
#######################################################
#                                                     #
#                        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   97 (  779),  selected   61 , name one
# Molecule2: number of CA atoms   61 (  480),  selected   61 , 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:    61      32_A - 98_A        0.56     0.56
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61      32_A - 98_A        0.56     0.56
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61      32_A - 98_A        0.56     0.56
  LCS_AVERAGE:    100.00

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   61
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     A    32_A     A    32_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    33_A     T    33_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    34_A     M    34_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    35_A     A    35_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    36_A     D    36_A     61   61   61     16   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    37_A     L    37_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    38_A     K    38_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    39_A     M    39_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    40_A     Q    40_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    41_A     A    41_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    42_A     V    42_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    43_A     K    43_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    44_A     E    44_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    45_A     I    45_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     C    46_A     C    46_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y    47_A     Y    47_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    48_A     E    48_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    49_A     V    49_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    50_A     A    50_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    51_A     L    51_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    52_A     A    52_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    53_A     D    53_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     F    54_A     F    54_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    55_A     R    55_A     61   61   61     29   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    56_A     H    56_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     G    57_A     G    57_A     61   61   61      9   55   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    58_A     R    58_A     61   61   61     44   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    59_A     A    59_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    60_A     E    60_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    61_A     I    61_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    62_A     E    62_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    63_A     A    63_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    64_A     L    64_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    65_A     A    65_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    66_A     A    66_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    67_A     L    67_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    68_A     K    68_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    69_A     M    69_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    70_A     R    70_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    71_A     E    71_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    72_A     L    72_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     C    73_A     C    73_A     61   61   61     44   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    74_A     R    74_A     61   61   61     38   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    75_A     T    75_A     61   61   61      8   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y    76_A     Y    76_A     61   61   61     25   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     G    83_A     G    83_A     61   61   61      3   24   37   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    84_A     D    84_A     61   61   61     14   53   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    85_A     A    85_A     61   61   61     25   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     W    86_A     W    86_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    87_A     R    87_A     61   61   61     35   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    88_A     A    88_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    89_A     V    89_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    90_A     A    90_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    91_A     R    91_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    92_A     D    92_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    93_A     V    93_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     W    94_A     W    94_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    95_A     D    95_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    96_A     T    96_A     61   61   61     43   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    97_A     V    97_A     61   61   61     47   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     G    98_A     G    98_A     61   61   61      3   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
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     47     58     60     61     61     61     61     61     61     61     61     61     61     61     61     61     61     61     61     61 
GDT PERCENT_AT  77.05  95.08  98.36 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.45   0.50   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56
GDT RMS_ALL_AT   0.59   0.57   0.57   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56

