
#######################################################
#                                                     #
#                        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   35 (  269),  selected   35 , name one
# Molecule2: number of CA atoms   35 (  269),  selected   35 , 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:    22      14_A - 35_A        4.99    10.61
  LCS_AVERAGE:     56.33

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11      24_A - 34_A        1.88    11.25
  LCS_AVERAGE:     20.82

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7      14_A - 20_A        0.63    11.36
  LONGEST_CONTINUOUS_SEGMENT:     7      24_A - 30_A        0.91    11.51
  LONGEST_CONTINUOUS_SEGMENT:     7      25_A - 31_A        0.83    11.82
  LCS_AVERAGE:     13.80

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   35
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     S     1_A     S     1_A      3    4   10      3    3    4    6    6    7    7    8   13   16   16   16   20   21   21   21   22   24   25   27 
LCS_GDT     D     2_A     D     2_A      3    4   11      3    3    3    6    6    7    7   10   13   16   16   18   20   21   22   22   22   24   25   27 
LCS_GDT     E     3_A     E     3_A      3    4   11      3    3    3    6    6    7    7    8    9   16   16   18   20   21   22   22   22   24   25   27 
LCS_GDT     M     4_A     M     4_A      3    4   11      3    3    4    4    5    6    6   10   12   16   17   18   20   21   22   22   23   24   25   27 
LCS_GDT     W     5_A     W     5_A      3    3   11      1    4    4    8   10   11   12   13   15   17   18   19   20   22   24   24   26   26   28   28 
LCS_GDT     F     6_A     F     6_A      3    3   16      3    7    8    8   10   11   12   13   15   17   18   19   21   23   24   25   26   26   28   28 
LCS_GDT     C     7_A     C     7_A      3    5   16      3    4    8    8   10   11   12   13   15   17   18   19   21   23   24   25   26   26   28   28 
LCS_GDT     E     8_A     E     8_A      3    5   20      3    3    3    5    5    6    6    7    8   11   17   19   21   23   24   25   26   26   28   28 
LCS_GDT     T     9_A     T     9_A      3    5   20      3    3    3    4    4    6    6    7    9   13   15   17   20   23   24   25   26   26   28   28 
LCS_GDT     L    10_A     L    10_A      3    5   20      1    3    3    4    4    5    5    6    9   13   16   19   21   23   24   25   26   26   27   28 
LCS_GDT     R    11_A     R    11_A      3    5   20      3    3    3    3    4    5    5    7    8    8   13   18   21   23   24   25   26   26   28   28 
LCS_GDT     R    12_A     R    12_A      3    4   20      3    3    3    5    5    9   13   13   14   16   16   16   21   23   24   25   26   26   28   28 
LCS_GDT     L    13_A     L    13_A      3    8   20      3    4    4    5    6    6   11   12   13   17   18   19   21   23   24   25   26   26   28   28 
LCS_GDT     L    14_A     L    14_A      7    8   22      5    7    8    8   10   11   13   13   15   17   18   19   21   23   24   25   26   26   28   28 
LCS_GDT     C    15_A     C    15_A      7    8   22      5    7    8    8   10   11   13   13   15   17   18   19   21   23   24   25   26   26   28   28 
