
#######################################################
#                                                     #
#                        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   61 (  460),  selected   60 , name one
# Molecule2: number of CA atoms   60 (  451),  selected   60 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.39     0.39
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.39     0.39
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.39     0.39
  LCS_AVERAGE:    100.00

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   60
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     D     1_A     D     1_A     60   60   60     26   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D     2_A     D     2_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K     3_A     K     3_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     4_A     A     4_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     5_A     A     5_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     C     6_A     C     6_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     7_A     A     7_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D     8_A     D     8_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G     9_A     G     9_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     I    10_A     I    10_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    11_A     A    11_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    12_A     A    12_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    13_A     V    13_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    14_A     K    14_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    15_A     A    15_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    16_A     R    16_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    17_A     V    17_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    18_A     E    18_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    19_A     K    19_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    20_A     L    20_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    21_A     A    21_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    22_A     P    22_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    23_A     E    23_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    24_A     A    24_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    25_A     V    25_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    26_A     P    26_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     Q    27_A     Q    27_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    28_A     K    28_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    29_A     L    29_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    30_A     K    30_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    31_A     R    31_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    32_A     A    32_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    33_A     L    33_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    34_A     K    34_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     I    35_A     I    35_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    36_A     A    36_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    37_A     E    37_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    38_A     R    38_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    39_A     E    39_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     Q    40_A     Q    40_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G    41_A     G    41_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    42_A     E    42_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G    43_A     G    43_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    44_A     E    44_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     F    45_A     F    45_A     60   60   60     52   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    46_A     D    46_A     60   60   60     50   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    47_A     E    47_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     C    48_A     C    48_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    49_A     L    49_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    50_A     E    50_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    51_A     A    51_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    52_A     L    52_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    53_A     D    53_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    54_A     D    54_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    55_A     A    55_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    56_A     K    56_A     60   60   60     36   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    57_A     R    57_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    58_A     A    58_A     60   60   60     43   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    59_A     L    59_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    60_A     P    60_A     60   60   60     35   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_AVERAGE  LCS_A: 100.00  ( 100.00  100.00  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     54     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60 
GDT PERCENT_AT  90.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.33   0.39   0.39   0.39   0.39   0.39   0.39   0.39   0.39   0.39   0.39   0.39   0.39   0.39   0.39   0.39   0.39   0.39   0.39   0.39
GDT RMS_ALL_AT   0.40   0.39   0.39   0.39   0.39   0.39   0.39   0.39   0.39   0.39   0.39   0.39   0.39   0.39   0.39   0.39   0.39   0.39   0.39   0.39

