
#######################################################
#                                                     #
#                        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   28 (  249),  selected   24 , name one
# Molecule2: number of CA atoms   26 (  234),  selected   24 , 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       8_F - 29_F        4.64     5.70
  LCS_AVERAGE:     84.29

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      11_F - 22_F        1.67     8.47
  LONGEST_CONTINUOUS_SEGMENT:    12      20_F - 31_F        1.73    16.82
  LCS_AVERAGE:     42.15

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11      12_F - 22_F        0.91     8.61
  LCS_AVERAGE:     36.22

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   24
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   22      0    3    3    3    3   10   13   15   15   17   19   19   20   21   22   22   22   23   24   24 
LCS_GDT     Q     9_D     Q     9_F      4    4   22      3    3    5    5    7    9   13   15   15   17   19   19   20   21   22   22   22   23   24   24 
LCS_GDT     K    10_D     K    10_F      4    4   22      3    3    5    5    7    7    8   11   13   15   16   16   20   21   22   22   22   23   24   24 
LCS_GDT     L    11_D     L    11_F      4   12   22      3    3    5    5   10   11   13   15   15   17   19   19   20   21   22   22   22   23   24   24 
LCS_GDT     N    12_D     N    12_F     11   12   22      3    9   11   11   12   12   13   15   15   17   19   19   20   21   22   22   22   23   24   24 
LCS_GDT     S    13_D     S    13_F     11   12   22      6    9   11   11   12   12   13   15   15   17   19   19   20   21   22   22   22   23   24   24 
LCS_GDT     W    14_D     W    14_F     11   12   22      6    9   11   11   12   12   13   15   15   17   19   19   20   21   22   22   22   23   24   24 
LCS_GDT     D    15_D     D    15_F     11   12   22      6    9   11   11   12   12   13   15   15   17   19   19   20   21   22   22   22   23   24   24 
LCS_GDT     V    16_D     V    16_F     11   12   22      6    9   11   11   12   12   13   15   15   17   19   19   20   21   22   22   22   23   24   24 
LCS_GDT     F    17_D     F    17_F     11   12   22      4    9   11   11   12   12   13   15   15   17   19   19   20   21   22   22   22   23   24   24 
LCS_GDT     G    18_D     G    18_F     11   12   22      6    9   11   11   12   12   13   15   15   17   19   19   20   21   22   22   22   23   24   24 
LCS_GDT     N    19_D     N    19_F     11   12   22      4    9   11   11   12   12   13   15   15   17   19   19   20   21   22   22   22   23   24   24 
LCS_GDT     W    20_D     W    20_F     11   12   22      3    9   11   11   12   12   13   15   15   17   19   19   20   21   22   22   22   23   24   24 
LCS_GDT     F    21_D     F    21_F     11   12   22      6    9   11   11   12   12   13   15   15   17   19   19   20   21   22   22   22   23   24   24 
LCS_GDT     D    22_D     D    22_F     11   12   22      4   10   11   11   12   12   13   15   15   17   19   19   20   21   22   22   22   23   24   24 
LCS_GDT     L    23_D     L    23_F     10   12   22      3   10   10   11   11   11   12   13   15   17   19   19   20   21   22   22   22   23   24   24 
LCS_GDT     A    24_D     A    24_F     10   12   22      4   10   10   11   11   11   12   12   13   14   15   17   20   21   22   22   22   23   24   24 
LCS_GDT     S    25_D     S    25_F     10   12   22      3   10   10   11   12   12   13   15   15   17   19   19   20   21   22   22   22   23   24   24 
LCS_GDT     W    26_D     W    26_F     10   12   22      5   10   10   11   11   11   12   12   15   17   19   19   20   21   22   22   22   23   24   24 
LCS_GDT     I    27_D     I    27_F     10   12   22      5   10   10   11   11   11   12   12   13   13   16   18   19   20   22   22   22   23   24   24 
LCS_GDT     K    28_D     K    28_F     10   12   22      4   10   10   11   11   11   12   13   14   16   19   19   20   21   22   22   22   23   24   24 
LCS_GDT     Y    29_D     Y    29_F     10   12   22      5   10   10   11   11   11   12   12   15   17   19   19   19   21   22   22   22   23   24   24 
LCS_GDT     I    30_D     I    30_F     10   12   21      5   10   10   11   11   11   12   12   13   13   14   16   16   17   20   20   20   23   24   24 
LCS_GDT     Q    31_D     Q    31_F     10   12   21      5   10   10   11   11   11   12   12   13   13   14   16   16   16   20   20   20   21   24   24 
LCS_AVERAGE  LCS_A:  54.22  (  36.22   42.15   84.29 )

