
#######################################################
#                                                     #
#                        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   58 (  481),  selected   58 , name one
# Molecule2: number of CA atoms   58 (  481),  selected   58 , 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:    29      30_A - 58_A        4.81    15.08
  LCS_AVERAGE:     43.19

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      34_A - 58_A        1.54    15.34
  LCS_AVERAGE:     32.52

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      35_A - 58_A        0.85    15.32
  LCS_AVERAGE:     27.23

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   58
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     1_A     A     1_A     10   14   17      4    9   29   32   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     E     2_A     E     2_A     10   14   17      6   29   33   34   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     Y     3_A     Y     3_A     10   14   17     14   30   33   34   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     V     4_A     V     4_A     10   14   17     12   30   33   34   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     R     5_A     R     5_A     10   14   17      7   30   33   34   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     A     6_A     A     6_A     10   14   17      6   30   33   34   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     L     7_A     L     7_A     10   14   17     14   30   33   34   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     F     8_A     F     8_A     10   14   17      6   30   33   34   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     D     9_A     D     9_A     10   14   17      3   13   33   34   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     H    10_A     H    10_A     10   14   17     14   30   33   34   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     T    11_A     T    11_A      5   14   17      3    5   22   34   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     G    12_A     G    12_A      5   14   17      3   30   33   34   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     H    13_A     H    13_A      4   14   24      3    5   12   23   33   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     D    14_A     D    14_A      4   14   24      3    4    5    7   12   20   23   31   36   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     E    15_A     E    15_A      4   16   24      3    4    5   10   14   17   23   27   32   37   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     Q    16_A     Q    16_A     14   16   24      8   14   14   14   14   15   18   26   29   37   39   41   42   42   42   43   44   45   46   46 
LCS_GDT     E    17_A     E    17_A     14   16   24      5   14   14   14   14   15   16   17   18   20   21   21   22   28   34   38   42   45   46   46 
LCS_GDT     L    18_A     L    18_A     14   16   24      5   14   14   14   14   15   16   17   18   20   21   21   22   22   24   24   25   28   35   38 
LCS_GDT     P    19_A     P    19_A     14   16   24      5   14   14   14   14   15   16   17   18   20   21   21   22   22   24   24   25   26   27   29 
LCS_GDT     F    20_A     F    20_A     14   16   24      5   14   14   14   14   15   16   17   18   20   21   21   22   22   24   24   25   26   27   29 
LCS_GDT     K    21_A     K    21_A     14   16   24      5   14   14   14   14   15   16   17   18   20   21   21   22   22   24   24   25   26   27   29 
LCS_GDT     K    22_A     K    22_A     14   16   24      5   14   14   14   14   15   16   17   18   20   21   21   22   22   24   24   25   26   27   29 
LCS_GDT     G    23_A     G    23_A     14   16   24      8   14   14   14   14   15   16   17   18   20   21   21   22   22   24   24   25   26   27   29 
LCS_GDT     E    24_A     E    24_A     14   16   24      8   14   14   14   14   15   16   17   18   20   21   21   22   22   24   24   25   26   27   29 
LCS_GDT     I    25_A     I    25_A     14   16   24      8   14   14   14   14   15   16   17   18   20   21   21   22   22   24   24   25   26   27   29 
LCS_GDT     L    26_A     L    26_A     14   16   24      8   14   14   14   14   15   16   17   18   20   21   21   22   22   24   24   25   26   27   29 
LCS_GDT     R    27_A     R    27_A     14   16   24      8   14   14   14   14   15   16   17   18   20   21   21   22   22   24   24   25   26   27   29 
LCS_GDT     I    28_A     I    28_A     14   16   24      8   14   14   14   14   15   16   17   18   20   21   21   22   22   24   24   28   30   35   36 
LCS_GDT     R    29_A     R    29_A     14   16   24      8   14   14   14   14   15   16   17   18   20   21   21   22   22   24   26   29   34   36   36 
LCS_GDT     D    30_A     D    30_A      6   16   29      3    3    6   11   14   15   16   17   18   20   21   21   27   27   34   35   41   44   46   46 
LCS_GDT     K    31_A     K    31_A      4    6   29      3    3    4    5    7    8   14   17   18   20   21   26   28   33   37   43   44   45   46   46 
LCS_GDT     P    32_A     P    32_A      4    6   29      3    3    4    5    7    8   14   17   18   20   21   21   28   39   41   43   44   45   46   46 
LCS_GDT     E    33_A     E    33_A      4    5   29      3    3    4    5    7    8   11   15   28   35   38   39   42   42   42   43   44   45   46   46 
LCS_GDT     E    34_A     E    34_A      4   25   29      3    3    5    5    6   12   31   36   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     Q    35_A     Q    35_A     24   25   29     11   30   33   34   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     L    36_A     L    36_A     24   25   29     10   30   33   34   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     W    37_A     W    37_A     24   25   29     14   30   33   34   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     N    38_A     N    38_A     24   25   29     14   30   33   34   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     A    39_A     A    39_A     24   25   29     12   30   33   34   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     E    40_A     E    40_A     24   25   29     14   30   33   34   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     N    41_A     N    41_A     24   25   29     13   30   33   34   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     V    42_A     V    42_A     24   25   29      9   30   33   34   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     E    43_A     E    43_A     24   25   29      7   30   33   34   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     G    44_A     G    44_A     24   25   29      9   30   33   34   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     K    45_A     K    45_A     24   25   29      7   30   33   34   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     R    46_A     R    46_A     24   25   29      7   30   33   34   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     G    47_A     G    47_A     24   25   29     14   30   33   34   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     L    48_A     L    48_A     24   25   29     14   30   33   34   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     I    49_A     I    49_A     24   25   29     14   30   33   34   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     H    50_A     H    50_A     24   25   29     14   30   33   34   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     V    51_A     V    51_A     24   25   29     14   30   33   34   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     V    52_A     V    52_A     24   25   29     14   30   33   34   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     L    53_A     L    53_A     24   25   29     14   30   33   34   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     V    54_A     V    54_A     24   25   29     14   30   33   34   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     E    55_A     E    55_A     24   25   29     11   30   33   34   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     K    56_A     K    56_A     24   25   29      7   30   33   34   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     Y    57_A     Y    57_A     24   25   29      7   30   33   34   35   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_GDT     G    58_A     G    58_A     24   25   29      3    3   11   26   33   37   37   37   37   38   40   41   42   42   42   43   44   45   46   46 
LCS_AVERAGE  LCS_A:  34.31  (  27.23   32.52   43.19 )

