
#######################################################
#                                                     #
#                        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   62 (  421),  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        0.75     0.75
  LCS_AVERAGE:     95.31

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61      25_A - 85_A        0.75     0.75
  LCS_AVERAGE:     95.31

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61      25_A - 85_A        0.75     0.75
  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      3   11   21   58   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     40   58   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   58   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   58   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   58   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   58   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   58   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   58   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   58   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   58   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   58   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   58   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   58   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   58   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   58   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   58   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   58   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   58   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   58   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   58   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   58   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   58   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   58   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   58   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   58   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   58   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   58   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   58   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     49   58   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   58   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   58   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   58   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   58   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   58   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   58   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   58   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   58   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   58   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   58   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     14   58   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     14   58   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     38   58   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     14   41   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     14   58   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   58   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   58   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   58   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   58   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   58   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     50   58   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   58   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   58   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   58   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   58   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   58   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   58   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   58   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   58   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   58   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   58   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   55   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     58     59     59     60     60     61     61     61     61     61     61     61     61     61     61     61     61     61     61 
GDT PERCENT_AT  78.12  90.62  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   0.38   0.41   0.41   0.55   0.55   0.75   0.75   0.75   0.75   0.75   0.75   0.75   0.75   0.75   0.75   0.75   0.75   0.75   0.75
GDT RMS_ALL_AT   0.75   0.75   0.75   0.75   0.76   0.76   0.75   0.75   0.75   0.75   0.75   0.75   0.75   0.75   0.75   0.75   0.75   0.75   0.75   0.75

