
#######################################################
#                                                     #
#                        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 (  542),  selected   63 , name one
# Molecule2: number of CA atoms  124 ( 1059),  selected   63 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:D  -ch2:D  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    57       7_D - 63_D        4.80     7.65
  LCS_AVERAGE:     43.28

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    51       7_D - 57_D        1.98     8.07
  LCS_AVERAGE:     35.19

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    27      30_D - 56_D        0.65     7.99
  LCS_AVERAGE:     14.95

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     K     7_D     K     7_D     19   51   57     20   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   53   55 
LCS_GDT     E     8_D     E     8_D     19   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     I     9_D     I     9_D     19   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     F    10_D     F    10_D     19   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     N    11_D     N    11_D     19   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     M    12_D     M    12_D     19   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     M    13_D     M    13_D     19   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     F    14_D     F    14_D     19   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     M    15_D     M    15_D     19   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     L    16_D     L    16_D     19   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     L    17_D     L    17_D     19   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     W    18_D     W    18_D     19   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     R    19_D     R    19_D     19   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     V    20_D     V    20_D     19   51   57     27   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     F    21_D     F    21_D     19   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     R    22_D     R    22_D     19   51   57     11   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     S    23_D     S    23_D     19   51   57     12   26   42   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     Q    24_D     Q    24_D     19   51   57     21   39   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     R    25_D     R    25_D     19   51   57      3    4    4   19   44   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     I    26_D     I    26_D      3   51   57      3    4    4    4    6    7   35   48   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     D    27_D     D    27_D      5   51   57      3    4    5    8   12   21   35   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     A    28_D     A    28_D      5   51   57      3    4    5    7    9   11   15   19   43   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     N    29_D     N    29_D      5   51   57      3    4    5    7   23   36   46   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     N    30_D     N    30_D     27   51   57     35   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     V    31_D     V    31_D     27   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     E    32_D     E    32_D     27   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     L    33_D     L    33_D     27   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     I    34_D     I    34_D     27   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     K    35_D     K    35_D     27   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     F    36_D     F    36_D     27   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     N    37_D     N    37_D     27   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     I    38_D     I    38_D     27   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     R    39_D     R    39_D     27   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     V    40_D     V    40_D     27   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     L    41_D     L    41_D     27   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     D    42_D     D    42_D     27   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     W    43_D     W    43_D     27   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     I    44_D     I    44_D     27   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     M    45_D     M    45_D     27   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     A    46_D     A    46_D     27   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     E    47_D     E    47_D     27   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     A    48_D     A    48_D     27   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     D    49_D     D    49_D     27   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     N    50_D     N    50_D     27   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     D    51_D     D    51_D     27   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     L    52_D     L    52_D     27   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     C    53_D     C    53_D     27   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     Y    54_D     Y    54_D     27   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     F    55_D     F    55_D     27   51   57     37   42   43   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     I    56_D     I    56_D     27   51   57      6   15   35   45   45   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     G    57_D     G    57_D      3   51   57      3    4   22   25   36   47   47   49   50   51   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     T    58_D     T    58_D      3   30   57      3    3    7    9   11   21   42   46   47   49   51   52   52   52   52   53   53   53   54   55 
LCS_GDT     H    59_D     H    59_D      5   11   57      3    3    6    8   11   13   14   16   22   25   30   32   35   42   52   53   53   53   54   55 
LCS_GDT     D    60_D     D    60_D      5   11   57      4    4    6    7   11   13   14   16   17   21   26   29   32   35   36   37   39   43   48   50 
LCS_GDT     K    61_D     K    61_D      5   11   57      4    4    6    8   11   13   14   16   17   21   23   29   32   35   36   37   39   43   48   49 
LCS_GDT     C    62_D     C    62_D      5   11   57      4    4    6    8   11   13   14   16   17   21   22   22   28   35   36   37   40   48   53   55 
LCS_GDT     E    63_D     E    63_D      5   11   57      4    6    7    9   11   13   14   16   17   21   22   22   25   27   28   30   34   39   44   46 
LCS_GDT     N    64_D     N    64_D      4   11   22      3    3    4    6   11   13   14   16   17   21   22   22   25   27   38   40   47   52   54   55 
LCS_GDT     P    65_D     P    65_D      5   11   22      5    6    7    9   11   13   14   16   17   21   22   22   25   27   33   36   39   43   49   55 
LCS_GDT     K    66_D     K    66_D      5   11   22      5    6    7    9   11   13   14   16   17   21   23   29   32   35   36   50   51   51   54   55 
LCS_GDT     E    67_D     E    67_D      5   11   22      5    6    7    9   11   13   14   16   17   21   22   22   25   28   33   36   38   41   43   49 
LCS_GDT     Q    68_D     Q    68_D      5   11   22      5    6    7    9   11   13   14   16   17   21   22   22   25   27   27   27   32   35   38   42 
LCS_GDT     W    69_D     W    69_D      5    8   22      5    6    7    9   11   13   14   16   17   21   22   22   25   27   31   35   38   40   41   42 
LCS_AVERAGE  LCS_A:  31.14  (  14.95   35.19   43.28 )

