
#######################################################
#                                                     #
#                        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   99 (  793),  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        0.52     0.52
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61      32_A - 98_A        0.52     0.52
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61      32_A - 98_A        0.52     0.52
  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     50   59   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     43   59   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     50   59   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     50   59   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      6   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     45   59   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     50   59   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     21   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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      6   59   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      7   44   60   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     50   59   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     35   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     50   59   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     21   59   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     50   59   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    3    3   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     50     59     60     61     61     61     61     61     61     61     61     61     61     61     61     61     61     61     61     61 
GDT PERCENT_AT  81.97  96.72  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   0.41   0.44   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52
GDT RMS_ALL_AT   0.53   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52

# Checking swapping
#   possible swapping detected:  Y    47_A      Y    47_A
#   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     0.374     0    0.447   0.451     1.782   90.833   87.238
LGA    T    33_A      T    33_A     0.725     0    0.074   0.291     1.201   90.476   89.184
LGA    M    34_A      M    34_A     0.519     0    0.043   0.210     1.222   92.857   94.107
LGA    A    35_A      A    35_A     0.485     0    0.091   0.109     0.916   95.238   94.286
LGA    D    36_A      D    36_A     0.958     0    0.124   0.200     2.496   95.238   81.012
LGA    L    37_A      L    37_A     0.249     0    0.032   0.188     0.638  100.000   98.810
LGA    K    38_A      K    38_A     0.427     0    0.056   0.690     1.885   97.619   90.794
LGA    M    39_A      M    39_A     0.416     0    0.024   0.848     2.687  100.000   89.286
LGA    Q    40_A      Q    40_A     0.269     0    0.008   0.828     4.009  100.000   83.492
LGA    A    41_A      A    41_A     0.304     0    0.080   0.091     0.494  100.000  100.000
LGA    V    42_A      V    42_A     0.376     0    0.066   0.113     0.616   97.619   98.639
LGA    K    43_A      K    43_A     0.312     0    0.042   0.079     0.508  100.000   98.942
LGA    E    44_A      E    44_A     0.378     0    0.165   0.238     1.110   92.976   96.878
LGA    I    45_A      I    45_A     0.150     0    0.024   0.093     0.771  100.000   98.810
LGA    C    46_A      C    46_A     0.187     0    0.098   0.111     0.645   97.619   98.413
LGA    Y    47_A      Y    47_A     0.122     0    0.061   1.249     7.975  100.000   62.103
LGA    E    48_A      E    48_A     0.208     0    0.019   0.856     2.654  100.000   83.492
LGA    V    49_A      V    49_A     0.412     0    0.057   0.073     0.597  100.000   98.639
LGA    A    50_A      A    50_A     0.311     0    0.059   0.056     0.501   97.619   98.095
LGA    L    51_A      L    51_A     0.311     0    0.123   0.319     1.851   97.619   88.512
LGA    A    52_A      A    52_A     0.418     0    0.032   0.031     0.546   97.619   96.190
LGA    D    53_A      D    53_A     0.290     0    0.029   0.151     0.933  100.000   96.429
LGA    F    54_A      F    54_A     0.355     0    0.067   0.084     0.520   97.619   99.134
LGA    R    55_A      R    55_A     0.742     0    0.122   1.493    10.241   95.238   54.242
