
#######################################################
#                                                     #
#                        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:    27       2_B - 28_B        4.86    15.90
  LONGEST_CONTINUOUS_SEGMENT:    27       3_B - 29_B        4.66    14.70
  LONGEST_CONTINUOUS_SEGMENT:    27       4_B - 30_B        4.84    13.90
  LONGEST_CONTINUOUS_SEGMENT:    27       5_B - 31_B        4.83    13.14
  LCS_AVERAGE:     62.58

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20       6_B - 25_B        1.91    14.83
  LONGEST_CONTINUOUS_SEGMENT:    20       7_B - 26_B        1.80    14.30
  LCS_AVERAGE:     38.43

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16       7_B - 22_B        0.97    15.29
  LONGEST_CONTINUOUS_SEGMENT:    16       8_B - 23_B        0.77    15.34
  LCS_AVERAGE:     26.41

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   27      4    4    4    5    5    6    9   11   11   13   15   16   19   20   21   22   23   24   24   25 
LCS_GDT     S     3_B     S     3_B      4    7   27      4    4    4    6   10   14   16   18   20   21   22   23   23   24   24   25   26   26   27   27 
LCS_GDT     Q     4_B     Q     4_B      4    7   27      4    4    4    5   10   14   16   18   20   21   22   23   23   24   25   25   26   26   27   27 
LCS_GDT     R     5_B     R     5_B      5   19   27      4    5    5   10   12   15   17   18   20   21   22   23   23   24   25   25   26   26   27   27 
LCS_GDT     L     6_B     L     6_B      5   20   27      4    7   10   13   17   17   19   19   20   21   22   23   23   24   25   25   26   26   27   27 
LCS_GDT     F     7_B     F     7_B     16   20   27      4    5   11   15   17   18   19   20   20   21   22   23   23   24   25   25   26   26   27   27 
LCS_GDT     V     8_B     V     8_B     16   20   27      5    5   15   16   17   18   19   20   20   21   22   23   23   24   25   25   26   26   27   27 
LCS_GDT     L     9_B     L     9_B     16   20   27     10   14   15   16   17   18   19   20   20   21   22   23   23   24   25   25   26   26   27   27 
LCS_GDT     D    10_B     D    10_B     16   20   27      7   14   15   16   17   18   19   20   20   21   22   23   23   24   25   25   26   26   27   27 
LCS_GDT     N    11_B     N    11_B     16   20   27     10   14   15   16   17   18   19   20   20   21   22   23   23   24   25   25   26   26   27   27 
LCS_GDT     E    12_B     E    12_B     16   20   27      9   14   15   16   17   18   19   20   20   21   22   23   23   24   25   25   26   26   27   27 
LCS_GDT     R    13_B     R    13_B     16   20   27     10   14   15   16   17   18   19   20   20   21   22   23   23   24   25   25   26   26   27   27 
LCS_GDT     Y    14_B     Y    14_B     16   20   27     10   14   15   16   17   18   19   20   20   21   22   23   23   24   25   25   26   26   27   27 
LCS_GDT     D    15_B     D    15_B     16   20   27     10   14   15   16   17   18   19   20   20   21   22   23   23   24   25   25   26   26   27   27 
LCS_GDT     S    16_B     S    16_B     16   20   27     10   14   15   16   17   18   19   20   20   21   22   23   23   24   25   25   26   26   27   27 
LCS_GDT     F    17_B     F    17_B     16   20   27     10   14   15   16   17   18   19   20   20   21   22   23   23   24   25   25   26   26   27   27 
LCS_GDT     I    18_B     I    18_B     16   20   27     10   14   15   16   17   18   19   20   20   21   22   23   23   24   25   25   26   26   27   27 
LCS_GDT     T    19_B     T    19_B     16   20   27     10   14   15   16   17   18   19   20   20   21   22   23   23   24   25   25   26   26   27   27 
