
#######################################################
#                                                     #
#                        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:    22      12_F - 33_F        4.83     7.37
  LCS_AVERAGE:     83.43

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13      21_F - 33_F        1.70    12.78
  LCS_AVERAGE:     44.38

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      22_F - 33_F        0.56    13.31
  LCS_AVERAGE:     39.79

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   20      0    3    3    3    3    3   12   14   16   17   18   18   19   21   23   24   24   24   25   25 
LCS_GDT     Q     9_D     Q     9_F      4    4   20      3    3    5    6    8   10   12   14   16   17   18   18   19   21   23   24   24   24   25   25 
LCS_GDT     K    10_D     K    10_F      4    4   20      3    3    5    6    6    6    8   10   11   14   15   15   17   17   19   20   21   23   25   25 
LCS_GDT     L    11_D     L    11_F      4   12   20      3    3    5    6    8   11   12   14   16   17   18   18   19   21   23   24   24   24   25   25 
LCS_GDT     N    12_D     N    12_F     11   12   22      5    9   11   11   11   11   12   14   16   17   18   19   20   21   23   24   24   24   25   25 
LCS_GDT     S    13_D     S    13_F     11   12   22      5    9   11   11   11   11   12   14   16   17   18   19   20   21   23   24   24   24   25   25 
LCS_GDT     W    14_D     W    14_F     11   12   22      5    9   11   11   11   11   12   14   16   17   18   19   20   21   23   24   24   24   25   25 
LCS_GDT     D    15_D     D    15_F     11   12   22      5    9   11   11   11   11   12   14   16   17   18   19   20   21   23   24   24   24   25   25 
LCS_GDT     V    16_D     V    16_F     11   12   22      5    9   11   11   11   11   14   15   16   17   18   19   20   21   23   24   24   24   25   25 
LCS_GDT     F    17_D     F    17_F     11   12   22      5    9   11   11   11   11   12   14   16   17   18   19   20   21   23   24   24   24   25   25 
LCS_GDT     G    18_D     G    18_F     11   12   22      5    9   11   11   11   11   12   15   16   17   18   19   20   21   23   24   24   24   25   25 
LCS_GDT     N    19_D     N    19_F     11   12   22      5    9   11   12   13   13   14   15   16   17   18   19   20   21   23   24   24   24   25   25 
LCS_GDT     W    20_D     W    20_F     11   12   22      3    9   11   11   11   11   12   14   16   17   18   19   20   21   23   24   24   24   25   25 
LCS_GDT     F    21_D     F    21_F     11   13   22      3    6   11   11   11   12   14   15   16   17   18   19   20   21   23   24   24   24   25   25 
LCS_GDT     D    22_D     D    22_F     12   13   22      9   11   12   12   13   13   14   15   16   17   18   18   19   20   22   24   24   24   25   25 
LCS_GDT     L    23_D     L    23_F     12   13   22      9   11   12   12   13   13   14   15   16   17   18   19   20   21   23   24   24   24   25   25 
LCS_GDT     A    24_D     A    24_F     12   13   22      9   11   12   12   13   13   14   15   15   16   17   19   20   21   23   24   24   24   25   25 
LCS_GDT     S    25_D     S    25_F     12   13   22      9   11   12   12   13   13   14   15   16   17   18   19   20   21   23   24   24   24   25   25 
LCS_GDT     W    26_D     W    26_F     12   13   22      9   11   12   12   13   13   14   15   15   17   18   19   20   21   23   24   24   24   25   25 
LCS_GDT     I    27_D     I    27_F     12   13   22      9   11   12   12   13   13   14   15   15   16   17   19   20   21   23   24   24   24   25   25 
LCS_GDT     K    28_D     K    28_F     12   13   22      9   11   12   12   13   13   14   15   15   16   17   19   20   21   23   24   24   24   25   25 
LCS_GDT     Y    29_D     Y    29_F     12   13   22      9   11   12   12   13   13   14   15   15   16   18   19   20   21   23   24   24   24   25   25 
LCS_GDT     I    30_D     I    30_F     12   13   22      9   11   12   12   13   13   14   15   15   16   17   18   20   20   23   24   24   24   25   25 
LCS_GDT     Q    31_D     Q    31_F     12   13   22      7   11   12   12   13   13   14   15   15   16   17   18   19   19   22   22   22   24   24   25 
LCS_GDT     R    32_D     R    32_F     12   13   22      4   11   12   12   13   13   14   15   15   16   17   19   20   20   23   24   24   24   25   25 
LCS_GDT     R    33_D     R    33_F     12   13   22      3    7   12   12   13   13   14   15   15   16   17   19   20   21   23   24   24   24   25   25 
LCS_AVERAGE  LCS_A:  55.87  (  39.79   44.38   83.43 )

