
#######################################################
#                                                     #
#                        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        0.38     0.38
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.38     0.38
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.38     0.38
  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     50   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     40   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     54   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     54   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     46   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     44   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     29   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    0.31   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38
GDT RMS_ALL_AT   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38

# 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    47_A      E    47_A
#   possible swapping detected:  E    50_A      E    50_A
#   possible swapping detected:  D    53_A      D    53_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_A      D     1_A     0.669     0    0.186   0.816     1.695   90.476   86.012
LGA    D     2_A      D     2_A     0.383     0    0.010   0.449     2.209   97.619   92.024
LGA    K     3_A      K     3_A     0.450     0    0.012   0.574     1.589  100.000   90.794
LGA    A     4_A      A     4_A     0.427     0    0.047   0.056     0.525  100.000   98.095
LGA    A     5_A      A     5_A     0.258     0    0.044   0.061     0.497  100.000  100.000
LGA    C     6_A      C     6_A     0.111     0    0.028   0.059     0.205  100.000  100.000
LGA    A     7_A      A     7_A     0.130     0    0.031   0.042     0.190  100.000  100.000
LGA    D     8_A      D     8_A     0.162     0    0.022   0.117     0.565  100.000   97.619
LGA    G     9_A      G     9_A     0.207     0    0.047   0.047     0.314  100.000  100.000
LGA    I    10_A      I    10_A     0.237     0    0.022   0.067     0.485  100.000  100.000
LGA    A    11_A      A    11_A     0.194     0    0.033   0.045     0.248  100.000  100.000
LGA    A    12_A      A    12_A     0.164     0    0.014   0.018     0.338  100.000  100.000
LGA    V    13_A      V    13_A     0.289     0    0.024   0.052     0.393  100.000  100.000
LGA    K    14_A      K    14_A     0.278     0    0.079   0.189     0.736   97.619   96.825
LGA    A    15_A      A    15_A     0.259     0    0.055   0.052     0.492  100.000  100.000
LGA    R    16_A      R    16_A     0.307     0    0.017   1.081     4.855  100.000   85.801
LGA    V    17_A      V    17_A     0.215     0    0.037   0.051     0.269  100.000  100.000
LGA    E    18_A      E    18_A     0.079     0    0.021   0.667     3.227  100.000   83.598
LGA    K    19_A      K    19_A     0.238     0    0.069   1.082     4.953   97.619   81.852
LGA    L    20_A      L    20_A     0.351     0    0.028   0.181     0.514  100.000   97.619
LGA    A    21_A      A    21_A     0.505     0    0.021   0.040     0.577   92.857   92.381
LGA    P    22_A      P    22_A     0.647     0    0.015   0.045     0.825   90.476   90.476
LGA    E    23_A      E    23_A     0.619     0    0.049   0.895     1.916   90.476   82.646
LGA    A    24_A      A    24_A     0.594     0    0.072   0.083     0.772   92.857   92.381
LGA    V    25_A      V    25_A     0.318     0    0.035   0.059     0.438  100.000  100.000
LGA    P    26_A      P    26_A     0.291     0    0.036   0.086     0.472  100.000  100.000
LGA    Q    27_A      Q    27_A     0.243     0    0.011   1.177     3.849  100.000   77.090
LGA    K    28_A      K    28_A     0.120     0    0.059   0.676     2.626  100.000   93.175
LGA    L    29_A      L    29_A     0.251     0    0.024   1.126     2.726  100.000   89.286
LGA    K    30_A      K    30_A     0.320     0    0.012   0.085     0.569  100.000   98.942
LGA    R    31_A      R    31_A     0.341     0    0.043   1.273     7.079  100.000   67.965
LGA    A    32_A      A    32_A     0.374     0    0.046   0.059     0.401  100.000  100.000
LGA    L    33_A      L    33_A     0.378     0    0.033   0.059     0.426  100.000  100.000
LGA    K    34_A      K    34_A     0.324     0    0.061   0.621     2.783  100.000   89.101
LGA    I    35_A      I    35_A     0.386     0    0.094   0.095     0.482  100.000  100.000
LGA    A    36_A      A    36_A     0.384     0    0.016   0.018     0.448  100.000  100.000
LGA    E    37_A      E    37_A     0.374     0    0.020   0.239     0.687  100.000   97.884
LGA    R    38_A      R    38_A     0.357     0    0.065   0.958     4.143   97.619   82.424
LGA    E    39_A      E    39_A     0.359     0    0.029   1.127     4.066  100.000   83.280
LGA    Q    40_A      Q    40_A     0.369     0    0.051   0.345     1.234   97.619   93.704
LGA    G    41_A      G    41_A     0.223     0    0.050   0.050     0.262  100.000  100.000
LGA    E    42_A      E    42_A     0.486     0    0.131   0.220     0.926  100.000   94.709
LGA    G    43_A      G    43_A     0.334     0    0.055   0.055     0.459  100.000  100.000
LGA    E    44_A      E    44_A     0.172     0    0.029   0.966     4.281  100.000   83.492
LGA    F    45_A      F    45_A     0.323     0    0.013   0.044     0.428  100.000  100.000
LGA    D    46_A      D    46_A     0.443     0    0.068   1.157     4.139  100.000   83.333
LGA    E    47_A      E    47_A     0.347     0    0.035   0.294     0.990  100.000   97.884
LGA    C    48_A      C    48_A     0.053     0    0.012   0.070     0.190  100.000  100.000
LGA    L    49_A      L    49_A     0.231     0    0.022   0.100     0.396  100.000  100.000
LGA    E    50_A      E    50_A     0.182     0    0.041   0.266     0.822  100.000   97.884
LGA    A    51_A      A    51_A     0.109     0    0.026   0.028     0.220  100.000  100.000
LGA    L    52_A      L    52_A     0.355     0    0.011   0.080     0.642  100.000   98.810
LGA    D    53_A      D    53_A     0.318     0    0.066   0.221     0.969  100.000   96.429
LGA    D    54_A      D    54_A     0.227     0    0.028   0.215     0.718  100.000   97.619
LGA    A    55_A      A    55_A     0.402     0    0.013   0.013     0.562   97.619   98.095
LGA    K    56_A      K    56_A     0.723     0    0.038   0.658     1.535   90.476   85.503
LGA    R    57_A      R    57_A     0.256     0    0.019   0.578     2.069  100.000   91.775
LGA    A    58_A      A    58_A     0.621     0    0.032   0.036     0.976   92.857   92.381
LGA    L    59_A      L    59_A     0.487     0    0.037   0.263     1.208   95.238   91.786
LGA    P    60_A      P    60_A     0.950     0    0.029   0.332     1.142   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):     0.376          0.377                  1.092           98.532   93.976

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   61   60    4.0     60    0.38   100.000   100.000    12.599

LGA_LOCAL      RMSD:   0.376  Number of atoms:   60  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.376  Number of assigned atoms:   60 
Std_ASGN_ATOMS RMSD:   0.376  Standard rmsd on all 60 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.500315 * X  +  -0.690462 * Y  +   0.522444 * Z  +  13.804423
  Y_new =  -0.325684 * X  +   0.709152 * Y  +   0.625326 * Z  +   6.950984
  Z_new =  -0.802256 * X  +   0.142709 * Y  +  -0.579672 * Z  +   9.024224 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.564544  0.931065  2.900204   [DEG: -146.9376   53.3461  166.1695 ]
ZXZ:  2.445593  2.189122 -1.394754   [DEG:  140.1221  125.4275  -79.9135 ]
 
# END of job
