
#######################################################
#                                                     #
#                        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        4.63     7.02
  LCS_AVERAGE:     83.58

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13      21_F - 33_F        1.65    11.75
  LCS_AVERAGE:     44.38

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      22_F - 33_F        0.46    12.29
  LCS_AVERAGE:     39.35

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    4   12   15   17   17   18   19   20   21   23   24   25   26   26 
LCS_GDT     Q     9_D     Q     9_F      3    4   20      3    3    5    5    5   10   13   13   15   17   17   18   19   20   23   23   24   25   26   26 
LCS_GDT     K    10_D     K    10_F      3    4   20      3    4    5    5    5    5    8   11   12   14   15   15   17   18   20   20   23   25   26   26 
LCS_GDT     L    11_D     L    11_F      3   12   21      3    4    5    6   10   11   13   13   15   17   17   18   19   20   23   23   24   25   26   26 
LCS_GDT     N    12_D     N    12_F     11   12   22      7    8   10   11   11   11   13   13   15   17   18   19   20   21   23   23   24   25   26   26 
LCS_GDT     S    13_D     S    13_F     11   12   22      7    8   10   11   11   11   13   13   15   17   18   19   20   21   23   23   24   25   26   26 
LCS_GDT     W    14_D     W    14_F     11   12   22      7    8   10   11   11   11   13   13   15   17   18   18   19   21   23   23   24   25   26   26 
LCS_GDT     D    15_D     D    15_F     11   12   22      7    8   10   11   11   11   13   13   15   17   18   19   20   21   23   23   24   25   26   26 
LCS_GDT     V    16_D     V    16_F     11   12   22      7    8   10   11   11   14   14   15   16   17   18   19   20   21   23   23   24   25   26   26 
LCS_GDT     F    17_D     F    17_F     11   12   22      7    8   10   11   11   11   13   13   15   17   18   19   20   21   23   23   24   25   26   26 
LCS_GDT     G    18_D     G    18_F     11   12   22      7    8   10   11   11   11   13   15   16   17   18   19   20   21   23   23   24   25   26   26 
LCS_GDT     N    19_D     N    19_F     11   12   22      4    8   12   13   13   14   14   15   16   17   17   19   20   21   23   23   24   25   26   26 
LCS_GDT     W    20_D     W    20_F     11   12   22      3    8   10   11   11   11   13   13   15   17   17   18   19   20   21   23   24   25   26   26 
LCS_GDT     F    21_D     F    21_F     11   13   22      3    4   10   11   11   12   14   15   16   17   18   19   20   21   23   23   24   25   26   26 
LCS_GDT     D    22_D     D    22_F     12   13   22     10   12   12   13   13   14   14   15   16   17   17   18   20   21   23   23   24   25   26   26 
LCS_GDT     L    23_D     L    23_F     12   13   22     10   12   12   13   13   14   14   15   16   17   18   19   20   21   23   23   24   25   26   26 
LCS_GDT     A    24_D     A    24_F     12   13   22     10   12   12   13   13   14   14   15   16   17   18   19   20   21   23   23   24   25   26   26 
LCS_GDT     S    25_D     S    25_F     12   13   22     10   12   12   13   13   14   14   15   16   17   18   19   20   21   23   23   24   25   26   26 
LCS_GDT     W    26_D     W    26_F     12   13   22     10   12   12   13   13   14   14   15   16   17   18   19   20   21   23   23   24   25   26   26 
LCS_GDT     I    27_D     I    27_F     12   13   22     10   12   12   13   13   14   14   15   16   17   18   19   20   21   23   23   24   25   26   26 
LCS_GDT     K    28_D     K    28_F     12   13   22     10   12   12   13   13   14   14   15   16   17   18   19   20   21   23   23   24   25   26   26 
LCS_GDT     Y    29_D     Y    29_F     12   13   22     10   12   12   13   13   14   14   15   16   17   18   19   20   21   23   23   24   25   26   26 
LCS_GDT     I    30_D     I    30_F     12   13   22     10   12   12   13   13   14   14   15   16   17   18   19   20   21   23   23   24   25   26   26 
LCS_GDT     Q    31_D     Q    31_F     12   13   22     10   12   12   13   13   14   14   15   16   16   18   19   20   21   23   23   24   25   26   26 
LCS_GDT     R    32_D     R    32_F     12   13   22     10   12   12   13   13   14   14   15   16   17   18   19   20   21   23   23   24   25   26   26 
LCS_GDT     R    33_D     R    33_F     12   13   22      3   12   12   13   13   14   14   15   16   17   18   19   20   21   23   23   24   25   26   26 
LCS_AVERAGE  LCS_A:  55.77  (  39.35   44.38   83.58 )

