
#######################################################
#                                                     #
#                        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   34 (  315),  selected   26 , name one
# Molecule2: number of CA atoms   26 (  234),  selected   26 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:D  -ch2:F  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25       9_F - 33_F        4.99     5.23
  LCS_AVERAGE:     95.86

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      11_F - 22_F        1.61     9.38
  LONGEST_CONTINUOUS_SEGMENT:    12      22_F - 33_F        1.12    16.52
  LCS_AVERAGE:     42.46

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11      22_F - 32_F        0.76    16.17
  LCS_AVERAGE:     36.24

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   26
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     L     8_D     L     8_F      3    3   23      0    3    3    3    3    3    5    8   14   18   18   19   22   23   24   25   26   26   26   26 
LCS_GDT     Q     9_D     Q     9_F      4    4   25      3    3    5    5    6    8   11   13   14   18   18   20   22   23   24   25   26   26   26   26 
LCS_GDT     K    10_D     K    10_F      4    4   25      3    4    5    5    6    7    9   10   12   15   19   20   22   23   24   25   26   26   26   26 
LCS_GDT     L    11_D     L    11_F      4   12   25      3    4    5    8    9   11   12   14   16   18   19   20   22   23   24   25   26   26   26   26 
LCS_GDT     N    12_D     N    12_F     10   12   25      4    8   10   11   11   11   12   14   16   18   19   20   22   23   24   25   26   26   26   26 
LCS_GDT     S    13_D     S    13_F     10   12   25      6    8   10   11   11   11   12   14   16   18   19   20   22   23   24   25   26   26   26   26 
LCS_GDT     W    14_D     W    14_F     10   12   25      6    8   10   11   11   11   12   14   16   18   19   20   22   23   24   25   26   26   26   26 
LCS_GDT     D    15_D     D    15_F     10   12   25      6    8   10   11   11   11   12   14   16   18   19   20   22   23   24   25   26   26   26   26 
LCS_GDT     V    16_D     V    16_F     10   12   25      6    8   10   11   11   11   12   14   16   18   19   20   22   23   24   25   26   26   26   26 
LCS_GDT     F    17_D     F    17_F     10   12   25      6    8   10   11   11   11   12   14   16   18   19   20   22   23   24   25   26   26   26   26 
LCS_GDT     G    18_D     G    18_F     10   12   25      6    8   10   11   11   11   12   14   16   18   19   20   22   23   24   25   26   26   26   26 
LCS_GDT     N    19_D     N    19_F     10   12   25      6    8   10   11   11   11   13   14   16   18   19   20   22   23   24   25   26   26   26   26 
LCS_GDT     W    20_D     W    20_F     10   12   25      6    8   10   11   11   11   12   14   16   18   19   20   22   23   24   25   26   26   26   26 
LCS_GDT     F    21_D     F    21_F     10   12   25      3    3    9   11   11   11   12   14   16   18   18   19   21   23   24   25   26   26   26   26 
LCS_GDT     D    22_D     D    22_F     11   12   25      3    9   11   11   12   12   13   14   16   18   19   20   22   23   24   25   26   26   26   26 
LCS_GDT     L    23_D     L    23_F     11   12   25      5    9   11   11   12   12   13   14   16   18   19   20   22   23   24   25   26   26   26   26 
LCS_GDT     A    24_D     A    24_F     11   12   25      7    9   11   11   12   12   13   13   14   16   19   20   22   23   24   25   26   26   26   26 
LCS_GDT     S    25_D     S    25_F     11   12   25      7    9   11   11   12   12   13   14   16   18   19   20   22   23   24   25   26   26   26   26 
LCS_GDT     W    26_D     W    26_F     11   12   25      7    9   11   11   12   12   13   14   16   18   19   20   22   23   24   25   26   26   26   26 
LCS_GDT     I    27_D     I    27_F     11   12   25      7    9   11   11   12   12   13   13   14   16   19   20   21   23   24   25   26   26   26   26 
LCS_GDT     K    28_D     K    28_F     11   12   25      7    9   11   11   12   12   13   14   16   17   19   20   22   23   24   25   26   26   26   26 
LCS_GDT     Y    29_D     Y    29_F     11   12   25      7    9   11   11   12   12   13   14   16   18   19   20   22   23   24   25   26   26   26   26 
LCS_GDT     I    30_D     I    30_F     11   12   25      7    9   11   11   12   12   13   13   14   15   17   18   21   23   23   25   26   26   26   26 
LCS_GDT     Q    31_D     Q    31_F     11   12   25      3    9   11   11   12   12   13   13   14   15   17   18   21   23   23   25   26   26   26   26 
LCS_GDT     R    32_D     R    32_F     11   12   25      3    9   11   11   12   12   13   14   16   17   19   20   22   23   24   25   26   26   26   26 
LCS_GDT     R    33_D     R    33_F      9   12   25      3    3    7   10   12   12   13   14   16   17   19   20   22   23   24   25   26   26   26   26 
LCS_AVERAGE  LCS_A:  58.19  (  36.24   42.46   95.86 )

