0.160   0.831    51.382    0.000    0.000
LGA    Q    19_A      Q    19_A    42.138     0    0.000   0.792    43.638    0.000    0.000
LGA    F    20_A      F    20_A    39.307     0    0.043   1.205    40.541    0.000    0.000
LGA    A    21_A      A    21_A    40.933     0    0.038   0.044    42.641    0.000    0.000
LGA    K    22_A      K    22_A    40.598     0    0.096   0.829    45.238    0.000    0.000
LGA    I    23_A      I    23_A    36.816     0    0.196   1.362    38.263    0.000    0.000
LGA    L    24_A      L    24_A    34.718     0    0.618   0.510    35.815    0.000    0.000
LGA    I    25_A      I    25_A    36.058     0    0.680   0.756    38.053    0.000    0.000
LGA    N    26_A      N    26_A    36.851     0    0.656   0.581    42.109    0.000    0.000
LGA    K    27_A      K    27_A    35.125     0    0.332   0.835    36.029    0.000    0.000
LGA    D    28_A      D    28_A    37.416     0    0.487   1.200    39.693    0.000    0.000
LGA    G    29_A      G    29_A    32.239     0    0.680   0.680    33.650    0.000    0.000
LGA    S    30_A      S    30_A    32.322     0    0.084   0.262    33.090    0.000    0.000
LGA    N    31_A      N    31_A    28.088     0    0.559   1.255    32.055    0.000    0.000
LGA    V    32_A      V    32_A    23.972     0    0.665   0.969    25.231    0.000    0.000
LGA    D    33_A      D    33_A    25.890     0    0.583   1.119    30.591    0.000    0.000
LGA    R    34_A      R    34_A    24.704     0    0.085   0.954    27.919    0.000    0.000
LGA    K    35_A      K    35_A    24.323     0    0.102   1.281    30.251    0.000    0.000
LGA    T    36_A      T    36_A    19.440     0    0.143   0.231    21.456    0.000    0.000
LGA    I    37_A      I    37_A    16.452     0    0.104   0.216    18.604    0.000    0.000
LGA    Q    38_A      Q    38_A    18.095     0    0.020   1.447    21.806    0.000    0.000
LGA    N    39_A      N    39_A    15.839     0    0.610   0.572    17.526    0.000    0.000
LGA    W    40_A      W    40_A    10.141     0    0.201   1.201    18.004    6.071    1.735
LGA    I    41_A      I    41_A     5.138     0    0.096   1.162     7.131   17.619   28.810
LGA    N    42_A      N    42_A    10.593     0    0.047   0.131    15.283    0.714    0.357
LGA    R    43_A      R    43_A    10.389     0    0.027   0.796    19.869    4.286    1.558
LGA    D    44_A      D    44_A     3.168     0    0.445   1.321     5.658   48.333   44.286
LGA    Q    45_A      Q    45_A     2.906     0    0.680   1.124     5.340   57.262   43.704
LGA    D    46_A      D    46_A     1.799     0    0.089   0.654     3.537   59.524   64.167
LGA    L    47_A      L    47_A     3.167     0    0.288   0.325     6.617   61.071   42.262
LGA    N    48_A      N    48_A     1.475     0    0.140   1.103     4.916   75.119   59.940
LGA    D    49_A      D    49_A     1.024     0    0.025   0.606     4.122   90.595   70.536
LGA    W    50_A      W    50_A     1.893     0    0.061   1.190     3.647   75.000   64.150
LGA    V    51_A      V    51_A     2.098     0    0.083   0.166     3.365   68.810   61.769
LGA    I    52_A      I    52_A     1.159     0    0.000   0.159     2.685   85.952   74.464
LGA    V    53_A      V    53_A     1.335     0    0.046   0.299     3.593   83.690   72.517
LGA    Q    54_A      Q    54_A     2.046     0    0.072   0.848     3.261   70.833   64.127
LGA    L    55_A      L    55_A     1.621     0    0.023   0.158     4.277   79.286   63.274
LGA    K    56_A      K    56_A     1.527     0    0.000   0.704     6.455   77.143   52.169
LGA    E    57_A      E    57_A     1.556     0    0.103   0.725     2.304   72.976   78.730
LGA    E    58_A      E    58_A     1.570     0    0.141   1.104     5.729   71.071   56.296
LGA    L    59_A      L    59_A     1.622     0    0.156   1.056     2.237   77.143   72.976
LGA    L    60_A      L    60_A     1.719     0    0.037   1.411     5.058   79.286   70.417
LGA    K    61_A      K    61_A     1.690     0    0.096   1.111     8.338   72.976   50.476
LGA    R    62_A      R    62_A     2.291     0    0.072   1.269     7.210   68.929   39.567
LGA    E    63_A      E    63_A     2.817     0    0.106   1.159     9.957   62.857   34.868
LGA    V    64_A      V    64_A     2.316     0    0.077   0.918     3.925   68.810   59.796
LGA    I    65_A      I    65_A     2.673     0    0.051   0.132     5.118   62.976   47.381
LGA    L    66_A      L    66_A     3.147     0    0.091   0.649     7.709   59.167   38.690
LGA    K    67_A      K    67_A     3.526     0    0.175   0.764    13.353   52.143   26.720
LGA    N    68_A      N    68_A     4.132     0    0.604   1.154     9.886   46.905   29.702
LGA    L    69_A      L    69_A     5.982     0    0.438   1.349    11.877   33.571   18.095
LGA    L    70_A      L    70_A     1.386     0    0.000   1.354     4.010   65.119   61.488
LGA    T    71_A      T    71_A     5.171     0    0.030   0.114     8.563   34.524   22.585
LGA    N    72_A      N    72_A     3.160     0    0.179   0.390     9.581   53.690   32.679
LGA    L    73_A      L    73_A     3.992     0    0.660   0.581     7.640   42.143   28.631
LGA    S    74_A      S    74_A     9.068     0    0.168   0.242    13.419    3.690    2.460
LGA    Q    75_A      Q    75_A    12.203     0    0.390   1.370    18.783    0.000    0.000
LGA    A    76_A      A    76_A    10.538     0    0.582   0.555    12.561    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       60     240    240  100.00     495    495  100.00                76
SUMMARY(RMSD_GDC):    13.863         13.635                 14.814           26.175   20.808

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)  102   76    4.0     28    2.40    29.276    27.834     1.119

LGA_LOCAL      RMSD:   2.402  Number of atoms:   28  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  20.831  Number of assigned atoms:   60 
Std_ASGN_ATOMS RMSD:  13.863  Standard rmsd on all 60 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.020869 * X  +  -0.552255 * Y  +   0.833414 * Z  + -86.637398
  Y_new =  -0.052678 * X  +   0.833045 * Y  +   0.550692 * Z  + -372.087677
  Z_new =  -0.998393 * X  +  -0.032410 * Y  +  -0.046476 * Z  +  98.450813 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.947993  1.514105 -2.532654   [DEG: -111.6118   86.7518 -145.1104 ]
ZXZ:  2.154703  1.617289 -1.603247   [DEG:  123.4554   92.6639  -91.8593 ]
 
# END of job