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     37     42     43     45     45     47     47     49     50     51     51     52     52     52     52     53     53     53     54     55 
GDT PERCENT_AT  29.84  33.87  34.68  36.29  36.29  37.90  37.90  39.52  40.32  41.13  41.13  41.94  41.94  41.94  41.94  42.74  42.74  42.74  43.55  44.35
GDT RMS_LOCAL    0.29   0.37   0.42   0.69   0.69   1.11   1.11   1.55   1.76   1.98   1.98   2.18   2.18   2.18   2.18   2.73   2.73   2.73   3.91   3.84
GDT RMS_ALL_AT   7.84   7.84   7.85   7.90   7.90   8.04   8.04   8.06   8.05   8.07   8.07   8.06   8.06   8.06   8.06   8.03   8.03   8.03   7.55   7.63

# Checking swapping
#   possible swapping detected:  F    10_D      F    10_D
#   possible swapping detected:  F    14_D      F    14_D
#   possible swapping detected:  D    27_D      D    27_D
#   possible swapping detected:  F    36_D      F    36_D
#   possible swapping detected:  D    51_D      D    51_D
#   possible swapping detected:  F    55_D      F    55_D
#   possible swapping detected:  D    60_D      D    60_D

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    K     7_D      K     7_D     0.989     0    0.087   0.828     2.105   90.476   82.646
LGA    E     8_D      E     8_D     0.643     0    0.110   0.522     1.547   90.476   89.630
LGA    I     9_D      I     9_D     0.481     0    0.029   0.093     0.741   95.238   92.857
LGA    F    10_D      F    10_D     0.665     0    0.018   0.116     0.939   90.476   91.342
LGA    N    11_D      N    11_D     0.773     0    0.033   0.963     2.956   90.476   80.893
LGA    M    12_D      M    12_D     0.550     0    0.028   0.775     2.542   90.476   84.167
LGA    M    13_D      M    13_D     0.566     0    0.024   0.871     2.594   90.476   86.310
LGA    F    14_D      F    14_D     0.501     0    0.030   0.141     0.804   90.476   90.476
LGA    M    15_D      M    15_D     0.652     0    0.029   1.173     3.508   90.476   77.321
LGA    L    16_D      L    16_D     0.486     0    0.058   0.082     0.829   95.238   94.048
LGA    L    17_D      L    17_D     0.492     0    0.040   1.109     2.611   97.619   87.857
LGA    W    18_D      W    18_D     0.388     0    0.022   1.493     5.458   95.238   75.544
LGA    R    19_D      R    19_D     0.912     0    0.028   1.357     4.691   88.214   72.900
LGA    V    20_D      V    20_D     0.885     0    0.023   0.062     1.133   88.214   89.184
LGA    F    21_D      F    21_D     0.530     0    0.080   0.353     1.490   95.238   90.563
LGA    R    22_D      R    22_D     1.539     0    0.118   1.124     6.664   75.238   56.450
LGA    S    23_D      S    23_D     2.284     0    0.398   0.690     3.835   70.833   61.667
LGA    Q    24_D      Q    24_D     1.282     0    0.590   0.817     2.738   81.429   78.730
LGA    R    25_D      R    25_D     3.446     0    0.647   1.403    15.329   44.167   19.048
LGA    I    26_D      I    26_D     6.335     0    0.471   1.076    11.421   20.357   10.714
LGA    D    27_D      D    27_D     5.614     0    0.681   1.366     9.535   27.738   17.024
LGA    A    28_D      A    28_D     6.965     0    0.729   0.666     8.783   15.238   12.762
LGA    N    29_D      N    29_D     5.003     0    0.018   0.890     9.761   35.238   21.012
LGA    N    30_D      N    30_D     0.417     0    0.374   0.461     4.725   86.190   66.786
LGA    V    31_D      V    31_D     0.725     0    0.030   1.301     3.322   90.476   81.020
LGA    E    32_D      E    32_D     0.848     0    0.021   0.805     3.737   88.214   71.534
LGA    L    33_D      L    33_D     0.975     0    0.020   1.055     5.538   90.476   72.440
LGA    I    34_D      I    34_D     0.621     0    0.042   0.101     0.702   90.476   90.476
LGA    K    35_D      K    35_D     0.555     0    0.023   0.581     1.656   90.476   86.508
LGA    F    36_D      F    36_D     0.514     0    0.031   0.160     1.894   95.238   84.935
LGA    N    37_D      N    37_D     0.304     0    0.042   1.113     2.439  100.000   90.000