LCS_GDT     Q    20_B     Q    20_B     16   20   27     10   14   15   16   17   18   19   20   20   21   22   23   23   24   25   25   26   26   27   27 
LCS_GDT     L    21_B     L    21_B     16   20   27     10   14   15   16   17   18   19   20   20   21   22   23   23   24   25   25   26   26   27   27 
LCS_GDT     E    22_B     E    22_B     16   20   27     10   14   15   16   17   18   19   20   20   21   22   23   23   24   25   25   26   26   27   27 
LCS_GDT     A    23_B     A    23_B     16   20   27      4   10   15   16   17   18   19   20   20   21   22   23   23   24   25   25   26   26   27   27 
LCS_GDT     P    24_B     P    24_B      4   20   27      3    4    4   11   16   18   19   20   20   21   21   22   23   24   25   25   26   26   27   27 
LCS_GDT     V    25_B     V    25_B      4   20   27      3    4    6   14   17   18   19   20   20   21   22   23   23   24   25   25   26   26   27   27 
LCS_GDT     Q    26_B     Q    26_B      3   20   27      3    7   13   16   16   18   19   20   20   21   22   23   23   24   25   25   26   26   27   27 
LCS_GDT     N    27_B     N    27_B     11   18   27      7   11   11   11   11   11   15   18   20   20   21   22   22   24   25   25   26   26   27   27 
LCS_GDT     A    28_B     A    28_B     11   13   27      7   11   11   11   11   11   15   17   19   20   21   22   22   23   25   25   26   26   27   27 
LCS_GDT     E    29_B     E    29_B     11   13   27      7   11   11   11   11   11   13   14   16   16   18   19   20   22   23   24   26   26   27   27 
LCS_GDT     G    30_B     G    30_B     11   13   27      7   11   11   11   11   11   13   14   16   16   18   19   20   20   21   22   24   25   26   27 
LCS_GDT     R    31_B     R    31_B     11   13   27      7   11   11   11   11   11   13   14   16   17   18   19   21   22   23   24   26   26   27   27 
LCS_GDT     E    32_B     E    32_B     11   13   25      7   11   11   11   11   11   13   14   16   16   18   19   20   20   21   22   23   25   26   27 
LCS_GDT     R    33_B     R    33_B     11   13   22      7   11   11   11   11   11   13   14   16   16   18   19   20   20   21   22   22   24   25   26 
LCS_GDT     L    34_B     L    34_B     11   13   22      7   11   11   11   11   11   13   14   16   16   18   19   20   20   21   22   22   24   25   26 
LCS_GDT     M    35_B     M    35_B     11   13   22      7   11   11   11   11   11   13   14   16   16   18   19   20   20   21   22   22   24   25   26 
LCS_GDT     A    36_B     A    36_B     11   13   22      6   11   11   11   11   11   13   14   16   16   18   19   20   20   21   22   22   24   25   26 
LCS_GDT     V    37_B     V    37_B     11   13   22      6   11   11   11   11   11   13   14   16   16   18   19   20   20   21   22   22   23   25   26 
LCS_GDT     K    38_B     K    38_B      4   13   22      3    4    4    5    7    9   13   14   16   16   18   18   20   20   21   22   22   23   25   26 
LCS_GDT     P    39_B     P    39_B      4   13   22      3    4    4    5    5   10   13   14   16   16   18   19   20   20   21   22   22   24   25   26 
LCS_GDT     E    40_B     E    40_B      4    5   22      3    4    4    5    5    6   10   14   15   15   16   18   18   20   21   22   22   24   25   26 
LCS_GDT     W    41_B     W    41_B      3    5   22      3    3    3    4    5    5    8    8    9   13   14   16   16   17   18   19   22   24   25   26 
LCS_GDT     K    42_B     K    42_B      3    4   19      0    3    3    4    4    4    5    6    7    7    7   10   10   12   15   15   18   18   18   18 
LCS_AVERAGE  LCS_A:  42.47  (  26.41   38.43   62.58 )