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      7      9     11     11     12     12     13     14     16     18     19     20     22     23     24     25     26     26     26     26 
GDT PERCENT_AT  26.92  34.62  42.31  42.31  46.15  46.15  50.00  53.85  61.54  69.23  73.08  76.92  84.62  88.46  92.31  96.15 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.22   0.42   0.76   0.76   1.12   1.12   1.83   2.73   2.99   3.59   3.79   3.88   4.43   4.48   4.75   4.97   5.17   5.17   5.17   5.17
GDT RMS_ALL_AT  16.03  15.38  16.17  16.17  16.52  16.52  14.87   7.03   6.53   6.75   5.38   5.58   5.32   5.76   5.27   5.20   5.17   5.17   5.17   5.17

# Checking swapping
#   possible swapping detected:  F    21_D      F    21_F

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    L     8_D      L     8_F     9.002     0    0.272   0.967    10.132    0.476    5.952
LGA    Q     9_D      Q     9_F    10.068     0    0.555   0.855    11.911    0.119    0.159
LGA    K    10_D      K    10_F    11.007     0    0.031   0.716    19.024    1.429    0.635
LGA    L    11_D      L    11_F     5.269     0    0.588   1.097     7.242   34.048   27.917
LGA    N    12_D      N    12_F     3.422     0    0.603   1.047     8.885   55.714   31.845
LGA    S    13_D      S    13_F     1.542     0    0.062   0.081     2.445   82.024   79.048
LGA    W    14_D      W    14_F     0.908     0    0.101   0.258     4.625   90.476   60.748
LGA    D    15_D      D    15_F     0.756     0    0.025   1.190     5.232   95.238   73.869
LGA    V    16_D      V    16_F     0.415     0    0.014   1.005     3.249   92.976   83.605
LGA    F    17_D      F    17_F     1.001     0    0.034   1.107     4.587   81.548   65.281
LGA    G    18_D      G    18_F     1.690     0    0.134   0.134     2.146   72.976   72.976
LGA    N    19_D      N    19_F     2.412     0    0.264   0.955     4.113   55.952   59.524
LGA    W    20_D      W    20_F     2.538     0    0.171   1.182     9.681   55.595   31.497
LGA    F    21_D      F    21_F     3.617     0    0.570   1.404     4.419   48.452   44.113
LGA    D    22_D      D    22_F     3.516     0    0.571   1.226     6.100   64.643   42.500
LGA    L    23_D      L    23_F     3.977     0    0.131   1.182     8.763   43.333   26.845
LGA    A    24_D      A    24_F     7.432     0    0.040   0.054     9.175   15.833   12.952
LGA    S    25_D      S    25_F     3.651     0    0.135   0.557     4.446   56.548   50.079
LGA    W    26_D      W    26_F     4.712     0    0.035   0.181    16.662   29.881    9.864
LGA    I    27_D      I    27_F    10.317     0    0.034   1.117    15.606    1.905    0.952
LGA    K    28_D      K    28_F     8.449     0    0.082   0.271    13.781    6.071    3.651
LGA    Y    29_D      Y    29_F     4.223     0    0.035   1.329    10.386   22.976   18.135
LGA    I    30_D      I    30_F    11.577     0    0.041   0.103    16.383    0.714    0.357
LGA    Q    31_D      Q    31_F    14.618     0    0.449   1.089    22.586    0.000    0.000
LGA    R    32_D      R    32_F    10.067     0    0.486   1.404    10.865    0.119    6.840
LGA    R    33_D      R    33_F    12.109     0    0.098   1.305    18.267    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       26     104    104  100.00     234    234  100.00                26
SUMMARY(RMSD_GDC):     5.169          4.912                  7.260           38.810   31.129

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   26    4.0     14    2.73    56.731    53.883     0.495

LGA_LOCAL      RMSD:   2.728  Number of atoms:   14  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   7.034  Number of assigned atoms:   26 
Std_ASGN_ATOMS RMSD:   5.169  Standard rmsd on all 26 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.295184 * X  +   0.041528 * Y  +   0.954538 * Z  +  84.131363
  Y_new =  -0.845721 * X  +   0.476198 * Y  +   0.240816 * Z  + -57.836796
  Z_new =  -0.444548 * X  +  -0.878357 * Y  +   0.175687 * Z  +   3.542954 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.234984  0.460669 -1.373384   [DEG:  -70.7594   26.3944  -78.6891 ]
ZXZ:  1.817924  1.394193 -2.673067   [DEG:  104.1594   79.8813 -153.1554 ]
 
# END of job
