
#######################################################
#                                                     #
#                        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        0.40     0.40
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.40     0.40
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.40     0.40
  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     40   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     50   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     28   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     49   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     49   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     51   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     49   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     51   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     51   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     27   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     51     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60 
GDT PERCENT_AT  85.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.31   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40
GDT RMS_ALL_AT   0.42   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40

# 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     0.883     0    0.253   0.824     1.680   88.214   87.202
LGA    D     2_A      D     2_A     0.491     0    0.009   0.482     2.463   97.619   90.893
LGA    K     3_A      K     3_A     0.546     0    0.020   0.564     1.635   92.857   88.571
LGA    A     4_A      A     4_A     0.559     0    0.045   0.054     0.664   95.238   94.286
LGA    A     5_A      A     5_A     0.368     0    0.050   0.066     0.615  100.000   98.095
LGA    C     6_A      C     6_A     0.082     0    0.016   0.047     0.158  100.000  100.000
LGA    A     7_A      A     7_A     0.114     0    0.033   0.043     0.190  100.000  100.000
LGA    D     8_A      D     8_A     0.174     0    0.025   0.105     0.584  100.000   97.619
LGA    G     9_A      G     9_A     0.208     0    0.055   0.055     0.293  100.000  100.000
LGA    I    10_A      I    10_A     0.217     0    0.022   0.042     0.352  100.000  100.000
LGA    A    11_A      A    11_A     0.194     0    0.032   0.044     0.264  100.000  100.000
LGA    A    12_A      A    12_A     0.163     0    0.013   0.017     0.357  100.000  100.000
LGA    V    13_A      V    13_A     0.300     0    0.024   0.054     0.415  100.000  100.000
LGA    K    14_A      K    14_A     0.277     0    0.079   0.193     0.715   97.619   96.825
LGA    A    15_A      A    15_A     0.292     0    0.055   0.051     0.518   97.619   98.095
LGA    R    16_A      R    16_A     0.376     0    0.016   0.149     0.757  100.000   98.268
LGA    V    17_A      V    17_A     0.293     0    0.037   0.049     0.343  100.000  100.000
LGA    E    18_A      E    18_A     0.174     0    0.022   0.777     3.742  100.000   82.857
LGA    K    19_A      K    19_A     0.367     0    0.052   1.054     5.095   97.619   80.423
LGA    L    20_A      L    20_A     0.369     0    0.032   0.156     0.460  100.000  100.000
LGA    A    21_A      A    21_A     0.526     0    0.018   0.032     0.606   92.857   92.381
LGA    P    22_A      P    22_A     0.644     0    0.038   0.057     0.940   90.476   90.476
LGA    E    23_A      E    23_A     0.660     0    0.053   0.639     1.700   90.476   85.503
LGA    A    24_A      A    24_A     0.608     0    0.082   0.095     0.777   90.476   90.476
LGA    V    25_A      V    25_A     0.321     0    0.030   0.065     0.404  100.000  100.000
LGA    P    26_A      P    26_A     0.310     0    0.039   0.087     0.478  100.000  100.000
LGA    Q    27_A      Q    27_A     0.302     0    0.012   1.164     4.472  100.000   84.339
LGA    K    28_A      K    28_A     0.194     0    0.052   0.685     2.596  100.000   92.116
LGA    L    29_A      L    29_A     0.290     0    0.026   1.128     2.789  100.000   89.286
LGA    K    30_A      K    30_A     0.451     0    0.013   0.080     0.676  100.000   97.884
LGA    R    31_A      R    31_A     0.434     0    0.037   1.255     6.942  100.000   68.788
LGA    A    32_A      A    32_A     0.406     0    0.040   0.054     0.447  100.000  100.000
LGA    L    33_A      L    33_A     0.429     0    0.037   0.063     0.465  100.000  100.000
LGA    K    34_A      K    34_A     0.382     0    0.060   0.648     2.650  100.000   91.058
LGA    I    35_A      I    35_A     0.427     0    0.089   0.090     0.495  100.000  100.000
LGA    A    36_A      A    36_A     0.423     0    0.015   0.018     0.448  100.000  100.000
LGA    E    37_A      E    37_A     0.314     0    0.020   0.201     0.580  100.000   97.884
LGA    R    38_A      R    38_A     0.337     0    0.060   1.045     4.130  100.000   81.255
LGA    E    39_A      E    39_A     0.375     0    0.037   1.125     3.910  100.000   84.868
LGA    Q    40_A      Q    40_A     0.305     0    0.041   0.179     0.759  100.000   98.942
LGA    G    41_A      G    41_A     0.208     0    0.041   0.041     0.275  100.000  100.000
LGA    E    42_A      E    42_A     0.477     0    0.119   0.227     1.000  100.000   94.709
LGA    G    43_A      G    43_A     0.338     0    0.047   0.047     0.465  100.000  100.000
LGA    E    44_A      E    44_A     0.262     0    0.052   0.983     4.231  100.000   85.185
LGA    F    45_A      F    45_A     0.368     0    0.016   0.037     0.536  100.000   99.134
LGA    D    46_A      D    46_A     0.457     0    0.070   1.159     4.181  100.000   83.333
LGA    E    47_A      E    47_A     0.350     0    0.026   1.073     3.482  100.000   85.608
LGA    C    48_A      C    48_A     0.057     0    0.021   0.074     0.190  100.000  100.000
LGA    L    49_A      L    49_A     0.177     0    0.035   0.113     0.407  100.000  100.000
LGA    E    50_A      E    50_A     0.151     0    0.024   0.269     0.975  100.000   98.942
LGA    A    51_A      A    51_A     0.147     0    0.015   0.022     0.251  100.000  100.000
LGA    L    52_A      L    52_A     0.343     0    0.019   0.053     0.591  100.000   98.810
LGA    D    53_A      D    53_A     0.230     0    0.017   0.769     3.290  100.000   84.940
LGA    D    54_A      D    54_A     0.181     0    0.023   0.200     0.669  100.000   97.619
LGA    A    55_A      A    55_A     0.366     0    0.010   0.015     0.462  100.000  100.000
LGA    K    56_A      K    56_A     0.661     0    0.043   0.568     1.587   97.619   87.725
LGA    R    57_A      R    57_A     0.352     0    0.015   1.164     4.604  100.000   81.602
LGA    A    58_A      A    58_A     0.608     0    0.037   0.039     0.927   92.857   92.381
LGA    L    59_A      L    59_A     0.439     0    0.032   0.166     1.272   95.238   90.595
LGA    P    60_A      P    60_A     0.972     0    0.026   0.092     1.033   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):     0.403          0.407                  1.118           98.454   93.803

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   61   60    4.0     60    0.40   100.000   100.000    11.922

LGA_LOCAL      RMSD:   0.403  Number of atoms:   60  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.403  Number of assigned atoms:   60 
Std_ASGN_ATOMS RMSD:   0.403  Standard rmsd on all 60 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.978519 * X  +  -0.188800 * Y  +  -0.082798 * Z  +  12.804992
  Y_new =  -0.119440 * X  +   0.191829 * Y  +   0.974133 * Z  +   7.484987
  Z_new =  -0.168034 * X  +   0.963097 * Y  +  -0.210258 * Z  +  10.385612 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -3.020132  0.168835  1.785738   [DEG: -173.0408    9.6735  102.3153 ]
ZXZ: -3.056799  1.782635 -0.172733   [DEG: -175.1417  102.1375   -9.8969 ]
 
# END of job