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      6     10     11     11     12     12     13     15     15     17     19     19     20     21     22     22     22     23     24     24 
GDT PERCENT_AT  23.08  38.46  42.31  42.31  46.15  46.15  50.00  57.69  57.69  65.38  73.08  73.08  76.92  80.77  84.62  84.62  84.62  88.46  92.31  92.31
GDT RMS_LOCAL    0.33   0.61   0.91   0.91   1.25   1.25   1.84   2.50   2.50   3.37   3.86   3.86   4.21   4.34   4.64   4.64   4.64   5.07   5.45   5.45
GDT RMS_ALL_AT   8.70  16.77   8.61   8.61   7.96   7.96   7.73   7.79   7.79   6.40   5.91   5.91   6.22   5.90   5.70   5.70   5.70   5.51   5.45   5.45

# Checking swapping
#   possible swapping detected:  F    17_D      F    17_F
#   possible swapping detected:  F    21_D      F    21_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     3.534     0    0.252   1.474     6.831   37.262   33.393
LGA    Q     9_D      Q     9_F     4.321     0    0.634   1.605     7.082   27.976   33.810
LGA    K    10_D      K    10_F     6.774     0    0.029   0.504    17.613   24.405   11.005
LGA    L    11_D      L    11_F     3.334     0    0.598   0.599     9.528   56.190   33.214
LGA    N    12_D      N    12_F     3.328     0    0.586   0.574     9.556   61.190   35.833
LGA    S    13_D      S    13_F     2.262     0    0.040   0.112     2.603   62.857   62.222
LGA    W    14_D      W    14_F     2.759     0    0.035   1.618    10.258   62.976   36.224
LGA    D    15_D      D    15_F     1.784     0    0.021   0.133     3.736   77.381   66.488
LGA    V    16_D      V    16_F     0.552     0    0.088   0.074     1.020   88.214   93.265
LGA    F    17_D      F    17_F     0.660     0    0.023   1.197     5.992   88.214   66.234
LGA    G    18_D      G    18_F     1.159     0    0.129   0.129     1.247   83.690   83.690
LGA    N    19_D      N    19_F     1.517     0    0.219   0.979     4.002   71.071   62.679
LGA    W    20_D      W    20_F     0.894     0    0.031   0.081     2.879   85.952   73.946
LGA    F    21_D      F    21_F     2.283     0    0.704   1.199     5.039   63.452   54.242
LGA    D    22_D      D    22_F     1.203     0    0.549   1.364     5.399   64.048   51.726
LGA    L    23_D      L    23_F     7.903     0    0.027   0.858    14.562    9.048    4.583
LGA    A    24_D      A    24_F     9.234     0    0.096   0.100    10.239    5.238    4.190
LGA    S    25_D      S    25_F     3.511     0    0.176   0.537     5.070   33.095   45.000
LGA    W    26_D      W    26_F     8.882     0    0.192   1.106    17.482    5.000    1.429
LGA    I    27_D      I    27_F    13.341     0    0.033   0.695    16.724    0.000    0.000
LGA    K    28_D      K    28_F    10.397     0    0.099   0.585    11.764    0.000    1.746
LGA    Y    29_D      Y    29_F    10.571     0    0.062   1.273    17.857    0.119    0.040
LGA    I    30_D      I    30_F    17.668     0    0.173   1.602    20.578    0.000    0.000
LGA    Q    31_D      Q    31_F    19.551     0    0.259   1.223    26.058    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       24      96     96  100.00     212    212  100.00                26
SUMMARY(RMSD_GDC):     5.446          5.192                  7.292           38.745   32.883

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   28   26    4.0     15    2.50    55.769    52.676     0.578

LGA_LOCAL      RMSD:   2.496  Number of atoms:   15  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   7.795  Number of assigned atoms:   24 
Std_ASGN_ATOMS RMSD:   5.446  Standard rmsd on all 24 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.363170 * X  +   0.099858 * Y  +   0.926356 * Z  +  30.163593
  Y_new =  -0.881575 * X  +   0.284955 * Y  +  -0.376332 * Z  + -55.356079
  Z_new =  -0.301550 * X  +  -0.953325 * Y  +  -0.015455 * Z  + -20.127058 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.961567  0.306318 -1.587006   [DEG: -112.3895   17.5507  -90.9288 ]
ZXZ:  1.184914  1.586252 -2.835237   [DEG:   67.8906   90.8855 -162.4471 ]
 
# END of job
