
#######################################################
#                                                     #
#                        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   69 (  472),  selected   61 , name one
# Molecule2: number of CA atoms   64 (  433),  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      25_A - 85_A        0.77     0.77
  LCS_AVERAGE:     95.31

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61      25_A - 85_A        0.77     0.77
  LCS_AVERAGE:     95.31

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61      25_A - 85_A        0.77     0.77
  LCS_AVERAGE:     95.31

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     D    25_A     D    25_A     61   61   61      4   11   14   51   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     G    26_A     G    26_A     61   61   61     42   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    27_A     Q    27_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     G    28_A     G    28_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    29_A     L    29_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y    30_A     Y    30_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    31_A     A    31_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    32_A     A    32_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     N    33_A     N    33_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     C    34_A     C    34_A     61   61   61     50   59   59   59   60   60   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     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    36_A     A    36_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     C    37_A     C    37_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    38_A     H    38_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     G    39_A     G    39_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    40_A     A    40_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    41_A     L    41_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    42_A     A    42_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    43_A     T    43_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     S    44_A     S    44_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    45_A     E    45_A     61   61   61     28   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    46_A     K    46_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    47_A     K    47_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     G    48_A     G    48_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    49_A     T    49_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    50_A     T    50_A     61   61   61     50   59   59   59   60   60   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     50   59   59   59   60   60   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     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    53_A     R    53_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    54_A     L    54_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    55_A     Q    55_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     S    56_A     S    56_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    57_A     A    57_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    58_A     V    58_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     S    59_A     S    59_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    60_A     A    60_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     N    61_A     N    61_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    62_A     A    62_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     G    63_A     G    63_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     G    64_A     G    64_A     61   61   61     16   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    65_A     M    65_A     61   61   61     16   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     G    66_A     G    66_A     61   61   61     46   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     F    67_A     F    67_A     61   61   61     16   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    68_A     L    68_A     61   61   61     16   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     S    69_A     S    69_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     S    70_A     S    70_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    71_A     L    71_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    72_A     T    72_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     S    73_A     S    73_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    74_A     A    74_A     61   61   61     46   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    75_A     Q    75_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    76_A     L    76_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    77_A     Q    77_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    78_A     A    78_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    79_A     I    79_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    80_A     V    80_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    81_A     D    81_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    82_A     V    82_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    83_A     L    83_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    84_A     A    84_A     61   61   61     50   59   59   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    85_A     V    85_A     61   61   61      3    4    5    5   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_AVERAGE  LCS_A:  95.31  (  95.31   95.31   95.31 )

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     50     59     59     59     60     60     61     61     61     61     61     61     61     61     61     61     61     61     61     61 
GDT PERCENT_AT  78.12  92.19  92.19  92.19  93.75  93.75  95.31  95.31  95.31  95.31  95.31  95.31  95.31  95.31  95.31  95.31  95.31  95.31  95.31  95.31
GDT RMS_LOCAL    0.31   0.41   0.41   0.41   0.57   0.57   0.77   0.77   0.77   0.77   0.77   0.77   0.77   0.77   0.77   0.77   0.77   0.77   0.77   0.77
GDT RMS_ALL_AT   0.78   0.78   0.78   0.78   0.78   0.78   0.77   0.77   0.77   0.77   0.77   0.77   0.77   0.77   0.77   0.77   0.77   0.77   0.77   0.77