LGA    I    38_D      I    38_D     0.307     0    0.029   0.211     0.879  100.000   97.619
LGA    R    39_D      R    39_D     0.240     0    0.014   0.918     4.265  100.000   87.749
LGA    V    40_D      V    40_D     0.140     0    0.027   0.034     0.254  100.000  100.000
LGA    L    41_D      L    41_D     0.316     0    0.051   0.256     0.970  100.000   97.619
LGA    D    42_D      D    42_D     0.218     0    0.027   0.131     0.547  100.000   98.810
LGA    W    43_D      W    43_D     0.144     0    0.031   0.374     1.540  100.000   92.041
LGA    I    44_D      I    44_D     0.270     0    0.029   0.067     0.417  100.000  100.000
LGA    M    45_D      M    45_D     0.191     0    0.024   0.156     0.569  100.000   98.810
LGA    A    46_D      A    46_D     0.275     0    0.025   0.030     0.362  100.000  100.000
LGA    E    47_D      E    47_D     0.678     0    0.049   0.272     1.538   92.857   88.571
LGA    A    48_D      A    48_D     0.732     0    0.025   0.026     1.016   88.214   88.667
LGA    D    49_D      D    49_D     0.520     0    0.024   0.198     0.713   90.476   94.048
LGA    N    50_D      N    50_D     0.746     0    0.054   1.228     4.555   90.476   73.869
LGA    D    51_D      D    51_D     0.933     0    0.031   0.091     1.341   90.476   87.083
LGA    L    52_D      L    52_D     0.816     0    0.073   1.253     2.707   90.476   81.964
LGA    C    53_D      C    53_D     0.845     0    0.039   0.688     2.784   90.476   84.921
LGA    Y    54_D      Y    54_D     1.145     0    0.083   0.148     3.309   83.690   69.286
LGA    F    55_D      F    55_D     1.059     0    0.586   0.615     3.706   77.619   64.242
LGA    I    56_D      I    56_D     2.471     0    0.466   0.440     4.781   62.976   51.726
LGA    G    57_D      G    57_D     4.140     0    0.296   0.296     4.140   43.452   43.452
LGA    T    58_D      T    58_D     6.892     0    0.716   0.998     8.914   11.310    9.932
LGA    H    59_D      H    59_D    12.940     0    0.539   1.245    15.554    0.000    0.000
LGA    D    60_D      D    60_D    17.435     0    0.155   1.125    19.768    0.000    0.000
LGA    K    61_D      K    61_D    19.821     0    0.164   1.029    23.526    0.000    0.000
LGA    C    62_D      C    62_D    16.035     0    0.185   0.825    16.980    0.000    0.000
LGA    E    63_D      E    63_D    17.785     0    0.120   1.127    25.744    0.000    0.000
LGA    N    64_D      N    64_D    15.072     0    0.455   0.803    17.525    0.000    0.000
LGA    P    65_D      P    65_D    16.521     0    0.117   0.151    18.311    0.000    0.000
LGA    K    66_D      K    66_D    15.472     0    0.042   0.560    19.617    0.000    0.000
LGA    E    67_D      E    67_D    20.800     0    0.033   1.068    25.334    0.000    0.000
LGA    Q    68_D      Q    68_D    25.218     0    0.082   1.093    28.786    0.000    0.000
LGA    W    69_D      W    69_D    24.251     0    0.599   1.295    27.225    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       63     252    252  100.00     542    542  100.00               124
SUMMARY(RMSD_GDC):     6.926          7.008                  7.462           34.622   31.591

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63  124    4.0     49    1.55    38.105    37.593     2.968

LGA_LOCAL      RMSD:   1.551  Number of atoms:   49  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   8.055  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   6.926  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.081177 * X  +   0.402625 * Y  +  -0.911758 * Z  +  -2.103040
  Y_new =   0.131527 * X  +  -0.902450 * Y  +  -0.410225 * Z  + -60.517639
  Z_new =  -0.987983 * X  +  -0.153221 * Y  +   0.020302 * Z  +  93.939438 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.123757  1.415614 -1.439064   [DEG:  121.6823   81.1087  -82.4523 ]
ZXZ: -1.148003  1.550493 -1.724656   [DEG:  -65.7757   88.8367  -98.8155 ]
 
# END of job
