
#######################################################
#                                                     #
#                        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   42 (  348),  selected   41 , name one
# Molecule2: number of CA atoms   41 (  336),  selected   41 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    35       2_B - 36_B        4.62     9.26
  LONGEST_CONTINUOUS_SEGMENT:    35       3_B - 37_B        4.91     9.08
  LCS_AVERAGE:     81.20

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23       6_B - 28_B        1.95    10.93
  LONGEST_CONTINUOUS_SEGMENT:    23       7_B - 29_B        1.86    10.93
  LCS_AVERAGE:     47.53

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18       8_B - 25_B        0.95    10.96
  LCS_AVERAGE:     34.80

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   41
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     2_B     A     2_B      4    5   35      3    4    4    4    7    8   10   11   11   14   23   26   28   30   32   33   34   35   35   35 
LCS_GDT     S     3_B     S     3_B      4    5   35      3    4    4    5    7    9   10   16   21   22   23   26   31   32   33   34   34   35   35   35 
LCS_GDT     Q     4_B     Q     4_B      4   20   35      3    4    4    4    9   18   18   21   24   26   28   29   31   32   33   34   34   35   35   35 
LCS_GDT     R     5_B     R     5_B     11   21   35      4    8   10   14   18   19   22   25   26   28   28   30   31   32   33   34   34   35   35   35 
LCS_GDT     L     6_B     L     6_B     11   23   35      4    8   10   14   18   21   22   25   26   28   28   30   31   32   33   34   34   35   35   35 
LCS_GDT     F     7_B     F     7_B     11   23   35      3    5   10   14   18   21   22   25   26   28   28   30   31   32   33   34   34   35   35   35 
LCS_GDT     V     8_B     V     8_B     18   23   35      4   10   18   18   20   21   22   25   26   28   28   30   31   32   33   34   34   35   35   35 
LCS_GDT     L     9_B     L     9_B     18   23   35      4   17   18   18   20   21   22   25   26   28   28   30   31   32   33   34   34   35   35   35 
LCS_GDT     D    10_B     D    10_B     18   23   35     15   17   18   18   20   21   22   25   26   28   28   30   31   32   33   34   34   35   35   35 
LCS_GDT     N    11_B     N    11_B     18   23   35     15   17   18   18   20   21   22   25   26   28   28   30   31   32   33   34   34   35   35   35 
LCS_GDT     E    12_B     E    12_B     18   23   35     15   17   18   18   20   21   22   25   26   28   28   30   31   32   33   34   34   35   35   35 
LCS_GDT     R    13_B     R    13_B     18   23   35     15   17   18   18   20   21   22   25   26   28   28   30   31   32   33   34   34   35   35   35 
LCS_GDT     Y    14_B     Y    14_B     18   23   35     15   17   18   18   20   21   22   25   26   28   28   30   31   32   33   34   34   35   35   35 
LCS_GDT     D    15_B     D    15_B     18   23   35     15   17   18   18   20   21   22   25   26   28   28   30   31   32   33   34   34   35   35   35 
LCS_GDT     S    16_B     S    16_B     18   23   35     15   17   18   18   20   21   22   25   26   28   28   30   31   32   33   34   34   35   35   35 
LCS_GDT     F    17_B     F    17_B     18   23   35     15   17   18   18   20   21   22   25   26   28   28   30   31   32   33   34   34   35   35   35 
LCS_GDT     I    18_B     I    18_B     18   23   35     15   17   18   18   20   21   22   25   26   28   28   30   31   32   33   34   34   35   35   35 
LCS_GDT     T    19_B     T    19_B     18   23   35     15   17   18   18   20   21   22   25   26   28   28   30   31   32   33   34   34   35   35   35 
