
#######################################################
#                                                     #
#                        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:    23      12_A - 34_A        4.98     7.75
  LCS_AVERAGE:     58.20

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10      16_A - 25_A        1.87    15.65
  LCS_AVERAGE:     18.12

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6      16_A - 21_A        0.94    14.80
  LONGEST_CONTINUOUS_SEGMENT:     6      17_A - 22_A        0.72    13.21
  LCS_AVERAGE:     12.08

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   12      3    3    3    3    4    4    4   12   13   15   18   19   22   23   26   27   29   31   33   33 
LCS_GDT     D     2_A     D     2_A      3    4   12      3    3    3    3    4    4    5    5   13   14   18   19   22   23   26   27   29   31   33   33 
LCS_GDT     E     3_A     E     3_A      3    4   12      3    3    3    3    4    4    6    8    9   10   11   15   21   23   26   27   29   31   33   33 
LCS_GDT     M     4_A     M     4_A      3    4   12      3    3    4    4    5    5    6    8    9   12   15   18   21   23   26   27   29   31   33   33 
LCS_GDT     W     5_A     W     5_A      3    3   12      3    3    4    4    5    5    6    8    9   10   11   14   19   23   26   27   29   31   33   33 
LCS_GDT     F     6_A     F     6_A      3    3   17      3    3    4    4    5    5    6    8    9   10   11   13   16   21   26   27   29   31   33   33 
LCS_GDT     C     7_A     C     7_A      5    5   17      4    5    5    5    5    5    6    8   10   10   11   14   15   17   21   26   29   31   33   33 
LCS_GDT     E     8_A     E     8_A      5    5   17      4    5    5    5    5    5    6   10   11   13   14   14   15   16   18   21   24   27   29   30 
LCS_GDT     T     9_A     T     9_A      5    5   17      4    5    5    5    5    5    7    8   11   13   14   14   15   16   18   18   18   27   28   29 
LCS_GDT     L    10_A     L    10_A      5    5   17      4    5    5    5    5    6    7    8   10   13   14   14   15   20   23   26   29   31   33   33 
LCS_GDT     R    11_A     R    11_A      5    5   19      4    5    5    5    5    6    6    9   14   17   18   19   21   21   26   27   29   31   33   33 
LCS_GDT     R    12_A     R    12_A      3    4   23      3    3    4    4    7    9   12   14   16   17   18   19   22   23   26   27   29   31   33   33 
LCS_GDT     L    13_A     L    13_A      3    4   23      3    3    5    6   11   11   12   14   16   17   18   19   22   23   26   27   29   31   33   33 
LCS_GDT     L    14_A     L    14_A      4    4   23      3    4    4    4    5    6    9   13   14   16   18   19   22   23   25   27   29   31   33   33 
LCS_GDT     C    15_A     C    15_A      4    8   23      3    4    4    4    7   10   10   12   14   16   18   19   21   23   24   25   26   29   33   33 
LCS_GDT     P    16_A     P    16_A      6   10   23      3    6    7    9   10   11   12   13   14   15   16   19   20   23   23   25   26   31   33   33 