# Checking swapping
#   possible swapping detected:  E    48_A      E    48_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    32_A      A    32_A     0.673     0    0.443   0.445     1.791   88.214   85.143
LGA    T    33_A      T    33_A     0.471     0    0.097   0.421     1.298   95.238   91.973
LGA    M    34_A      M    34_A     0.147     0    0.053   0.225     1.311  100.000   96.488
LGA    A    35_A      A    35_A     0.535     0    0.104   0.112     0.962   92.857   92.381
LGA    D    36_A      D    36_A     0.920     0    0.133   0.331     2.934   95.238   82.143
LGA    L    37_A      L    37_A     0.233     0    0.039   0.123     0.305  100.000  100.000
LGA    K    38_A      K    38_A     0.327     0    0.065   0.680     1.953  100.000   92.910
LGA    M    39_A      M    39_A     0.354     0    0.047   0.855     2.075  100.000   92.083
LGA    Q    40_A      Q    40_A     0.290     0    0.020   0.141     0.546  100.000   98.942
LGA    A    41_A      A    41_A     0.187     0    0.074   0.084     0.426  100.000  100.000
LGA    V    42_A      V    42_A     0.397     0    0.087   0.179     0.683   97.619   98.639
LGA    K    43_A      K    43_A     0.378     0    0.031   0.172     1.388  100.000   93.757
LGA    E    44_A      E    44_A     0.446     0    0.162   0.346     1.586   92.976   91.746
LGA    I    45_A      I    45_A     0.191     0    0.010   0.110     0.824  100.000   97.619
LGA    C    46_A      C    46_A     0.149     0    0.093   0.113     0.658   97.619   98.413
LGA    Y    47_A      Y    47_A     0.105     0    0.038   0.217     1.076  100.000   93.690
LGA    E    48_A      E    48_A     0.165     0    0.009   0.864     3.045  100.000   80.159
LGA    V    49_A      V    49_A     0.349     0    0.054   0.068     0.465  100.000  100.000
LGA    A    50_A      A    50_A     0.396     0    0.115   0.119     0.833   97.619   98.095
LGA    L    51_A      L    51_A     0.335     0    0.079   0.274     1.662   97.619   90.714
LGA    A    52_A      A    52_A     0.575     0    0.074   0.067     0.800   90.476   90.476
LGA    D    53_A      D    53_A     0.615     0    0.078   0.138     1.491   88.214   84.821
LGA    F    54_A      F    54_A     0.459     0    0.085   0.104     0.982   95.238   97.403
LGA    R    55_A      R    55_A     0.997     0    0.163   1.428    10.059   92.857   53.506
LGA    H    56_A      H    56_A     0.254     0    0.090   0.310     1.078   90.595   92.524
LGA    G    57_A      G    57_A     1.105     0    0.076   0.076     1.105   90.595   90.595
LGA    R    58_A      R    58_A     0.525     0    0.030   1.130     5.398   95.238   70.260
LGA    A    59_A      A    59_A     0.388     0    0.047   0.044     0.429  100.000  100.000
LGA    E    60_A      E    60_A     0.390     0    0.013   0.348     1.146  100.000   95.820
LGA    I    61_A      I    61_A     0.184     0    0.025   0.090     0.317  100.000  100.000
LGA    E    62_A      E    62_A     0.254     0    0.046   0.262     0.969  100.000   98.942
LGA    A    63_A      A    63_A     0.413     0    0.025   0.023     0.472  100.000  100.000
LGA    L    64_A      L    64_A     0.394     0    0.201   0.424     1.578   97.619   90.714
LGA    A    65_A      A    65_A     0.282     0    0.023   0.022     0.514   97.619   98.095
LGA    A    66_A      A    66_A     0.388     0    0.053   0.055     0.609   97.619   96.190
LGA    L    67_A      L    67_A     0.251     0    0.035   0.783     2.845  100.000   91.131
LGA    K    68_A      K    68_A     0.420     0    0.034   0.733     1.544  100.000   91.746
LGA    M    69_A      M    69_A     0.434     0    0.058   0.559     1.311  100.000   94.167
LGA    R    70_A      R    70_A     0.311     0    0.069   1.277     3.870   97.619   78.009
LGA    E    71_A      E    71_A     0.458     0    0.096   0.981     3.262   97.619   87.143
LGA    L    72_A      L    72_A     0.485     0    0.016   0.129     0.643   95.238   97.619
LGA    C    73_A      C    73_A     0.533     0    0.084   0.222     0.961   90.476   90.476
LGA    R    74_A      R    74_A     0.748     0    0.278   1.387     8.929   81.786   58.831
LGA    T    75_A      T    75_A     0.608     0    0.233   0.922     2.968   95.238   87.143
LGA    Y    76_A      Y    76_A     0.589     0    0.689   0.734     2.378   86.429   86.905
LGA    G    83_A      G    83_A     2.027     0    0.431   0.431     3.764   67.738   67.738
LGA    D    84_A      D    84_A     1.280     0    0.045   0.142     1.799   81.429   79.286
LGA    A    85_A      A    85_A     0.731     0    0.022   0.024     1.116   95.238   92.476
LGA    W    86_A      W    86_A     0.266     0    0.035   0.100     1.234  100.000   91.939
LGA    R    87_A      R    87_A     0.682     0    0.021   0.880     2.111   92.857   85.758
LGA    A    88_A      A    88_A     0.403     0    0.191   0.213     1.107   92.976   92.476
LGA    V    89_A      V    89_A     0.290     0    0.075   0.118     0.539   97.619   97.279
LGA    A    90_A      A    90_A     0.241     0    0.054   0.058     0.323  100.000  100.000
LGA    R    91_A      R    91_A     0.314     0    0.038   1.403     6.448  100.000   70.736
LGA    D    92_A      D    92_A     0.302     0    0.051   0.226     1.159  100.000   95.298
LGA    V    93_A      V    93_A     0.351     0    0.049   0.073     0.530  100.000   98.639
LGA    W    94_A      W    94_A     0.235     0    0.009   0.125     1.302  100.000   93.299
LGA    D    95_A      D    95_A     0.345     0    0.120   0.473     1.253   97.619   94.107
LGA    T    96_A      T    96_A     0.604     0    0.029   1.049     2.587   95.238   85.918
LGA    V    97_A      V    97_A     0.275     0    0.547   1.387     2.784   86.905   81.156
LGA    G    98_A      G    98_A     1.058     0    0.666   0.666     2.908   75.357   75.357

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       61     244    244  100.00     480    480  100.00                61
SUMMARY(RMSD_GDC):     0.563          0.675                  1.441           95.384   90.145

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   97   61    4.0     61    0.56    98.770    99.490     9.198

LGA_LOCAL      RMSD:   0.563  Number of atoms:   61  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.563  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   0.563  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.152456 * X  +   0.913089 * Y  +  -0.378186 * Z  +  -8.296340
  Y_new =  -0.436637 * X  +  -0.281060 * Y  +  -0.854607 * Z  +  18.815325
  Z_new =  -0.886626 * X  +   0.295420 * Y  +   0.355839 * Z  +   2.793437 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.234870  1.089998  0.692890   [DEG:  -70.7528   62.4523   39.6997 ]
ZXZ: -0.416621  1.206984 -1.249169   [DEG:  -23.8706   69.1551  -71.5721 ]
 
# END of job