LCS_GDT     Q    20_B     Q    20_B     18   23   35     15   17   18   18   20   21   22   25   26   28   28   30   31   32   33   34   34   35   35   35 
LCS_GDT     L    21_B     L    21_B     18   23   35     15   17   18   18   20   21   22   25   26   28   28   30   31   32   33   34   34   35   35   35 
LCS_GDT     E    22_B     E    22_B     18   23   35     15   17   18   18   20   21   22   25   26   28   28   30   31   32   33   34   34   35   35   35 
LCS_GDT     A    23_B     A    23_B     18   23   35     15   17   18   18   20   21   22   25   26   28   28   30   31   32   33   34   34   35   35   35 
LCS_GDT     P    24_B     P    24_B     18   23   35     15   17   18   18   20   21   22   25   26   28   28   30   31   32   33   34   34   35   35   35 
LCS_GDT     V    25_B     V    25_B     18   23   35      4    6   13   18   20   20   22   25   26   28   28   30   31   32   33   34   34   35   35   35 
LCS_GDT     Q    26_B     Q    26_B     14   23   35      3    6   13   17   19   20   21   22   25   28   28   30   30   32   33   34   34   35   35   35 
LCS_GDT     N    27_B     N    27_B     14   23   35     11   12   16   18   20   20   22   23   26   28   28   30   31   32   33   34   34   35   35   35 
LCS_GDT     A    28_B     A    28_B     14   23   35     12   17   18   18   20   21   22   25   26   28   28   30   31   32   33   34   34   35   35   35 
LCS_GDT     E    29_B     E    29_B     14   23   35     11   12   14   14   19   21   22   25   26   28   28   30   31   32   33   34   34   35   35   35 
LCS_GDT     G    30_B     G    30_B     14   16   35     11   12   14   14   15   15   15   16   26   28   28   30   31   32   33   34   34   35   35   35 
LCS_GDT     R    31_B     R    31_B     14   16   35     11   12   14   14   15   15   15   25   26   28   28   30   31   32   33   34   34   35   35   35 
LCS_GDT     E    32_B     E    32_B     14   16   35     11   12   14   14   15   15   17   25   26   28   28   30   31   32   33   34   34   35   35   35 
LCS_GDT     R    33_B     R    33_B     14   16   35     11   12   14   14   15   15   15   16   16   16   27   30   31   32   33   34   34   35   35   35 
LCS_GDT     L    34_B     L    34_B     14   16   35     10   12   14   14   15   15   15   16   16   16   17   18   30   32   33   34   34   35   35   35 
LCS_GDT     M    35_B     M    35_B     14   16   35     11   12   14   14   15   15   15   16   16   19   27   30   31   32   33   34   34   35   35   35 
LCS_GDT     A    36_B     A    36_B     14   16   35     11   12   14   14   15   15   15   16   16   16   17   18   30   32   33   34   34   35   35   35 
LCS_GDT     V    37_B     V    37_B     14   16   35     11   12   14   14   15   15   15   16   16   16   17   17   17   19   22   23   33   34   35   35 
LCS_GDT     K    38_B     K    38_B     14   16   21     11   12   14   14   15   15   15   16   16   16   17   17   17   18   20   21   23   24   27   33 
LCS_GDT     P    39_B     P    39_B     14   16   21      3    3   14   14   15   15   15   16   16   16   17   17   17   18   18   18   19   21   21   24 
LCS_GDT     E    40_B     E    40_B     14   16   21      3    8   14   14   15   15   15   16   16   16   17   17   17   18   18   18   19   20   21   22 
LCS_GDT     W    41_B     W    41_B      3   16   21      3    3    3    3    4    4    7    9   15   15   16   17   17   18   18   18   19   19   20   20 
LCS_GDT     K    42_B     K    42_B      3    4   21      0    3    3    3    4    4    7    8   10   15   16   17   17   18   18   18   19   19   19   19 
LCS_AVERAGE  LCS_A:  54.51  (  34.80   47.53   81.20 )