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      9     11     12     12     13     13     14     15     16     17     18     19     20     21     23     24     24     24     25     25 
GDT PERCENT_AT  34.62  42.31  46.15  46.15  50.00  50.00  53.85  57.69  61.54  65.38  69.23  73.08  76.92  80.77  88.46  92.31  92.31  92.31  96.15  96.15
GDT RMS_LOCAL    0.23   0.38   0.56   0.56   0.95   0.95   1.74   2.25   3.34   3.68   3.99   4.38   4.48   5.17   5.43   5.56   5.56   5.56   5.82   5.82
GDT RMS_ALL_AT  13.01  13.32  13.31  13.31  12.35  12.35  12.16  10.94   9.69   8.78   7.92   6.98   7.04   6.21   6.10   6.12   6.12   6.12   6.11   6.11

# Checking swapping
#   possible swapping detected:  F    17_D      F    17_F
#   possible swapping detected:  D    22_D      D    22_F

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    L     8_D      L     8_F    28.051     0    0.293   0.445    30.192    0.000    0.000
LGA    Q     9_D      Q     9_F    21.793     0    0.604   0.601    24.302    0.000    0.000
LGA    K    10_D      K    10_F    22.045     0    0.073   0.381    26.453    0.000    0.000
LGA    L    11_D      L    11_F    18.830     0    0.594   0.854    20.127    0.000    0.000
LGA    N    12_D      N    12_F    15.270     0    0.672   0.586    18.270    0.000    0.000
LGA    S    13_D      S    13_F    13.408     0    0.046   0.665    16.893    0.000    0.000
LGA    W    14_D      W    14_F    15.241     0    0.012   1.319    23.525    0.000    0.000
LGA    D    15_D      D    15_F    10.889     0    0.035   0.489    15.221    5.119    2.560
LGA    V    16_D      V    16_F     4.747     0    0.052   0.112     7.108   26.190   30.068
LGA    F    17_D      F    17_F     9.176     0    0.022   1.240    17.885    5.714    2.078
LGA    G    18_D      G    18_F     6.760     0    0.198   0.198     7.601   28.452   28.452
LGA    N    19_D      N    19_F     1.538     0    0.217   1.004     6.977   54.643   42.083
LGA    W    20_D      W    20_F     6.382     0    0.145   1.217    16.443   20.595    6.088
LGA    F    21_D      F    21_F     4.514     0    0.606   1.215    11.902   44.405   19.307
LGA    D    22_D      D    22_F     2.792     0    0.576   1.382     8.007   62.976   38.690
LGA    L    23_D      L    23_F     2.169     0    0.103   0.900     4.187   68.810   64.405
LGA    A    24_D      A    24_F     1.762     0    0.031   0.030     2.004   75.000   72.952
LGA    S    25_D      S    25_F     1.760     0    0.143   0.725     2.437   79.405   77.302
LGA    W    26_D      W    26_F     1.403     0    0.039   0.230     2.710   81.548   71.361
LGA    I    27_D      I    27_F     0.557     0    0.030   0.122     1.152   95.238   91.786
LGA    K    28_D      K    28_F     0.419     0    0.109   0.217     1.547   97.619   89.683
LGA    Y    29_D      Y    29_F     0.232     0    0.029   0.300     1.327   97.619   91.389
LGA    I    30_D      I    30_F     1.131     0    0.070   0.649     2.901   83.690   76.369
LGA    Q    31_D      Q    31_F     1.914     0    0.036   1.259     6.561   72.976   52.275
LGA    R    32_D      R    32_F     1.538     0    0.370   0.850     6.221   72.976   59.827
LGA    R    33_D      R    33_F     1.351     0    0.611   0.409     9.071   77.143   40.303

# 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):     6.071          5.895                  7.919           44.235   36.807

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   26    4.0     15    2.25    59.615    55.207     0.640

LGA_LOCAL      RMSD:   2.245  Number of atoms:   15  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  10.941  Number of assigned atoms:   26 
Std_ASGN_ATOMS RMSD:   6.071  Standard rmsd on all 26 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.033360 * X  +  -0.561873 * Y  +   0.826551 * Z  +  40.073597
  Y_new =  -0.885614 * X  +  -0.399922 * Y  +  -0.236115 * Z  + -68.517326
  Z_new =   0.463222 * X  +  -0.724128 * Y  +  -0.510944 * Z  +  -6.620655 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.533145 -0.481627 -2.185270   [DEG:  -87.8427  -27.5952 -125.2068 ]
ZXZ:  1.292544  2.107079  2.572495   [DEG:   74.0573  120.7267  147.3931 ]
 
# END of job