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     10     14     15     16     17     18     19     20     20     21     22     23     23     24     25     25     26     26     27     27 
GDT PERCENT_AT  24.39  34.15  36.59  39.02  41.46  43.90  46.34  48.78  48.78  51.22  53.66  56.10  56.10  58.54  60.98  60.98  63.41  63.41  65.85  65.85
GDT RMS_LOCAL    0.34   0.49   0.61   0.77   1.02   1.28   1.53   1.80   1.80   2.05   2.97   3.14   3.02   3.38   3.77   3.68   4.13   4.13   4.76   4.76
GDT RMS_ALL_AT  15.10  15.14  15.54  15.34  15.16  14.93  15.17  14.30  14.30  14.57  16.43  16.13  15.30  15.89  14.59  15.67  15.13  15.13  13.75  13.75

# Checking swapping
#   possible swapping detected:  F     7_B      F     7_B
#   possible swapping detected:  D    10_B      D    10_B
#   possible swapping detected:  E    12_B      E    12_B
#   possible swapping detected:  F    17_B      F    17_B
#   possible swapping detected:  E    22_B      E    22_B
#   possible swapping detected:  E    32_B      E    32_B
#   possible swapping detected:  E    40_B      E    40_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     2_B      A     2_B    20.554     0    0.242   0.344    21.952    0.000    0.000
LGA    S     3_B      S     3_B    13.489     0    0.258   0.643    16.267    0.000    0.000
LGA    Q     4_B      Q     4_B    11.728     0    0.122   1.216    16.452    2.143    0.952
LGA    R     5_B      R     5_B     8.157     0    0.670   1.291    18.063   14.881    5.455
LGA    L     6_B      L     6_B     5.182     0    0.188   1.281    10.303   18.929   12.381
LGA    F     7_B      F     7_B     3.174     0    0.084   0.098    10.076   63.571   31.299
LGA    V     8_B      V     8_B     3.047     0    0.096   1.142     5.931   51.786   39.456
LGA    L     9_B      L     9_B     0.943     0    0.022   0.873     2.922   85.952   79.702
LGA    D    10_B      D    10_B     1.001     0    0.097   0.435     1.472   88.214   84.821
LGA    N    11_B      N    11_B     0.509     0    0.072   1.138     3.314   95.238   81.726
LGA    E    12_B      E    12_B     0.649     0    0.071   1.155     3.093   92.857   83.069
LGA    R    13_B      R    13_B     0.337     0    0.054   1.210     4.803   95.238   75.628
LGA    Y    14_B      Y    14_B     0.581     0    0.013   0.267     1.708   90.476   86.825
LGA    D    15_B      D    15_B     0.495     0    0.039   0.367     1.193   95.238   92.917
LGA    S    16_B      S    16_B     0.994     0    0.026   0.798     2.452   88.214   83.175
LGA    F    17_B      F    17_B     1.080     0    0.051   0.275     2.586   85.952   74.069
LGA    I    18_B      I    18_B     0.458     0    0.030   1.818     4.360   97.619   79.107
LGA    T    19_B      T    19_B     0.790     0    0.043   0.207     1.170   90.595   87.959
LGA    Q    20_B      Q    20_B     1.295     0    0.054   1.062     5.165   81.429   66.614
LGA    L    21_B      L    21_B     0.825     0    0.044   1.340     3.261   90.476   77.143
LGA    E    22_B      E    22_B     0.727     0    0.229   1.133     3.267   88.214   76.402
LGA    A    23_B      A    23_B     1.374     0    0.273   0.360     2.524   83.810   78.476
LGA    P    24_B      P    24_B     4.023     0    0.203   0.499     6.211   54.167   40.340
LGA    V    25_B      V    25_B     2.955     0    0.565   1.479     7.455   61.190   40.884
LGA    Q    26_B      Q    26_B     3.069     0    0.102   0.206     6.500   45.833   37.937
LGA    N    27_B      N    27_B     7.423     0    0.410   1.428     9.883   10.833    6.964
LGA    A    28_B      A    28_B     8.975     0    0.077   0.074    11.868    2.500    2.095
LGA    E    29_B      E    29_B    11.895     0    0.056   1.216    15.104    0.000    0.000
LGA    G    30_B      G    30_B    12.919     0    0.106   0.106    14.176    0.000    0.000
LGA    R    31_B      R    31_B    11.929     0    0.053   1.385    15.302    0.000    1.515
LGA    E    32_B      E    32_B    17.083     0    0.089   1.167    20.392    0.000    0.000
LGA    R    33_B      R    33_B    19.630     0    0.038   1.273    22.081    0.000    0.000
LGA    L    34_B      L    34_B    18.624     0    0.041   1.392    21.174    0.000    0.000
LGA    M    35_B      M    35_B    20.502     0    0.147   0.694    24.744    0.000    0.000
LGA    A    36_B      A    36_B    25.967     0    0.199   0.200    29.068    0.000    0.000
LGA    V    37_B      V    37_B    27.240     0    0.593   0.999    28.960    0.000    0.000
LGA    K    38_B      K    38_B    29.260     4    0.035   0.068    29.855    0.000    0.000
LGA    P    39_B      P    39_B    28.925     0    0.645   0.594    29.751    0.000    0.000
LGA    E    40_B      E    40_B    30.505     0    0.428   0.782    37.048    0.000    0.000
LGA    W    41_B      W    41_B    25.248     0    0.567   1.184    27.129    0.000    0.000
LGA    K    42_B      K    42_B    27.869     0    0.447   1.298    33.591    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):    11.113         11.003                 11.157           40.862   34.803

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   42   41    4.0     20    1.80    45.732    44.438     1.053

LGA_LOCAL      RMSD:   1.799  Number of atoms:   20  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  14.300  Number of assigned atoms:   41 
Std_ASGN_ATOMS RMSD:  11.113  Standard rmsd on all 41 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.082046 * X  +   0.695091 * Y  +   0.714225 * Z  +  20.250135
  Y_new =  -0.649025 * X  +   0.506586 * Y  +  -0.567571 * Z  +  14.361160
  Z_new =  -0.756330 * X  +  -0.510117 * Y  +   0.409568 * Z  +  62.323059 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.696544  0.857685 -0.894296   [DEG:  -97.2048   49.1417  -51.2394 ]
ZXZ:  0.899315  1.148816 -2.164177   [DEG:   51.5270   65.8223 -123.9982 ]
 
# END of job