# Checking swapping

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D    25_A      D    25_A     2.986     0    0.496   1.168     5.101   45.833   45.298
LGA    G    26_A      G    26_A     0.678     0    0.067   0.067     0.865   90.476   90.476
LGA    Q    27_A      Q    27_A     0.497     0    0.022   1.169     3.582   97.619   82.593
LGA    G    28_A      G    28_A     0.293     0    0.004   0.004     0.391  100.000  100.000
LGA    L    29_A      L    29_A     0.324     0    0.026   0.128     0.478  100.000  100.000
LGA    Y    30_A      Y    30_A     0.258     0    0.031   0.083     0.375  100.000  100.000
LGA    A    31_A      A    31_A     0.262     0    0.037   0.040     0.377  100.000  100.000
LGA    A    32_A      A    32_A     0.226     0    0.030   0.037     0.336  100.000  100.000
LGA    N    33_A      N    33_A     0.315     0    0.045   0.110     0.588  100.000   98.810
LGA    C    34_A      C    34_A     0.189     0    0.012   0.092     0.476  100.000  100.000
LGA    A    35_A      A    35_A     0.400     0    0.024   0.023     0.647   95.238   96.190
LGA    A    36_A      A    36_A     0.418     0    0.014   0.016     0.501   97.619   98.095
LGA    C    37_A      C    37_A     0.426     0    0.037   0.041     0.634  100.000   98.413
LGA    H    38_A      H    38_A     0.469     0    0.033   0.257     0.985   97.619   93.333
LGA    G    39_A      G    39_A     0.534     0    0.071   0.071     0.759   90.476   90.476
LGA    A    40_A      A    40_A     0.334     0    0.030   0.031     0.388  100.000  100.000
LGA    L    41_A      L    41_A     0.145     0    0.019   0.069     0.390  100.000  100.000
LGA    A    42_A      A    42_A     0.194     0    0.056   0.062     0.272  100.000  100.000
LGA    T    43_A      T    43_A     0.244     0    0.139   0.137     0.651   97.619   97.279
LGA    S    44_A      S    44_A     0.285     0    0.078   0.088     0.454  100.000  100.000
LGA    E    45_A      E    45_A     0.612     0    0.062   0.725     2.600   90.476   78.201
LGA    K    46_A      K    46_A     0.162     0    0.035   0.422     3.137  100.000   87.407
LGA    K    47_A      K    47_A     0.112     0    0.030   0.127     1.113  100.000   93.757
LGA    G    48_A      G    48_A     0.189     0    0.034   0.034     0.189  100.000  100.000
LGA    T    49_A      T    49_A     0.053     0    0.055   0.071     0.340  100.000  100.000
LGA    T    50_A      T    50_A     0.320     0    0.025   0.102     0.894  100.000   95.918
LGA    L    51_A      L    51_A     0.319     0    0.030   0.098     0.794  100.000   98.810
LGA    A    52_A      A    52_A     0.512     0    0.020   0.027     0.703   97.619   96.190
LGA    R    53_A      R    53_A     0.548     0    0.014   0.998     4.325   95.238   77.316
LGA    L    54_A      L    54_A     0.284     0    0.029   0.111     0.452  100.000  100.000
LGA    Q    55_A      Q    55_A     0.247     0    0.035   0.235     0.642  100.000   98.942
LGA    S    56_A      S    56_A     0.427     0    0.016   0.050     0.592   95.238   96.825
LGA    A    57_A      A    57_A     0.496     0    0.054   0.054     0.780  100.000   98.095
LGA    V    58_A      V    58_A     0.401     0    0.013   0.040     0.535  100.000   97.279
LGA    S    59_A      S    59_A     0.182     0    0.013   0.548     1.886  100.000   95.476
LGA    A    60_A      A    60_A     0.080     0    0.017   0.034     0.204  100.000  100.000
LGA    N    61_A      N    61_A     0.272     0    0.020   0.205     1.299  100.000   94.107
LGA    A    62_A      A    62_A     0.176     0    0.033   0.033     0.770   97.619   96.190
LGA    G    63_A      G    63_A     0.301     0    0.030   0.030     0.736   95.238   95.238
LGA    G    64_A      G    64_A     0.638     0    0.056   0.056     0.683   92.857   92.857
LGA    M    65_A      M    65_A     0.683     0    0.051   0.606     1.873   90.476   87.143
LGA    G    66_A      G    66_A     0.595     0    0.056   0.056     0.654   92.857   92.857
LGA    F    67_A      F    67_A     1.228     0    0.028   0.182     1.994   81.429   78.312
LGA    L    68_A      L    68_A     1.031     0    0.038   0.123     1.802   85.952   80.476
LGA    S    69_A      S    69_A     0.363     0    0.044   0.049     0.586   97.619   96.825
LGA    S    70_A      S    70_A     0.440     0    0.012   0.057     0.536   97.619   95.238
LGA    L    71_A      L    71_A     0.280     0    0.074   0.101     0.472  100.000  100.000
LGA    T    72_A      T    72_A     0.239     0    0.043   0.092     0.607  100.000   98.639
LGA    S    73_A      S    73_A     0.391     0    0.019   0.037     0.565   97.619   95.238
LGA    A    74_A      A    74_A     0.421     0    0.034   0.041     0.513  100.000   98.095
LGA    Q    75_A      Q    75_A     0.219     0    0.006   0.326     1.077  100.000   96.878
LGA    L    76_A      L    76_A     0.193     0    0.018   0.068     0.394  100.000  100.000
LGA    Q    77_A      Q    77_A     0.119     0    0.070   0.180     0.508  100.000   98.942
LGA    A    78_A      A    78_A     0.161     0    0.026   0.029     0.365  100.000  100.000
LGA    I    79_A      I    79_A     0.366     0    0.011   0.046     0.497  100.000  100.000
LGA    V    80_A      V    80_A     0.271     0    0.025   0.054     0.336  100.000  100.000
LGA    D    81_A      D    81_A     0.469     0    0.021   0.122     1.061  100.000   94.107
LGA    V    82_A      V    82_A     0.304     0    0.058   1.241     2.602   97.619   86.395
LGA    L    83_A      L    83_A     0.404     0    0.057   0.139     1.016   92.976   96.488
LGA    A    84_A      A    84_A     0.428     0    0.660   0.608     2.294   86.548   87.333
LGA    V    85_A      V    85_A     3.837     0    0.559   1.064     8.417   46.905   30.068

# 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):     0.746          0.793                  1.181           91.319   89.010

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   62   64    4.0     61    0.75    93.359    94.291     7.209

LGA_LOCAL      RMSD:   0.746  Number of atoms:   61  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.746  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   0.746  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.983200 * X  +  -0.132697 * Y  +   0.125338 * Z  +  35.369087
  Y_new =  -0.168593 * X  +   0.397005 * Y  +  -0.902199 * Z  + -34.848843
  Z_new =   0.069960 * X  +  -0.908173 * Y  +  -0.412707 * Z  + -27.398397 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.971770 -0.070017 -1.997333   [DEG: -170.2699   -4.0117 -114.4388 ]
ZXZ:  0.138041  1.996220  3.064711   [DEG:    7.9092  114.3750  175.5950 ]
 
# END of job