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     12     12     13     13     14     14     15     16     17     18     19     20     21     23     23     24     25     26     26 
GDT PERCENT_AT  38.46  46.15  46.15  50.00  50.00  53.85  53.85  57.69  61.54  65.38  69.23  73.08  76.92  80.77  88.46  88.46  92.31  96.15 100.00 100.00
GDT RMS_LOCAL    0.30   0.46   0.46   0.89   0.89   1.76   1.76   2.13   2.59   3.74   3.84   3.97   4.12   4.40   5.07   5.07   5.36   5.56   5.80   5.80
GDT RMS_ALL_AT  12.37  12.29  12.29  11.39  11.39  10.06  10.06  10.13   9.39   6.79   6.96   7.08   7.21   6.94   6.10   6.10   5.86   5.84   5.80   5.80

# Checking swapping
#   possible swapping detected:  F    17_D      F    17_F
#   possible swapping detected:  D    22_D      D    22_F
#   possible swapping detected:  Y    29_D      Y    29_F

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    L     8_D      L     8_F    25.805     0    0.281   0.901    28.015    0.000    0.000
LGA    Q     9_D      Q     9_F    19.970     0    0.577   0.593    22.329    0.000    0.000
LGA    K    10_D      K    10_F    20.586     0    0.044   0.757    27.423    0.000    0.000
LGA    L    11_D      L    11_F    16.934     0    0.608   0.628    18.340    0.000    0.000
LGA    N    12_D      N    12_F    13.338     0    0.565   0.965    14.647    0.119    0.060
LGA    S    13_D      S    13_F    12.523     0    0.032   0.076    14.783    0.000    0.000
LGA    W    14_D      W    14_F    14.686     0    0.071   0.382    22.868    0.000    0.000
LGA    D    15_D      D    15_F    10.182     0    0.056   0.133    15.291    6.786    3.393
LGA    V    16_D      V    16_F     4.381     0    0.047   0.129     6.524   28.452   31.429
LGA    F    17_D      F    17_F     9.191     0    0.029   1.444    16.657    5.714    2.078
LGA    G    18_D      G    18_F     6.851     0    0.133   0.133     7.628   28.452   28.452
LGA    N    19_D      N    19_F     1.416     0    0.266   1.110     7.080   56.786   43.333
LGA    W    20_D      W    20_F     6.442     0    0.110   1.192    16.876   20.595    6.088
LGA    F    21_D      F    21_F     4.418     0    0.570   1.086    11.106   45.833   21.082
LGA    D    22_D      D    22_F     2.811     0    0.566   1.352     7.646   64.881   39.524
LGA    L    23_D      L    23_F     2.142     0    0.105   0.760     2.961   68.810   66.905
LGA    A    24_D      A    24_F     1.816     0    0.041   0.051     1.965   75.000   74.571
LGA    S    25_D      S    25_F     1.737     0    0.127   0.122     2.712   79.405   73.254
LGA    W    26_D      W    26_F     1.309     0    0.042   1.654     7.214   85.952   58.197
LGA    I    27_D      I    27_F     0.543     0    0.028   1.082     2.326   95.238   83.214
LGA    K    28_D      K    28_F     0.501     0    0.063   0.952     6.336   95.238   69.683
LGA    Y    29_D      Y    29_F     0.212     0    0.000   0.207     1.058   97.619   95.278
LGA    I    30_D      I    30_F     0.819     0    0.070   0.746     2.744   90.595   82.976
LGA    Q    31_D      Q    31_F     1.571     0    0.065   1.292     6.651   75.000   58.360
LGA    R    32_D      R    32_F     1.332     0    0.510   0.570     2.570   75.357   74.632
LGA    R    33_D      R    33_F     1.194     0    0.199   1.312     9.778   71.071   38.182

# 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):     5.799          5.628                  7.279           44.881   36.565

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   26    4.0     15    2.13    60.577    56.000     0.672

LGA_LOCAL      RMSD:   2.132  Number of atoms:   15  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  10.134  Number of assigned atoms:   26 
Std_ASGN_ATOMS RMSD:   5.799  Standard rmsd on all 26 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.891216 * X  +   0.022572 * Y  +  -0.453018 * Z  + -95.863228
  Y_new =   0.374446 * X  +  -0.600264 * Y  +   0.706734 * Z  + -144.789062
  Z_new =  -0.255978 * X  +  -0.799483 * Y  +  -0.543417 * Z  +  35.919399 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.397757  0.258859 -2.167775   [DEG:   22.7898   14.8315 -124.2044 ]
ZXZ: -2.571569  2.145299 -2.831727   [DEG: -147.3401  122.9166 -162.2460 ]
 
# END of job
