
#######################################################
#                                                     #
#                        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        0.35     0.35
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.35     0.35
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.35     0.35
  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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     56   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     41   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     56   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     19   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     30   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     41   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     56     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60 
GDT PERCENT_AT  93.33 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.31   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35
GDT RMS_ALL_AT   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35

# 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     0.511     0    0.169   0.849     2.223   92.857   83.988
LGA    D     2_A      D     2_A     0.189     0    0.006   0.498     2.094  100.000   94.405
LGA    K     3_A      K     3_A     0.397     0    0.015   0.559     1.552  100.000   91.852
LGA    A     4_A      A     4_A     0.396     0    0.024   0.033     0.491  100.000  100.000
LGA    A     5_A      A     5_A     0.121     0    0.036   0.056     0.330  100.000  100.000
LGA    C     6_A      C     6_A     0.195     0    0.038   0.067     0.229  100.000  100.000
LGA    A     7_A      A     7_A     0.215     0    0.033   0.045     0.290  100.000  100.000
LGA    D     8_A      D     8_A     0.275     0    0.018   0.110     0.651  100.000   96.429
LGA    G     9_A      G     9_A     0.065     0    0.045   0.045     0.179  100.000  100.000
LGA    I    10_A      I    10_A     0.223     0    0.024   0.042     0.352  100.000  100.000
LGA    A    11_A      A    11_A     0.277     0    0.033   0.044     0.318  100.000  100.000
LGA    A    12_A      A    12_A     0.100     0    0.017   0.018     0.259  100.000  100.000
LGA    V    13_A      V    13_A     0.194     0    0.027   0.057     0.312  100.000  100.000
LGA    K    14_A      K    14_A     0.242     0    0.078   0.185     0.528   97.619   96.825
LGA    A    15_A      A    15_A     0.127     0    0.059   0.055     0.365  100.000  100.000
LGA    R    16_A      R    16_A     0.259     0    0.018   0.247     1.205  100.000   95.714
LGA    V    17_A      V    17_A     0.260     0    0.037   0.048     0.287  100.000  100.000
LGA    E    18_A      E    18_A     0.125     0    0.022   0.812     3.912  100.000   83.810
LGA    K    19_A      K    19_A     0.294     0    0.051   1.067     4.904   97.619   81.799
LGA    L    20_A      L    20_A     0.356     0    0.030   0.199     0.591  100.000   96.429
LGA    A    21_A      A    21_A     0.327     0    0.016   0.031     0.423  100.000  100.000
LGA    P    22_A      P    22_A     0.498     0    0.030   0.045     0.743   95.238   97.279
LGA    E    23_A      E    23_A     0.408     0    0.055   0.967     2.312  100.000   85.079
LGA    A    24_A      A    24_A     0.423     0    0.062   0.074     0.612  100.000   98.095
LGA    V    25_A      V    25_A     0.286     0    0.037   0.062     0.402  100.000  100.000
LGA    P    26_A      P    26_A     0.341     0    0.038   0.091     0.452  100.000  100.000
LGA    Q    27_A      Q    27_A     0.292     0    0.014   1.168     4.475  100.000   84.339
LGA    K    28_A      K    28_A     0.212     0    0.046   0.830     3.646  100.000   80.476
LGA    L    29_A      L    29_A     0.281     0    0.021   1.124     2.721  100.000   89.286
LGA    K    30_A      K    30_A     0.383     0    0.013   0.077     0.545  100.000   98.942
LGA    R    31_A      R    31_A     0.375     0    0.037   1.267     7.038  100.000   68.485
LGA    A    32_A      A    32_A     0.401     0    0.041   0.054     0.434  100.000  100.000
LGA    L    33_A      L    33_A     0.405     0    0.030   0.054     0.440  100.000  100.000
LGA    K    34_A      K    34_A     0.332     0    0.058   0.655     2.868  100.000   91.058
LGA    I    35_A      I    35_A     0.410     0    0.089   0.091     0.518   97.619   98.810
LGA    A    36_A      A    36_A     0.454     0    0.015   0.018     0.519   97.619   98.095
LGA    E    37_A      E    37_A     0.314     0    0.027   0.240     0.722  100.000   97.884
LGA    R    38_A      R    38_A     0.332     0    0.067   1.258     4.872  100.000   80.952
LGA    E    39_A      E    39_A     0.403     0    0.047   1.083     3.923  100.000   83.968
LGA    Q    40_A      Q    40_A     0.403     0    0.074   1.074     3.723   97.619   83.810
LGA    G    41_A      G    41_A     0.182     0    0.041   0.041     0.235  100.000  100.000
LGA    E    42_A      E    42_A     0.389     0    0.144   0.285     1.033  100.000   95.820
LGA    G    43_A      G    43_A     0.233     0    0.061   0.061     0.381  100.000  100.000
LGA    E    44_A      E    44_A     0.225     0    0.075   0.998     4.397  100.000   84.339
LGA    F    45_A      F    45_A     0.397     0    0.010   0.037     0.587  100.000   96.537
LGA    D    46_A      D    46_A     0.469     0    0.066   1.151     4.146  100.000   82.143
LGA    E    47_A      E    47_A     0.321     0    0.031   1.059     3.405  100.000   86.667
LGA    C    48_A      C    48_A     0.074     0    0.014   0.089     0.191  100.000  100.000
LGA    L    49_A      L    49_A     0.251     0    0.028   0.073     0.423  100.000  100.000
LGA    E    50_A      E    50_A     0.154     0    0.037   0.206     0.775  100.000   98.942
LGA    A    51_A      A    51_A     0.170     0    0.020   0.025     0.299  100.000  100.000
LGA    L    52_A      L    52_A     0.386     0    0.017   0.035     0.532  100.000   98.810
LGA    D    53_A      D    53_A     0.343     0    0.050   0.121     0.466  100.000  100.000
LGA    D    54_A      D    54_A     0.225     0    0.016   0.390     1.464  100.000   95.298
LGA    A    55_A      A    55_A     0.403     0    0.005   0.008     0.538   97.619   98.095
LGA    K    56_A      K    56_A     0.719     0    0.042   0.659     1.512   90.476   85.503
LGA    R    57_A      R    57_A     0.305     0    0.021   0.200     0.684  100.000   97.403
LGA    A    58_A      A    58_A     0.616     0    0.034   0.038     1.026   90.595   90.571
LGA    L    59_A      L    59_A     0.558     0    0.042   0.165     1.367   95.238   90.595
LGA    P    60_A      P    60_A     0.681     0    0.028   0.341     1.074   90.476   89.184

# 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):     0.348          0.354                  1.119           99.010   94.129

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   61   60    4.0     60    0.35   100.000   100.000    13.386

LGA_LOCAL      RMSD:   0.348  Number of atoms:   60  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.348  Number of assigned atoms:   60 
Std_ASGN_ATOMS RMSD:   0.348  Standard rmsd on all 60 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.261992 * X  +  -0.373923 * Y  +   0.889686 * Z  +  14.229851
  Y_new =  -0.704513 * X  +   0.704154 * Y  +   0.088483 * Z  +   6.893916
  Z_new =  -0.659562 * X  +  -0.603613 * Y  +  -0.447916 * Z  +   7.256443 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.926826  0.720236 -2.209195   [DEG: -110.3990   41.2665 -126.5776 ]
ZXZ:  1.669925  2.035229 -2.311931   [DEG:   95.6797  116.6101 -132.4639 ]
 
# END of job
