
#######################################################
#                                                     #
#                        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        0.36     0.36
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.36     0.36
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.36     0.36
  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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     30   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     30   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     31   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     53   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     53   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     50   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     53   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     53     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60 
GDT PERCENT_AT  88.33 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36
GDT RMS_ALL_AT   0.37   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36

# Checking swapping
#   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
#   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     0.612     0    0.515   0.941     5.778   86.905   63.155
LGA    D     2_A      D     2_A     0.208     0    0.038   0.352     1.861  100.000   95.417
LGA    K     3_A      K     3_A     0.443     0    0.034   0.533     1.752  100.000   90.741
LGA    A     4_A      A     4_A     0.419     0    0.050   0.061     0.544  100.000   98.095
LGA    A     5_A      A     5_A     0.214     0    0.051   0.070     0.465  100.000  100.000
LGA    C     6_A      C     6_A     0.258     0    0.018   0.032     0.398  100.000  100.000
LGA    A     7_A      A     7_A     0.177     0    0.035   0.044     0.249  100.000  100.000
LGA    D     8_A      D     8_A     0.262     0    0.027   0.090     0.709  100.000   96.429
LGA    G     9_A      G     9_A     0.177     0    0.047   0.047     0.311  100.000  100.000
LGA    I    10_A      I    10_A     0.249     0    0.022   0.036     0.372  100.000  100.000
LGA    A    11_A      A    11_A     0.243     0    0.035   0.047     0.267  100.000  100.000
LGA    A    12_A      A    12_A     0.195     0    0.013   0.020     0.284  100.000  100.000
LGA    V    13_A      V    13_A     0.289     0    0.021   0.045     0.464  100.000  100.000
LGA    K    14_A      K    14_A     0.294     0    0.073   0.171     0.644   97.619   96.825
LGA    A    15_A      A    15_A     0.134     0    0.054   0.050     0.397  100.000  100.000
LGA    R    16_A      R    16_A     0.201     0    0.017   0.808     3.977  100.000   83.074
LGA    V    17_A      V    17_A     0.178     0    0.033   0.042     0.218  100.000  100.000
LGA    E    18_A      E    18_A     0.128     0    0.020   0.919     3.277  100.000   81.852
LGA    K    19_A      K    19_A     0.253     0    0.061   1.090     4.869   97.619   82.646
LGA    L    20_A      L    20_A     0.338     0    0.027   0.195     0.475  100.000  100.000
LGA    A    21_A      A    21_A     0.483     0    0.016   0.033     0.546   95.238   94.286
LGA    P    22_A      P    22_A     0.601     0    0.032   0.047     0.839   90.476   90.476
LGA    E    23_A      E    23_A     0.616     0    0.058   0.961     2.249   90.476   81.746
LGA    A    24_A      A    24_A     0.565     0    0.058   0.071     0.759   92.857   92.381
LGA    V    25_A      V    25_A     0.270     0    0.030   0.059     0.354  100.000  100.000
LGA    P    26_A      P    26_A     0.292     0    0.036   0.089     0.430  100.000  100.000
LGA    Q    27_A      Q    27_A     0.253     0    0.010   0.943     3.508  100.000   85.026
LGA    K    28_A      K    28_A     0.136     0    0.061   0.829     3.771  100.000   80.476
LGA    L    29_A      L    29_A     0.232     0    0.032   1.128     2.781  100.000   89.286
LGA    K    30_A      K    30_A     0.359     0    0.012   0.098     0.681  100.000   98.942
LGA    R    31_A      R    31_A     0.346     0    0.035   1.241     6.907  100.000   68.788
LGA    A    32_A      A    32_A     0.301     0    0.049   0.062     0.326  100.000  100.000
LGA    L    33_A      L    33_A     0.341     0    0.032   0.069     0.532  100.000   97.619
LGA    K    34_A      K    34_A     0.326     0    0.081   0.637     2.740  100.000   91.058
LGA    I    35_A      I    35_A     0.354     0    0.105   0.107     0.504   97.619   98.810
LGA    A    36_A      A    36_A     0.348     0    0.016   0.019     0.445  100.000  100.000
LGA    E    37_A      E    37_A     0.325     0    0.026   0.197     0.535  100.000   98.942
LGA    R    38_A      R    38_A     0.292     0    0.063   0.142     0.976   97.619   95.671
LGA    E    39_A      E    39_A     0.328     0    0.049   1.091     3.920  100.000   85.714
LGA    Q    40_A      Q    40_A     0.357     0    0.079   1.154     4.413   97.619   84.127
LGA    G    41_A      G    41_A     0.182     0    0.038   0.038     0.225  100.000  100.000
LGA    E    42_A      E    42_A     0.409     0    0.154   0.259     1.152   97.619   92.646
LGA    G    43_A      G    43_A     0.306     0    0.039   0.039     0.427  100.000  100.000
LGA    E    44_A      E    44_A     0.375     0    0.084   0.958     4.187  100.000   84.339
LGA    F    45_A      F    45_A     0.529     0    0.008   0.046     0.765   95.238   92.208
LGA    D    46_A      D    46_A     0.592     0    0.061   0.427     1.158   92.857   90.536
LGA    E    47_A      E    47_A     0.447     0    0.022   1.041     3.144   97.619   84.550
LGA    C    48_A      C    48_A     0.160     0    0.022   0.099     0.281  100.000  100.000
LGA    L    49_A      L    49_A     0.327     0    0.032   0.087     0.553  100.000   98.810
LGA    E    50_A      E    50_A     0.236     0    0.033   0.219     0.981  100.000   98.942
LGA    A    51_A      A    51_A     0.150     0    0.022   0.025     0.275  100.000  100.000
LGA    L    52_A      L    52_A     0.391     0    0.022   0.063     0.585  100.000   98.810
LGA    D    53_A      D    53_A     0.360     0    0.049   0.083     0.467  100.000  100.000
LGA    D    54_A      D    54_A     0.247     0    0.016   0.465     1.641  100.000   93.095
LGA    A    55_A      A    55_A     0.400     0    0.008   0.013     0.545   97.619   98.095
LGA    K    56_A      K    56_A     0.733     0    0.046   0.668     1.585   90.476   84.550
LGA    R    57_A      R    57_A     0.265     0    0.017   0.251     0.844  100.000   97.403
LGA    A    58_A      A    58_A     0.525     0    0.037   0.040     0.869   92.857   92.381
LGA    L    59_A      L    59_A     0.507     0    0.043   0.184     1.358   97.619   91.786
LGA    P    60_A      P    60_A     0.620     0    0.030   0.339     1.072   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):     0.364          0.401                  1.145           98.274   93.482

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   61   60    4.0     60    0.36   100.000   100.000    12.918

LGA_LOCAL      RMSD:   0.364  Number of atoms:   60  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.364  Number of assigned atoms:   60 
Std_ASGN_ATOMS RMSD:   0.364  Standard rmsd on all 60 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.114075 * X  +   0.417075 * Y  +   0.901685 * Z  +  12.777916
  Y_new =  -0.992789 * X  +  -0.081503 * Y  +  -0.087902 * Z  +   4.710424
  Z_new =   0.036828 * X  +  -0.905210 * Y  +   0.423365 * Z  +  10.317858 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.685198 -0.036836 -1.133323   [DEG:  -96.5547   -2.1106  -64.9346 ]
ZXZ:  1.473617  1.133640  3.100931   [DEG:   84.4321   64.9528  177.6702 ]
 
# END of job