# Checking swapping
#   possible swapping detected:  D    25_A      D    25_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D    25_A      D    25_A     3.187     0    0.451   1.056     5.257   45.833   37.976
LGA    G    26_A      G    26_A     0.693     0    0.038   0.038     0.890   90.476   90.476
LGA    Q    27_A      Q    27_A     0.395     0    0.027   1.154     3.599   97.619   83.651
LGA    G    28_A      G    28_A     0.140     0    0.012   0.012     0.301  100.000  100.000
LGA    L    29_A      L    29_A     0.337     0    0.029   0.114     0.801  100.000   97.619
LGA    Y    30_A      Y    30_A     0.239     0    0.025   0.080     0.340  100.000  100.000
LGA    A    31_A      A    31_A     0.196     0    0.036   0.038     0.305  100.000  100.000
LGA    A    32_A      A    32_A     0.193     0    0.024   0.027     0.288  100.000  100.000
LGA    N    33_A      N    33_A     0.229     0    0.025   0.097     0.470  100.000  100.000
LGA    C    34_A      C    34_A     0.128     0    0.013   0.103     0.579  100.000   98.413
LGA    A    35_A      A    35_A     0.339     0    0.024   0.023     0.603   97.619   98.095
LGA    A    36_A      A    36_A     0.424     0    0.012   0.016     0.494  100.000  100.000
LGA    C    37_A      C    37_A     0.403     0    0.046   0.046     0.648  100.000   98.413
LGA    H    38_A      H    38_A     0.425     0    0.032   0.281     0.961   97.619   93.333
LGA    G    39_A      G    39_A     0.506     0    0.074   0.074     0.652   95.238   95.238
LGA    A    40_A      A    40_A     0.321     0    0.035   0.032     0.413  100.000  100.000
LGA    L    41_A      L    41_A     0.186     0    0.026   0.079     0.376  100.000  100.000
LGA    A    42_A      A    42_A     0.267     0    0.047   0.052     0.384  100.000  100.000
LGA    T    43_A      T    43_A     0.155     0    0.132   0.121     0.709   97.619   97.279
LGA    S    44_A      S    44_A     0.265     0    0.083   0.095     0.550   97.619   98.413
LGA    E    45_A      E    45_A     0.667     0    0.071   0.728     2.708   90.476   77.354
LGA    K    46_A      K    46_A     0.210     0    0.040   0.444     3.169  100.000   86.455
LGA    K    47_A      K    47_A     0.144     0    0.035   0.165     1.078  100.000   94.762
LGA    G    48_A      G    48_A     0.129     0    0.045   0.045     0.224  100.000  100.000
LGA    T    49_A      T    49_A     0.089     0    0.052   0.063     0.293  100.000  100.000
LGA    T    50_A      T    50_A     0.317     0    0.028   0.096     0.890  100.000   95.918
LGA    L    51_A      L    51_A     0.299     0    0.028   0.112     0.791  100.000   98.810
LGA    A    52_A      A    52_A     0.503     0    0.021   0.029     0.673   97.619   96.190
LGA    R    53_A      R    53_A     0.561     0    0.013   1.012     4.125   95.238   78.052
LGA    L    54_A      L    54_A     0.306     0    0.016   0.109     0.470  100.000  100.000
LGA    Q    55_A      Q    55_A     0.280     0    0.034   0.210     0.490  100.000  100.000
LGA    S    56_A      S    56_A     0.448     0    0.017   0.049     0.554   95.238   96.825
LGA    A    57_A      A    57_A     0.514     0    0.035   0.036     0.744   95.238   94.286
LGA    V    58_A      V    58_A     0.433     0    0.020   0.061     0.601  100.000   95.918
LGA    S    59_A      S    59_A     0.217     0    0.019   0.540     1.863  100.000   95.476
LGA    A    60_A      A    60_A     0.185     0    0.012   0.030     0.313  100.000  100.000
LGA    N    61_A      N    61_A     0.320     0    0.023   0.227     1.340  100.000   94.107
LGA    A    62_A      A    62_A     0.087     0    0.027   0.028     0.755   97.619   98.095
LGA    G    63_A      G    63_A     0.480     0    0.026   0.026     0.890   95.238   95.238
LGA    G    64_A      G    64_A     0.767     0    0.036   0.036     0.767   90.476   90.476
LGA    M    65_A      M    65_A     0.686     0    0.041   0.649     1.872   90.476   87.143
LGA    G    66_A      G    66_A     0.560     0    0.020   0.020     0.655   92.857   92.857
LGA    F    67_A      F    67_A     1.147     0    0.069   0.177     1.956   83.690   79.913
LGA    L    68_A      L    68_A     1.071     0    0.069   0.117     1.669   85.952   81.548
LGA    S    69_A      S    69_A     0.372     0    0.027   0.066     0.682   97.619   98.413
LGA    S    70_A      S    70_A     0.461     0    0.008   0.031     0.736   97.619   95.238
LGA    L    71_A      L    71_A     0.343     0    0.034   0.097     0.587  100.000   95.238
LGA    T    72_A      T    72_A     0.252     0    0.047   0.080     0.628  100.000   98.639
LGA    S    73_A      S    73_A     0.481     0    0.022   0.619     3.005   95.238   86.905
LGA    A    74_A      A    74_A     0.512     0    0.042   0.052     0.625   97.619   96.190
LGA    Q    75_A      Q    75_A     0.193     0    0.011   0.220     1.083  100.000   96.878
LGA    L    76_A      L    76_A     0.227     0    0.016   0.078     0.477  100.000  100.000
LGA    Q    77_A      Q    77_A     0.130     0    0.068   0.147     0.353  100.000  100.000
LGA    A    78_A      A    78_A     0.095     0    0.038   0.034     0.367  100.000  100.000
LGA    I    79_A      I    79_A     0.344     0    0.009   0.054     0.505  100.000   98.810
LGA    V    80_A      V    80_A     0.214     0    0.023   0.053     0.297  100.000  100.000
LGA    D    81_A      D    81_A     0.349     0    0.025   0.112     0.871  100.000   96.429
LGA    V    82_A      V    82_A     0.265     0    0.039   1.230     2.609   97.619   86.395
LGA    L    83_A      L    83_A     0.420     0    0.036   0.101     0.800   95.238   97.619
LGA    A    84_A      A    84_A     0.464     0    0.627   0.564     1.863   88.571   88.952
LGA    V    85_A      V    85_A     3.974     0    0.463   1.044     8.397   39.524   26.190

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       61     244    244  100.00     416    416  100.00                64
SUMMARY(RMSD_GDC):     0.772          0.842                  1.233           91.231   88.754

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   69   64    4.0     61    0.77    93.750    94.415     6.993

LGA_LOCAL      RMSD:   0.772  Number of atoms:   61  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.772  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   0.772  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.696524 * X  +  -0.646034 * Y  +  -0.312239 * Z  +  21.530767
  Y_new =  -0.232623 * X  +   0.614965 * Y  +  -0.753462 * Z  + -33.925159
  Z_new =   0.678778 * X  +  -0.452170 * Y  +  -0.578620 * Z  + -34.768806 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.819263 -0.746098 -2.478257   [DEG: -161.5319  -42.7483 -141.9937 ]
ZXZ: -0.392864  2.187833  2.158443   [DEG:  -22.5094  125.3536  123.6697 ]
 
# END of job