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     30     33     34     35     37     37     37     37     38     40     41     42     42     42     43     44     45     46     46 
GDT PERCENT_AT  24.14  51.72  56.90  58.62  60.34  63.79  63.79  63.79  63.79  65.52  68.97  70.69  72.41  72.41  72.41  74.14  75.86  77.59  79.31  79.31
GDT RMS_LOCAL    0.38   0.63   0.71   0.84   0.94   1.32   1.32   1.32   1.32   1.76   2.44   2.66   3.02   3.02   3.02   3.49   3.94   4.28   4.71   4.71
GDT RMS_ALL_AT  15.30  15.36  15.37  15.34  15.35  15.26  15.26  15.26  15.26  15.16  15.02  14.93  14.92  14.92  14.92  14.88  14.80  14.68  14.58  14.58

# Checking swapping
#   possible swapping detected:  E     2_A      E     2_A
#   possible swapping detected:  Y     3_A      Y     3_A
#   possible swapping detected:  F     8_A      F     8_A
#   possible swapping detected:  E    15_A      E    15_A
#   possible swapping detected:  E    17_A      E    17_A
#   possible swapping detected:  F    20_A      F    20_A
#   possible swapping detected:  E    24_A      E    24_A
#   possible swapping detected:  D    30_A      D    30_A
#   possible swapping detected:  E    34_A      E    34_A
#   possible swapping detected:  E    40_A      E    40_A
#   possible swapping detected:  E    43_A      E    43_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     1_A      A     1_A     2.684     0    0.524   0.595     4.990   68.929   61.429
LGA    E     2_A      E     2_A     1.408     0    0.094   0.806     5.276   77.262   63.280
LGA    Y     3_A      Y     3_A     0.606     0    0.105   0.188     1.552   90.476   87.540
LGA    V     4_A      V     4_A     0.670     0    0.038   0.110     1.124   88.214   89.184
LGA    R     5_A      R     5_A     1.106     0    0.017   0.922     4.837   88.214   76.580
LGA    A     6_A      A     6_A     0.966     0    0.035   0.058     1.670   85.952   83.333
LGA    L     7_A      L     7_A     0.681     0    0.019   0.731     2.613   95.238   85.357
LGA    F     8_A      F     8_A     1.307     0    0.635   1.466     5.166   75.833   62.424
LGA    D     9_A      D     9_A     1.434     0    0.098   1.035     3.636   86.190   73.810
LGA    H    10_A      H    10_A     0.859     0    0.605   1.175     3.484   79.881   70.333
LGA    T    11_A      T    11_A     2.362     0    0.296   1.123     5.804   66.905   56.735
LGA    G    12_A      G    12_A     1.007     0    0.517   0.517     1.409   81.429   81.429
LGA    H    13_A      H    13_A     4.376     0    0.547   0.918    10.490   33.214   18.714
LGA    D    14_A      D    14_A     7.557     0    0.089   0.882    10.221    8.452    4.524
LGA    E    15_A      E    15_A     9.444     0    0.623   1.298    14.222    6.548    2.910
LGA    Q    16_A      Q    16_A     8.430     0    0.591   0.495    10.497    2.619    1.587
LGA    E    17_A      E    17_A    12.489     0    0.027   0.810    16.458    0.000    0.000
LGA    L    18_A      L    18_A    19.412     0    0.055   1.383    23.642    0.000    0.000
LGA    P    19_A      P    19_A    24.936     0    0.104   0.183    27.920    0.000    0.000
LGA    F    20_A      F    20_A    30.329     0    0.054   1.425    32.416    0.000    0.000
LGA    K    21_A      K    21_A    36.941     0    0.151   1.420    42.731    0.000    0.000
LGA    K    22_A      K    22_A    40.561     0    0.582   1.150    49.828    0.000    0.000
LGA    G    23_A      G    23_A    41.669     0    0.232   0.232    42.173    0.000    0.000
LGA    E    24_A      E    24_A    38.289     0    0.039   1.078    38.947    0.000    0.000
LGA    I    25_A      I    25_A    36.419     0    0.023   0.617    42.463    0.000    0.000
LGA    L    26_A      L    26_A    30.370     0    0.136   0.267    32.331    0.000    0.000
LGA    R    27_A      R    27_A    28.272     0    0.073   1.293    32.045    0.000    0.000