LCS_GDT     P    16_A     P    16_A      7    8   22      4    7    8    8   10   11   12   13   15   17   18   19   21   23   24   25   26   26   28   28 
LCS_GDT     K    17_A     K    17_A      7    8   22      5    7    8    8   10   12   13   13   15   17   19   19   21   23   24   25   26   26   28   28 
LCS_GDT     S    18_A     S    18_A      7    8   22      5    7    8    8   10   11   12   13   15   17   19   19   21   23   24   25   26   26   28   28 
LCS_GDT     C    19_A     C    19_A      7    8   22      5    7    8    8   10   11   12   14   16   17   19   19   21   23   24   25   26   26   28   28 
LCS_GDT     S    20_A     S    20_A      7    8   22      3    7    7    8   10   11   12   14   16   17   19   19   21   23   24   25   26   26   28   28 
LCS_GDT     I    21_A     I    21_A      3    3   22      3    3    3    5    6    6   11   14   16   17   19   19   21   23   24   25   26   26   28   28 
LCS_GDT     E    22_A     E    22_A      3    4   22      3    3    4    5    7    9   12   14   16   17   19   19   21   23   24   25   26   26   28   28 
LCS_GDT     G    23_A     G    23_A      3    4   22      3    3    3    5    6    7   10   13   16   17   19   19   21   23   24   25   26   26   28   28 
LCS_GDT     G    24_A     G    24_A      7   11   22      4    6    6    8   10   12   13   14   16   17   19   19   21   23   24   25   26   26   28   28 
LCS_GDT     C    25_A     C    25_A      7   11   22      4    6    7    8   10   12   13   14   16   17   19   19   21   23   24   25   26   26   28   28 
LCS_GDT     P    26_A     P    26_A      7   11   22      4    6    7    8   10   12   13   14   16   17   19   19   21   23   24   25   26   26   28   28 
LCS_GDT     E    27_A     E    27_A      7   11   22      4    6    7    8   10   12   13   14   16   17   19   19   21   23   24   25   26   26   28   28 
LCS_GDT     V    28_A     V    28_A      7   11   22      4    6    7    8   10   12   13   14   16   17   19   19   20   22   24   25   26   26   28   28 
LCS_GDT     C    29_A     C    29_A      7   11   22      4    6    7    8   10   12   13   14   16   17   19   19   20   23   24   25   26   26   28   28 
LCS_GDT     S    30_A     S    30_A      7   11   22      3    6    7    8   10   12   13   14   16   17   19   19   20   21   24   25   26   26   28   28 
LCS_GDT     H    31_A     H    31_A      7   11   22      3    4    7    8   10   12   13   14   16   17   19   19   20   21   22   23   26   26   28   28 
LCS_GDT     M    32_A     M    32_A      4   11   22      3    4    5    8   10   12   13   14   16   17   19   19   20   21   22   23   26   26   28   28 
LCS_GDT     C    33_A     C    33_A      4   11   22      3    4    5    8   10   12   13   14   16   17   19   19   20   20   21   23   24   26   28   28 
LCS_GDT     P    34_A     P    34_A      4   11   22      3    4    4    7    8   12   13   14   16   17   19   19   20   20   21   23   24   26   28   28 
LCS_GDT     L    35_A     L    35_A      4    8   22      3    4    4    7    8   11   13   13   16   17   19   19   20   20   21   21   22   23   23   24 
LCS_AVERAGE  LCS_A:  30.31  (  13.80   20.82   56.33 )