LCS_GDT     K    17_A     K    17_A      6   10   23      5    6    7    9   10   12   12   13   14   16   18   19   22   23   26   27   29   31   33   33 
LCS_GDT     S    18_A     S    18_A      6   10   23      5    5    6    9   10   12   12   13   14   17   18   19   22   23   26   27   29   31   33   33 
LCS_GDT     C    19_A     C    19_A      6   10   23      5    5    6    8   11   12   12   14   16   17   18   19   22   23   26   27   29   31   33   33 
LCS_GDT     S    20_A     S    20_A      6   10   23      5    5    6    8   11   12   12   14   16   17   18   19   22   23   26   27   29   31   33   33 
LCS_GDT     I    21_A     I    21_A      6   10   23      5    6    7    9   11   12   12   14   16   17   18   19   22   23   26   27   29   31   33   33 
LCS_GDT     E    22_A     E    22_A      6   10   23      4    6    7    9   11   12   12   14   16   17   18   19   22   23   26   27   29   29   33   33 
LCS_GDT     G    23_A     G    23_A      5   10   23      3    3    7    9   11   12   12   14   16   17   18   19   22   23   26   27   29   31   33   33 
LCS_GDT     G    24_A     G    24_A      5   10   23      3    5    7    9   11   12   12   14   16   17   18   19   22   23   26   27   29   31   33   33 
LCS_GDT     C    25_A     C    25_A      5   10   23      3    6    7    9   11   12   12   14   16   17   18   19   22   23   26   27   29   31   33   33 
LCS_GDT     P    26_A     P    26_A      4    9   23      3    4    5    8    9   10   12   13   14   17   18   19   22   23   26   27   29   31   33   33 
LCS_GDT     E    27_A     E    27_A      4    9   23      3    6    7    9   11   12   12   14   16   17   18   19   22   23   26   27   29   31   33   33 
LCS_GDT     V    28_A     V    28_A      4    6   23      3    4    6    7   11   12   12   14   16   17   18   19   22   23   26   27   29   31   33   33 
LCS_GDT     C    29_A     C    29_A      4    6   23      3    4    6    8   11   12   12   14   16   17   18   19   22   23   26   27   29   31   33   33 
LCS_GDT     S    30_A     S    30_A      3    5   23      3    3    4    5    5    7    7   13   16   17   18   19   22   23   26   27   29   31   33   33 
LCS_GDT     H    31_A     H    31_A      3    4   23      3    3    4    5    6    9   12   14   16   17   18   19   22   23   26   27   29   31   33   33 
LCS_GDT     M    32_A     M    32_A      3    4   23      3    3    3    4    4    6   10   14   16   17   18   19   22   23   26   27   29   31   33   33 
LCS_GDT     C    33_A     C    33_A      3    4   23      3    3    4    4    5    6   10   13   16   17   18   19   22   23   26   27   29   31   33   33 
LCS_GDT     P    34_A     P    34_A      3    4   23      3    3    3    4    5    5    6    9    9    9   15   19   21   21   23   25   29   31   33   33 
LCS_GDT     L    35_A     L    35_A      3    4   20      0    3    3    4    4    6    6    9   12   17   18   19   21   21   24   26   29   31   33   33 
LCS_AVERAGE  LCS_A:  29.47  (  12.08   18.12   58.20 )