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     15     17     18     18     20     21     22     25     26     28     28     30     31     32     33     34     34     35     35     35 
GDT PERCENT_AT  36.59  41.46  43.90  43.90  48.78  51.22  53.66  60.98  63.41  68.29  68.29  73.17  75.61  78.05  80.49  82.93  82.93  85.37  85.37  85.37
GDT RMS_LOCAL    0.27   0.43   0.65   0.65   1.11   1.55   1.71   2.39   2.49   2.80   2.80   3.46   3.81   3.90   4.15   4.46   4.32   4.62   4.62   4.62
GDT RMS_ALL_AT  10.91  10.85  10.71  10.71  11.19  10.32  10.39  10.02  10.12  10.18  10.18   9.81   9.44   9.48   9.39   9.24   9.40   9.26   9.26   9.26

# Checking swapping
#   possible swapping detected:  F     7_B      F     7_B
#   possible swapping detected:  F    17_B      F    17_B
#   possible swapping detected:  E    22_B      E    22_B
#   possible swapping detected:  E    29_B      E    29_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     2_B      A     2_B    12.518     0    0.532   0.545    14.839    0.000    0.000
LGA    S     3_B      S     3_B    10.941     0    0.507   0.430    11.279    2.500    2.143
LGA    Q     4_B      Q     4_B     7.131     0    0.348   1.166    12.737   11.071    5.291
LGA    R     5_B      R     5_B     4.039     0    0.653   0.970     9.323   41.786   27.056
LGA    L     6_B      L     6_B     3.249     0    0.032   0.076     3.541   48.333   49.167
LGA    F     7_B      F     7_B     3.100     0    0.593   0.446     4.562   47.143   44.329
LGA    V     8_B      V     8_B     0.977     0    0.287   0.422     2.387   77.381   81.701
LGA    L     9_B      L     9_B     1.113     0    0.093   1.399     3.156   88.214   79.881
LGA    D    10_B      D    10_B     1.295     0    0.092   0.901     2.663   81.429   79.583
LGA    N    11_B      N    11_B     1.503     0    0.019   0.944     3.993   75.000   70.298
LGA    E    12_B      E    12_B     1.475     0    0.033   0.994     4.405   81.429   66.878
LGA    R    13_B      R    13_B     1.547     0    0.032   1.129     3.748   75.000   74.242
LGA    Y    14_B      Y    14_B     1.430     0    0.049   0.178     2.135   81.429   76.508
LGA    D    15_B      D    15_B     1.248     0    0.013   0.457     1.628   81.429   80.357
LGA    S    16_B      S    16_B     1.098     0    0.022   0.171     1.283   81.429   81.429
LGA    F    17_B      F    17_B     1.478     0    0.023   0.263     2.381   79.286   72.987
LGA    I    18_B      I    18_B     1.399     0    0.019   0.113     1.528   81.429   80.357
LGA    T    19_B      T    19_B     1.079     0    0.031   0.244     1.377   81.429   81.429
LGA    Q    20_B      Q    20_B     1.275     0    0.015   1.146     4.020   81.429   72.963
LGA    L    21_B      L    21_B     1.484     0    0.074   0.277     2.298   77.143   75.060
LGA    E    22_B      E    22_B     1.432     0    0.022   0.737     2.878   81.429   70.635
LGA    A    23_B      A    23_B     1.022     0    0.067   0.101     1.464   81.429   83.238
LGA    P    24_B      P    24_B     1.574     0    0.659   0.602     3.548   65.595   72.449
LGA    V    25_B      V    25_B     3.675     0    0.089   1.288     5.415   48.452   42.925
LGA    Q    26_B      Q    26_B     5.731     0    0.685   1.189    10.734   17.381   11.323
LGA    N    27_B      N    27_B     4.591     0    0.356   0.422     7.178   38.810   30.536
LGA    A    28_B      A    28_B     1.579     0    0.018   0.018     2.722   71.071   71.429
LGA    E    29_B      E    29_B     2.392     0    0.118   0.804     4.980   57.500   48.624
LGA    G    30_B      G    30_B     6.004     0    0.157   0.157     6.976   21.190   21.190
LGA    R    31_B      R    31_B     5.175     0    0.027   1.170     6.940   25.000   30.303
LGA    E    32_B      E    32_B     5.212     0    0.061   0.822     7.940   20.952   30.794
LGA    R    33_B      R    33_B     8.559     0    0.058   1.195    10.776    3.333    8.095
LGA    L    34_B      L    34_B    10.032     0    0.015   1.397    13.339    0.357    0.238
LGA    M    35_B      M    35_B     8.647     0    0.049   1.137    10.606    1.548   12.321
LGA    A    36_B      A    36_B    11.569     0    0.041   0.042    14.354    0.000    0.000
LGA    V    37_B      V    37_B    14.793     0    0.037   0.083    16.555    0.000    0.000
LGA    K    38_B      K    38_B    17.767     4    0.159   0.183    21.275    0.000    0.000
LGA    P    39_B      P    39_B    20.806     0    0.646   0.657    24.379    0.000    0.000
LGA    E    40_B      E    40_B    24.644     0    0.385   1.087    26.839    0.000    0.000
LGA    W    41_B      W    41_B    25.116     0    0.669   1.453    29.581    0.000    0.000
LGA    K    42_B      K    42_B    31.080     0    0.391   1.181    37.626    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       41     164    164  100.00     336    336  100.00                41
SUMMARY(RMSD_GDC):     8.551          8.679                  9.231           44.106   42.336

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   42   41    4.0     25    2.39    57.317    55.261     1.005

LGA_LOCAL      RMSD:   2.386  Number of atoms:   25  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  10.016  Number of assigned atoms:   41 
Std_ASGN_ATOMS RMSD:   8.551  Standard rmsd on all 41 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.383851 * X  +   0.684148 * Y  +  -0.620161 * Z  +   6.148498
  Y_new =  -0.733303 * X  +  -0.182311 * Y  +  -0.655003 * Z  + -21.115049
  Z_new =  -0.561181 * X  +   0.706190 * Y  +   0.431707 * Z  +  45.446842 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.088561  0.595812  1.022095   [DEG:  -62.3700   34.1375   58.5618 ]
ZXZ: -0.758082  1.124411 -0.671477   [DEG:  -43.4349   64.4240  -38.4728 ]
 
# END of job