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      5      7      8      8     10     12     13     14     16     17     19     19     21     23     24     25     26     26     28     28 
GDT PERCENT_AT  14.29  20.00  22.86  22.86  28.57  34.29  37.14  40.00  45.71  48.57  54.29  54.29  60.00  65.71  68.57  71.43  74.29  74.29  80.00  80.00
GDT RMS_LOCAL    0.37   0.63   0.83   0.83   1.56   2.11   2.24   2.98   3.17   3.32   3.75   3.75   4.90   5.15   5.28   5.46   5.59   5.59   6.50   6.16
GDT RMS_ALL_AT  11.14  11.36  10.73  10.73  11.37  12.06  11.15  13.53  13.87  13.70  12.69  12.69  10.95  11.05  10.95  10.79  10.54  10.54   9.35  10.12

# Checking swapping
#   possible swapping detected:  D     2_A      D     2_A
#   possible swapping detected:  E    22_A      E    22_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     1_A      S     1_A    18.052     0    0.315   0.343    20.248    0.000    0.000
LGA    D     2_A      D     2_A    18.285     0    0.444   1.151    20.491    0.000    0.000
LGA    E     3_A      E     3_A    21.546     0    0.568   1.287    27.405    0.000    0.000
LGA    M     4_A      M     4_A    16.496     0    0.608   1.084    18.227    0.000    0.179
LGA    W     5_A      W     5_A    19.578     0    0.567   1.178    28.012    0.000    0.000
LGA    F     6_A      F     6_A    23.390     0    0.604   1.043    26.727    0.000    0.000
LGA    C     7_A      C     7_A    21.707     0    0.572   0.898    21.746    0.000    0.000
LGA    E     8_A      E     8_A    22.370     0    0.434   0.990    25.010    0.000    0.000
LGA    T     9_A      T     9_A    26.003     0    0.587   0.545    30.226    0.000    0.000
LGA    L    10_A      L    10_A    24.291     0    0.540   0.430    28.644    0.000    0.000
LGA    R    11_A      R    11_A    18.765     0    0.544   1.001    20.623    0.000    0.000
LGA    R    12_A      R    12_A    18.813     0    0.507   1.188    26.853    0.000    0.000
LGA    L    13_A      L    13_A    18.163     0    0.622   1.033    21.698    0.000    0.000
LGA    L    14_A      L    14_A    15.992     0    0.581   0.475    20.588    0.000    0.000
LGA    C    15_A      C    15_A    10.931     0    0.068   0.825    12.797    0.000    1.429
LGA    P    16_A      P    16_A    11.144     0    0.059   0.098    11.853    2.857    1.633
LGA    K    17_A      K    17_A     7.918     0    0.058   0.601    10.944   12.738    6.402
LGA    S    18_A      S    18_A     6.997     0    0.086   0.557    10.140   16.548   11.270
LGA    C    19_A      C    19_A     3.530     0    0.525   0.897     4.799   47.262   47.063
LGA    S    20_A      S    20_A     3.704     0    0.539   0.850     5.888   43.214   36.746
LGA    I    21_A      I    21_A     3.778     0    0.553   0.483     8.620   53.810   33.571
LGA    E    22_A      E    22_A     2.529     0    0.300   1.081     5.678   49.167   45.238
LGA    G    23_A      G    23_A     4.675     0    0.694   0.694     4.675   40.476   40.476
LGA    G    24_A      G    24_A     2.178     0    0.492   0.492     2.802   62.976   62.976
LGA    C    25_A      C    25_A     3.443     0    0.137   0.762     4.573   63.333   54.683
LGA    P    26_A      P    26_A     2.601     0    0.073   0.074     4.397   67.143   55.170
LGA    E    27_A      E    27_A     2.044     0    0.036   1.040     6.312   64.762   47.090
LGA    V    28_A      V    28_A     2.687     0    0.056   0.992     5.277   66.905   56.327
LGA    C    29_A      C    29_A     1.803     0    0.198   0.734     2.879   71.071   67.698
LGA    S    30_A      S    30_A     3.031     0    0.320   0.318     4.861   51.071   46.508
LGA    H    31_A      H    31_A     2.608     0    0.063   1.244     4.603   64.881   56.714
LGA    M    32_A      M    32_A     3.238     0    0.632   1.477     4.812   50.476   47.321
LGA    C    33_A      C    33_A     3.652     0    0.220   0.251     4.669   40.357   38.333
LGA    P    34_A      P    34_A     4.447     0    0.535   0.512     4.536   38.690   39.932
LGA    L    35_A      L    35_A     4.965     0    0.431   0.537     6.354   30.119   24.167

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       35     140    140  100.00     269    269  100.00                35
SUMMARY(RMSD_GDC):     8.668          8.664                  9.583           26.796   23.455

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   35   35    4.0     14    2.98    38.571    34.991     0.454

LGA_LOCAL      RMSD:   2.984  Number of atoms:   14  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  13.525  Number of assigned atoms:   35 
Std_ASGN_ATOMS RMSD:   8.668  Standard rmsd on all 35 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.584890 * X  +  -0.587321 * Y  +   0.559426 * Z  +  -6.715756
  Y_new =   0.545695 * X  +  -0.795205 * Y  +  -0.264321 * Z  +  -3.702465
  Z_new =   0.600100 * X  +   0.150677 * Y  +   0.785606 * Z  +   2.559121 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.390848 -0.643626  0.189497   [DEG:  136.9855  -36.8771   10.8574 ]
ZXZ:  1.129401  0.667122  1.324795   [DEG:   64.7099   38.2233   75.9051 ]
 
# END of job