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      6      7      9     11     12     12     14     16     17     18     19     22     23     26     27     29     31     33     33 
GDT PERCENT_AT  14.29  17.14  20.00  25.71  31.43  34.29  34.29  40.00  45.71  48.57  51.43  54.29  62.86  65.71  74.29  77.14  82.86  88.57  94.29  94.29
GDT RMS_LOCAL    0.41   0.72   0.91   1.24   1.98   2.18   2.02   2.96   3.29   3.47   3.62   3.89   4.45   4.61   5.38   5.48   5.92   6.38   6.52   6.52
GDT RMS_ALL_AT  13.52  16.53  16.24  16.11   8.94  12.75  16.13   7.66   7.66   7.66   7.64   8.59   7.73   7.68   7.28   7.27   7.15   7.05   7.07   7.07

# Checking swapping
#   possible swapping detected:  D     2_A      D     2_A
#   possible swapping detected:  E     3_A      E     3_A
#   possible swapping detected:  E     8_A      E     8_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     8.604     0    0.188   0.230    11.423    2.619    1.746
LGA    D     2_A      D     2_A     8.025     0    0.432   1.120    10.761    8.810    4.821
LGA    E     3_A      E     3_A     8.403     0    0.562   0.782    10.843    4.881    2.646
LGA    M     4_A      M     4_A     6.865     0    0.618   1.122     9.673   16.548   11.845
LGA    W     5_A      W     5_A     9.402     0    0.571   1.123    17.965    2.619    0.748
LGA    F     6_A      F     6_A    10.435     0    0.595   0.651    13.155    0.000    0.000
LGA    C     7_A      C     7_A    11.690     0    0.585   0.564    13.499    0.000    0.000
LGA    E     8_A      E     8_A    12.779     0    0.101   0.989    19.302    0.000    0.000
LGA    T     9_A      T     9_A    14.628     0    0.029   0.209    18.103    0.000    0.000
LGA    L    10_A      L    10_A    11.834     0    0.129   0.122    16.651    0.476    0.238
LGA    R    11_A      R    11_A     8.485     0    0.450   0.472    20.469    9.881    3.593
LGA    R    12_A      R    12_A     3.452     0    0.665   1.441    10.072   59.881   27.619
LGA    L    13_A      L    13_A     3.590     0    0.624   1.019     7.060   39.048   34.762
LGA    L    14_A      L    14_A     8.685     0    0.662   0.556    12.482    5.476    2.917
LGA    C    15_A      C    15_A     9.679     0    0.017   0.869    10.658    2.024    1.349
LGA    P    16_A      P    16_A    10.241     0    0.621   0.643    12.878    2.143    1.224
LGA    K    17_A      K    17_A     9.047     0    0.081   0.721    14.746    8.333    3.704
LGA    S    18_A      S    18_A     6.106     0    0.104   0.124     9.655   28.571   20.317
LGA    C    19_A      C    19_A     1.897     0    0.023   0.216     3.518   72.262   71.111
LGA    S    20_A      S    20_A     3.381     0    0.075   0.683     5.852   51.071   41.984
LGA    I    21_A      I    21_A     1.891     0    0.119   0.225     6.288   73.214   57.917
LGA    E    22_A      E    22_A     2.746     0    0.191   1.081     5.873   57.262   43.757
LGA    G    23_A      G    23_A     2.731     0    0.684   0.684     2.731   66.905   66.905
LGA    G    24_A      G    24_A     2.792     0    0.242   0.242     4.222   54.048   54.048
LGA    C    25_A      C    25_A     1.895     0    0.303   0.769     3.855   59.762   61.746
LGA    P    26_A      P    26_A     5.707     0    0.280   0.301     9.036   25.357   17.551
LGA    E    27_A      E    27_A     2.921     0    0.026   0.996     5.508   50.119   44.180
LGA    V    28_A      V    28_A     2.912     0    0.481   0.417     4.190   57.262   52.313
LGA    C    29_A      C    29_A     2.337     0    0.581   0.984     4.376   55.952   51.746
LGA    S    30_A      S    30_A     5.590     0    0.597   0.588     9.610   29.405   20.873
LGA    H    31_A      H    31_A     3.560     0    0.395   1.451     9.280   45.000   26.714
LGA    M    32_A      M    32_A     4.255     0    0.579   1.397     4.892   42.143   38.988
LGA    C    33_A      C    33_A     5.787     0    0.279   0.303     9.665   12.619   12.302
LGA    P    34_A      P    34_A    10.664     0    0.547   0.485    11.637    1.190    2.177
LGA    L    35_A      L    35_A    12.051     0    0.373   0.648    14.363    0.000    0.000

# 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):     7.016          6.831                  8.457           26.997   22.338

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   35   35    4.0     14    2.96    40.000    34.606     0.457

LGA_LOCAL      RMSD:   2.965  Number of atoms:   14  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   7.657  Number of assigned atoms:   35 
Std_ASGN_ATOMS RMSD:   7.016  Standard rmsd on all 35 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.685742 * X  +   0.616659 * Y  +  -0.386639 * Z  + -12.635478
  Y_new =   0.586555 * X  +  -0.153688 * Y  +   0.795194 * Z  +  -2.336180
  Z_new =   0.430941 * X  +  -0.772083 * Y  +  -0.467095 * Z  +  -4.091644 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.707596 -0.445536 -2.114870   [DEG:   40.5423  -25.5273 -121.1731 ]
ZXZ: -2.689030  2.056798  2.632511   [DEG: -154.0701  117.8459  150.8318 ]
 
# END of job