LGA    I    28_A      I    28_A    21.434     0    0.096   0.696    24.130    0.000    0.000
LGA    R    29_A      R    29_A    21.735     0    0.599   0.865    31.071    0.000    0.000
LGA    D    30_A      D    30_A    17.879     0    0.686   1.244    22.845    0.000    0.000
LGA    K    31_A      K    31_A    15.758     0    0.236   0.957    18.390    0.000    0.000
LGA    P    32_A      P    32_A    14.353     0    0.056   0.310    16.926    0.000    0.000
LGA    E    33_A      E    33_A    11.246     0    0.718   1.043    16.316    0.119    0.053
LGA    E    34_A      E    34_A     7.295     0    0.242   0.929     9.638   16.905   10.794
LGA    Q    35_A      Q    35_A     0.628     0    0.604   0.753     4.563   82.143   67.090
LGA    L    36_A      L    36_A     0.467     0    0.067   1.154     3.091   95.238   86.964
LGA    W    37_A      W    37_A     0.333     0    0.043   0.219     1.325   97.619   93.946
LGA    N    38_A      N    38_A     0.433     0    0.148   1.138     3.814   97.619   87.024
LGA    A    39_A      A    39_A     0.554     0    0.044   0.060     1.113   88.214   88.667
LGA    E    40_A      E    40_A     0.413     0    0.023   0.491     1.988  100.000   90.794
LGA    N    41_A      N    41_A     0.922     0    0.064   1.224     4.174   90.476   79.405
LGA    V    42_A      V    42_A     0.815     0    0.054   0.137     0.980   90.476   91.837
LGA    E    43_A      E    43_A     1.148     0    0.222   0.885     2.377   88.214   81.693
LGA    G    44_A      G    44_A     0.804     0    0.126   0.126     0.970   92.857   92.857
LGA    K    45_A      K    45_A     1.019     0    0.037   0.883     3.838   83.690   74.444
LGA    R    46_A      R    46_A     1.060     0    0.096   0.942     2.655   81.429   80.866
LGA    G    47_A      G    47_A     0.437     0    0.056   0.056     0.557   97.619   97.619
LGA    L    48_A      L    48_A     0.443     0    0.035   0.856     2.269   95.238   87.440
LGA    I    49_A      I    49_A     0.297     0    0.045   0.622     1.386  100.000   92.976
LGA    H    50_A      H    50_A     0.522     0    0.065   0.582     2.287   92.857   86.286
LGA    V    51_A      V    51_A     0.527     0    0.040   0.102     0.680   90.476   91.837
LGA    V    52_A      V    52_A     0.431     0    0.149   1.103     2.408   95.238   87.211
LGA    L    53_A      L    53_A     0.337     0    0.082   0.098     0.670  100.000   97.619
LGA    V    54_A      V    54_A     0.339     0    0.024   0.073     0.425  100.000  100.000
LGA    E    55_A      E    55_A     0.657     0    0.090   0.579     2.798   88.214   82.751
LGA    K    56_A      K    56_A     1.014     0    0.151   0.873     3.793   88.214   72.487
LGA    Y    57_A      Y    57_A     0.583     0    0.587   0.511     2.823   86.071   75.437
LGA    G    58_A      G    58_A     3.318     0    0.397   0.397     4.450   46.905   46.905

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       58     232    232  100.00     481    481  100.00                58
SUMMARY(RMSD_GDC):    13.179         13.125                 13.576           55.538   51.106

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   58   58    4.0     37    1.32    62.069    55.650     2.612

LGA_LOCAL      RMSD:   1.317  Number of atoms:   37  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  15.257  Number of assigned atoms:   58 
Std_ASGN_ATOMS RMSD:  13.179  Standard rmsd on all 58 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.627883 * X  +   0.018205 * Y  +  -0.778094 * Z  + -33.489132
  Y_new =  -0.082663 * X  +  -0.992512 * Y  +  -0.089926 * Z  +  19.545307
  Z_new =  -0.773905 * X  +   0.120782 * Y  +  -0.621677 * Z  +  -1.631623 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.130900  0.884985  2.949699   [DEG:   -7.5000   50.7059  169.0053 ]
ZXZ: -1.455735  2.241678 -1.415977   [DEG:  -83.4075  128.4387  -81.1295 ]
 
# END of job
