
#######################################################
#                                                     #
#                        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:    26       8_F - 33_F        4.75     4.75
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13      21_F - 33_F        1.65     8.91
  LCS_AVERAGE:     44.38

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      22_F - 33_F        0.66     8.65
  LCS_AVERAGE:     36.83

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   26      0    3    3    3    3    4    4   11   15   16   18   21   24   24   25   26   26   26   26   26 
LCS_GDT     Q     9_D     Q     9_F      4    4   26      3    3    4    5    6   12   13   15   16   18   20   21   24   24   25   26   26   26   26   26 
LCS_GDT     K    10_D     K    10_F      4    4   26      3    4    4    5    6    6    7    9   12   13   15   15   20   23   25   26   26   26   26   26 
LCS_GDT     L    11_D     L    11_F      4   12   26      3    4    4    7    9   11   12   13   15   16   19   21   24   24   25   26   26   26   26   26 
LCS_GDT     N    12_D     N    12_F      9   12   26      4    8    8   11   11   12   14   16   17   19   20   21   24   24   25   26   26   26   26   26 
LCS_GDT     S    13_D     S    13_F      9   12   26      4    8    9   11   11   11   14   14   18   19   20   21   24   24   25   26   26   26   26   26 
LCS_GDT     W    14_D     W    14_F      9   12   26      4    8    9   11   11   11   12   13   15   16   19   21   24   24   25   26   26   26   26   26 
LCS_GDT     D    15_D     D    15_F      9   12   26      4    8    9   11   11   12   14   16   17   18   20   21   24   24   25   26   26   26   26   26 
LCS_GDT     V    16_D     V    16_F      9   12   26      6    9   11   14   14   14   14   16   18   19   20   21   24   24   25   26   26   26   26   26 
LCS_GDT     F    17_D     F    17_F      9   12   26      4    8    9   11   11   11   12   15   18   19   20   21   24   24   25   26   26   26   26   26 
LCS_GDT     G    18_D     G    18_F      9   12   26      4    8    9   11   11   11   14   15   18   19   20   21   24   24   25   26   26   26   26   26 
LCS_GDT     N    19_D     N    19_F      9   12   26      4    8    9   14   14   14   14   16   18   19   20   21   24   24   25   26   26   26   26   26 
LCS_GDT     W    20_D     W    20_F      9   12   26      4    8    9   11   11   11   14   14   16   16   17   20   21   21   24   26   26   26   26   26 
LCS_GDT     F    21_D     F    21_F      9   13   26      4    8    9   11   11   11   14   15   18   19   20   21   24   24   25   26   26   26   26   26 
LCS_GDT     D    22_D     D    22_F     12   13   26     10   11   12   14   14   14   14   16   18   19   20   21   24   24   25   26   26   26   26   26 
LCS_GDT     L    23_D     L    23_F     12   13   26     10   11   12   14   14   14   14   16   18   19   20   21   24   24   25   26   26   26   26   26 
LCS_GDT     A    24_D     A    24_F     12   13   26     10   11   12   14   14   14   14   16   18   19   20   21   24   24   25   26   26   26   26   26 
LCS_GDT     S    25_D     S    25_F     12   13   26     10   11   12   14   14   14   14   16   18   19   20   21   24   24   25   26   26   26   26   26 
LCS_GDT     W    26_D     W    26_F     12   13   26     10   11   12   14   14   14   14   16   18   19   20   21   24   24   25   26   26   26   26   26 
LCS_GDT     I    27_D     I    27_F     12   13   26     10   11   12   14   14   14   14   16   18   19   20   21   24   24   25   26   26   26   26   26 
LCS_GDT     K    28_D     K    28_F     12   13   26     10   11   12   14   14   14   14   16   18   19   20   21   24   24   25   26   26   26   26   26 
LCS_GDT     Y    29_D     Y    29_F     12   13   26     10   11   12   14   14   14   14   16   18   19   20   21   24   24   25   26   26   26   26   26 
LCS_GDT     I    30_D     I    30_F     12   13   26     10   11   12   14   14   14   14   16   18   19   20   21   24   24   25   26   26   26   26   26 
LCS_GDT     Q    31_D     Q    31_F     12   13   26     10   11   12   14   14   14   14   16   18   19   20   21   24   24   25   26   26   26   26   26 
LCS_GDT     R    32_D     R    32_F     12   13   26      6   11   12   14   14   14   14   16   18   19   20   21   24   24   25   26   26   26   26   26 
LCS_GDT     R    33_D     R    33_F     12   13   26      3    9   12   14   14   14   14   16   18   19   20   21   24   24   25   26   26   26   26   26 
LCS_AVERAGE  LCS_A:  60.40  (  36.83   44.38  100.00 )