# Checking swapping
#   possible swapping detected:  E    18_A      E    18_A
#   possible swapping detected:  E    37_A      E    37_A
#   possible swapping detected:  E    39_A      E    39_A
#   possible swapping detected:  E    42_A      E    42_A
#   possible swapping detected:  E    44_A      E    44_A
#   possible swapping detected:  E    50_A      E    50_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_A      D     1_A     0.997     0    0.217   0.857     1.867   90.476   86.071
LGA    D     2_A      D     2_A     0.421     0    0.006   0.457     2.246   97.619   90.893
LGA    K     3_A      K     3_A     0.567     0    0.014   0.575     1.796   92.857   86.561
LGA    A     4_A      A     4_A     0.563     0    0.027   0.035     0.744   95.238   94.286
LGA    A     5_A      A     5_A     0.331     0    0.052   0.070     0.614  100.000   98.095
LGA    C     6_A      C     6_A     0.283     0    0.027   0.066     0.380  100.000  100.000
LGA    A     7_A      A     7_A     0.271     0    0.028   0.039     0.368  100.000  100.000
LGA    D     8_A      D     8_A     0.201     0    0.026   0.108     0.585  100.000   97.619
LGA    G     9_A      G     9_A     0.161     0    0.042   0.042     0.272  100.000  100.000
LGA    I    10_A      I    10_A     0.269     0    0.022   0.040     0.392  100.000  100.000
LGA    A    11_A      A    11_A     0.250     0    0.034   0.046     0.284  100.000  100.000
LGA    A    12_A      A    12_A     0.128     0    0.015   0.018     0.287  100.000  100.000
LGA    V    13_A      V    13_A     0.240     0    0.023   0.052     0.345  100.000  100.000
LGA    K    14_A      K    14_A     0.269     0    0.073   0.177     0.640   97.619   96.825
LGA    A    15_A      A    15_A     0.156     0    0.057   0.053     0.357  100.000  100.000
LGA    R    16_A      R    16_A     0.306     0    0.021   0.186     1.284  100.000   95.714
LGA    V    17_A      V    17_A     0.277     0    0.038   0.051     0.300  100.000  100.000
LGA    E    18_A      E    18_A     0.141     0    0.023   0.790     3.881  100.000   83.810
LGA    K    19_A      K    19_A     0.220     0    0.052   1.058     4.620  100.000   83.704
LGA    L    20_A      L    20_A     0.333     0    0.028   0.173     0.525  100.000   97.619
LGA    A    21_A      A    21_A     0.343     0    0.016   0.040     0.428  100.000  100.000
LGA    P    22_A      P    22_A     0.513     0    0.038   0.050     0.755   92.857   94.558
LGA    E    23_A      E    23_A     0.357     0    0.057   1.006     2.708  100.000   83.492
LGA    A    24_A      A    24_A     0.388     0    0.075   0.087     0.557  100.000   98.095
LGA    V    25_A      V    25_A     0.263     0    0.041   0.065     0.352  100.000  100.000
LGA    P    26_A      P    26_A     0.259     0    0.032   0.083     0.431  100.000  100.000
LGA    Q    27_A      Q    27_A     0.234     0    0.014   1.157     4.367  100.000   85.185
LGA    K    28_A      K    28_A     0.186     0    0.045   0.824     3.519  100.000   81.217
LGA    L    29_A      L    29_A     0.282     0    0.025   1.129     2.720  100.000   89.286
LGA    K    30_A      K    30_A     0.362     0    0.015   0.076     0.474  100.000  100.000
LGA    R    31_A      R    31_A     0.374     0    0.035   1.283     7.178  100.000   67.489
LGA    A    32_A      A    32_A     0.430     0    0.042   0.055     0.451  100.000  100.000
LGA    L    33_A      L    33_A     0.422     0    0.037   0.056     0.456  100.000  100.000
LGA    K    34_A      K    34_A     0.365     0    0.058   0.646     2.919  100.000   90.053
LGA    I    35_A      I    35_A     0.450     0    0.088   0.090     0.572   97.619   98.810
LGA    A    36_A      A    36_A     0.498     0    0.015   0.021     0.544   95.238   96.190
LGA    E    37_A      E    37_A     0.388     0    0.025   0.275     0.755  100.000   97.884
LGA    R    38_A      R    38_A     0.391     0    0.069   1.215     4.774   97.619   79.221
LGA    E    39_A      E    39_A     0.419     0    0.044   1.080     4.038  100.000   83.280
LGA    Q    40_A      Q    40_A     0.475     0    0.073   1.099     3.921   95.238   81.852
LGA    G    41_A      G    41_A     0.309     0    0.040   0.040     0.361  100.000  100.000
LGA    E    42_A      E    42_A     0.296     0    0.136   0.259     0.909  100.000   95.767
LGA    G    43_A      G    43_A     0.226     0    0.055   0.055     0.334  100.000  100.000
LGA    E    44_A      E    44_A     0.308     0    0.069   0.990     4.189  100.000   85.185
LGA    F    45_A      F    45_A     0.532     0    0.009   0.035     0.971   95.238   92.208
LGA    D    46_A      D    46_A     0.608     0    0.065   1.145     4.066   92.857   79.583
LGA    E    47_A      E    47_A     0.410     0    0.031   1.071     3.313   97.619   84.550
LGA    C    48_A      C    48_A     0.125     0    0.016   0.097     0.238  100.000  100.000
LGA    L    49_A      L    49_A     0.309     0    0.041   0.110     0.571  100.000   97.619
LGA    E    50_A      E    50_A     0.180     0    0.019   0.263     1.031  100.000   95.820
LGA    A    51_A      A    51_A     0.151     0    0.011   0.024     0.291  100.000  100.000
LGA    L    52_A      L    52_A     0.357     0    0.026   0.044     0.641  100.000   97.619
LGA    D    53_A      D    53_A     0.266     0    0.012   0.763     3.185  100.000   85.952
LGA    D    54_A      D    54_A     0.177     0    0.016   0.323     1.133  100.000   94.167
LGA    A    55_A      A    55_A     0.396     0    0.012   0.019     0.490  100.000  100.000
LGA    K    56_A      K    56_A     0.691     0    0.047   0.580     1.688   95.238   86.667
LGA    R    57_A      R    57_A     0.349     0    0.020   1.213     4.904   97.619   80.000
LGA    A    58_A      A    58_A     0.576     0    0.041   0.042     0.976   92.857   92.381
LGA    L    59_A      L    59_A     0.425     0    0.041   0.159     1.340  100.000   92.976
LGA    P    60_A      P    60_A     0.853     0    0.032   0.344     1.049   90.476   87.891

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       60     240    240  100.00     451    451  100.00                60
SUMMARY(RMSD_GDC):     0.392          0.388                  1.200           98.571   93.103

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   61   60    4.0     60    0.39   100.000   100.000    12.193

LGA_LOCAL      RMSD:   0.392  Number of atoms:   60  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.392  Number of assigned atoms:   60 
Std_ASGN_ATOMS RMSD:   0.392  Standard rmsd on all 60 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.947969 * X  +  -0.245325 * Y  +   0.202907 * Z  +  10.560298
  Y_new =   0.222077 * X  +  -0.052882 * Y  +   0.973594 * Z  +   8.534663
  Z_new =  -0.228117 * X  +   0.967997 * Y  +   0.104611 * Z  +   6.222552 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.911476  0.230143  1.463144   [DEG:  166.8153   13.1862   83.8320 ]
ZXZ:  2.936124  1.465993 -0.231436   [DEG:  168.2275   83.9952  -13.2603 ]
 
# END of job