LGA    H    56_A      H    56_A     0.280     0    0.068   0.327     0.967   97.619   96.190
LGA    G    57_A      G    57_A     0.729     0    0.075   0.075     0.729   95.238   95.238
LGA    R    58_A      R    58_A     0.410     0    0.056   1.104     5.091   97.619   73.939
LGA    A    59_A      A    59_A     0.263     0    0.054   0.050     0.311  100.000  100.000
LGA    E    60_A      E    60_A     0.148     0    0.016   0.414     1.084  100.000   95.820
LGA    I    61_A      I    61_A     0.208     0    0.018   0.060     0.418  100.000  100.000
LGA    E    62_A      E    62_A     0.205     0    0.030   0.208     0.758  100.000   96.825
LGA    A    63_A      A    63_A     0.356     0    0.018   0.020     0.436  100.000  100.000
LGA    L    64_A      L    64_A     0.310     0    0.220   0.440     1.696   97.619   89.583
LGA    A    65_A      A    65_A     0.226     0    0.019   0.019     0.454  100.000  100.000
LGA    A    66_A      A    66_A     0.430     0    0.045   0.046     0.636   97.619   96.190
LGA    L    67_A      L    67_A     0.216     0    0.034   0.772     2.979  100.000   91.131
LGA    K    68_A      K    68_A     0.233     0    0.040   0.259     1.702  100.000   92.857
LGA    M    69_A      M    69_A     0.370     0    0.038   0.551     1.461  100.000   95.357
LGA    R    70_A      R    70_A     0.255     0    0.081   1.249     3.081   97.619   84.589
LGA    E    71_A      E    71_A     0.506     0    0.086   0.824     2.710   97.619   88.942
LGA    L    72_A      L    72_A     0.471     0    0.030   0.169     0.567  100.000   98.810
LGA    C    73_A      C    73_A     0.351     0    0.090   0.229     1.006  100.000   96.905
LGA    R    74_A      R    74_A     0.525     0    0.286   0.719     5.990   88.452   64.892
LGA    T    75_A      T    75_A     0.419     0    0.139   0.201     1.362   97.619   93.265
LGA    Y    76_A      Y    76_A     0.800     0    0.670   0.660     2.518   82.143   86.944
LGA    G    83_A      G    83_A     1.236     0    0.235   0.235     1.236   88.214   88.214
LGA    D    84_A      D    84_A     0.239     0    0.069   0.459     0.936   95.238   94.048
LGA    A    85_A      A    85_A     0.588     0    0.036   0.036     0.864   95.238   94.286
LGA    W    86_A      W    86_A     0.316     0    0.045   0.079     0.819  100.000   96.599
LGA    R    87_A      R    87_A     0.473     0    0.022   0.236     0.932   97.619   93.074
LGA    A    88_A      A    88_A     0.323     0    0.147   0.169     0.992   97.619   98.095
LGA    V    89_A      V    89_A     0.278     0    0.070   0.120     0.546   97.619   97.279
LGA    A    90_A      A    90_A     0.325     0    0.058   0.067     0.396  100.000  100.000
LGA    R    91_A      R    91_A     0.323     0    0.041   0.479     1.345  100.000   94.848
LGA    D    92_A      D    92_A     0.100     0    0.044   0.267     1.045  100.000   97.679
LGA    V    93_A      V    93_A     0.268     0    0.024   0.068     0.492  100.000  100.000
LGA    W    94_A      W    94_A     0.270     0    0.025   0.098     0.452  100.000  100.000
LGA    D    95_A      D    95_A     0.362     0    0.112   0.467     1.036   97.619   95.298
LGA    T    96_A      T    96_A     0.648     0    0.058   1.160     2.639   97.619   86.122
LGA    V    97_A      V    97_A     0.640     0    0.442   0.359     2.089   86.429   86.871
LGA    G    98_A      G    98_A     2.211     0    0.407   0.407     2.211   77.381   77.381

# 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):     0.520          0.549                  1.359           96.983   92.033

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   99   61    4.0     61    0.52    99.180    99.619     9.831

LGA_LOCAL      RMSD:   0.520  Number of atoms:   61  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.520  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   0.520  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.789865 * X  +  -0.166199 * Y  +  -0.590331 * Z  +   2.580099
  Y_new =   0.529026 * X  +   0.302280 * Y  +  -0.792942 * Z  +  26.157784
  Z_new =   0.310232 * X  +  -0.938618 * Y  +  -0.150837 * Z  + -13.060800 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.551446 -0.315437 -1.730135   [DEG:  146.1871  -18.0732  -99.1294 ]
ZXZ: -0.639960  1.722211  2.822376   [DEG:  -36.6670   98.6754  161.7103 ]
 
# END of job