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     11     12     14     14     14     14     16     18     19     20     21     24     24     25     26     26     26     26     26 
GDT PERCENT_AT  38.46  42.31  46.15  53.85  53.85  53.85  53.85  61.54  69.23  73.08  76.92  80.77  92.31  92.31  96.15 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.36   0.44   0.66   1.06   1.06   1.06   1.06   2.46   2.82   3.15   3.32   3.64   4.33   4.33   4.51   4.75   4.75   4.75   4.75   4.75
GDT RMS_ALL_AT   8.90   8.78   8.65   7.70   7.70   7.70   7.70   5.86   7.14   6.15   5.78   5.21   4.77   4.77   4.77   4.75   4.75   4.75   4.75   4.75

# Checking swapping
#   possible swapping detected:  D    15_D      D    15_F
#   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    13.214     0    0.269   1.521    15.110    0.000    0.000
LGA    Q     9_D      Q     9_F     7.837     0    0.552   1.571    10.038    2.262    7.566
LGA    K    10_D      K    10_F    11.067     0    0.078   0.957    15.930    0.119    0.053
LGA    L    11_D      L    11_F     8.829     0    0.601   1.231    12.824    5.119    2.917
LGA    N    12_D      N    12_F     4.786     0    0.583   1.514     6.208   39.167   34.107
LGA    S    13_D      S    13_F     7.049     0    0.018   0.699    10.598   12.143    8.175
LGA    W    14_D      W    14_F     9.486     0    0.078   1.629    15.852    6.071    1.735
LGA    D    15_D      D    15_F     4.860     0    0.046   0.881     9.669   46.548   26.786
LGA    V    16_D      V    16_F     2.884     0    0.035   1.094     6.322   50.476   41.973
LGA    F    17_D      F    17_F     8.118     0    0.053   1.373    17.071   10.833    3.939
LGA    G    18_D      G    18_F     5.199     0    0.148   0.148     5.726   42.381   42.381
LGA    N    19_D      N    19_F     2.937     0    0.195   0.909     7.753   44.524   31.369
LGA    W    20_D      W    20_F     9.064     0    0.199   1.530    18.437    5.357    1.531
LGA    F    21_D      F    21_F     6.599     0    0.596   1.283    11.862   25.238   10.476
LGA    D    22_D      D    22_F     3.023     0    0.557   1.351     7.448   53.810   35.238
LGA    L    23_D      L    23_F     2.495     0    0.042   0.862     3.488   66.905   63.155
LGA    A    24_D      A    24_F     1.079     0    0.049   0.057     1.672   86.190   85.238
LGA    S    25_D      S    25_F     1.495     0    0.174   0.702     2.690   85.952   78.968
LGA    W    26_D      W    26_F     1.370     0    0.049   1.657     5.011   81.429   61.259
LGA    I    27_D      I    27_F     1.190     0    0.025   1.173     4.108   81.429   68.095
LGA    K    28_D      K    28_F     0.786     0    0.035   1.344     3.437   88.214   77.302
LGA    Y    29_D      Y    29_F     0.609     0    0.038   1.435     7.220   90.595   62.381
LGA    I    30_D      I    30_F     1.110     0    0.087   0.544     2.054   83.690   80.536
LGA    Q    31_D      Q    31_F     2.072     0    0.034   1.193     7.750   68.810   45.556
LGA    R    32_D      R    32_F     1.799     0    0.474   1.440     8.674   75.000   49.784
LGA    R    33_D      R    33_F     1.356     0    0.200   1.372    10.837   71.071   37.013

# 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):     4.751          4.525                  6.589           47.051   36.828

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   26    4.0     16    2.46    64.423    58.986     0.624

LGA_LOCAL      RMSD:   2.464  Number of atoms:   16  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.857  Number of assigned atoms:   26 
Std_ASGN_ATOMS RMSD:   4.751  Standard rmsd on all 26 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.264081 * X  +   0.647606 * Y  +  -0.714750 * Z  + 143.832748
  Y_new =   0.911526 * X  +   0.074640 * Y  +   0.404412 * Z  + -125.245140
  Z_new =   0.315248 * X  +  -0.758311 * Y  +  -0.570599 * Z  +  75.780243 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.288804 -0.320718 -2.215870   [DEG:   73.8430  -18.3758 -126.9600 ]
ZXZ: -2.085696  2.178031  2.747605   [DEG: -119.5015  124.7920  157.4262 ]
 
# END of job
