
#######################################################
#                                                     #
#                        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   65 (  516),  selected   51 , name one
# Molecule2: number of CA atoms   51 (  404),  selected   51 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:C  -ch2:C  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    51       6_C - 56_C        1.58     1.58
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    51       6_C - 56_C        1.58     1.58
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    46       6_C - 51_C        0.97     1.82
  LONGEST_CONTINUOUS_SEGMENT:    46       7_C - 52_C        0.96     1.73
  LONGEST_CONTINUOUS_SEGMENT:    46       8_C - 53_C        0.86     1.66
  LCS_AVERAGE:     86.39

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   51
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     P     6_C     P     6_C     46   51   51      4    6   16   32   45   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     T     7_C     T     7_C     46   51   51      4    6    8   32   41   46   46   48   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     K     8_C     K     8_C     46   51   51      4   33   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     I     9_C     I     9_C     46   51   51     24   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     L    10_C     L    10_C     46   51   51     29   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     P    11_C     P    11_C     46   51   51     33   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     C    12_C     C    12_C     46   51   51     33   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     P    13_C     P    13_C     46   51   51     33   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     R    14_C     R    14_C     46   51   51     33   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     C    15_C     C    15_C     46   51   51     33   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     N    16_C     N    16_C     46   51   51     33   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     S    17_C     S    17_C     46   51   51     33   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     M    18_C     M    18_C     46   51   51     33   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     E    19_C     E    19_C     46   51   51     29   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     T    20_C     T    20_C     46   51   51     14   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     K    21_C     K    21_C     46   51   51     33   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     F    22_C     F    22_C     46   51   51     33   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     C    23_C     C    23_C     46   51   51     33   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     Y    24_C     Y    24_C     46   51   51     33   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     Y    25_C     Y    25_C     46   51   51     33   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     N    26_C     N    26_C     46   51   51     10   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     N    27_C     N    27_C     46   51   51     13   40   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     Y    28_C     Y    28_C     46   51   51     24   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     N    29_C     N    29_C     46   51   51     33   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     V    30_C     V    30_C     46   51   51     33   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     N    31_C     N    31_C     46   51   51     33   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     Q    32_C     Q    32_C     46   51   51     33   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     P    33_C     P    33_C     46   51   51     33   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     R    34_C     R    34_C     46   51   51     33   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     H    35_C     H    35_C     46   51   51     33   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     F    36_C     F    36_C     46   51   51     33   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     C    37_C     C    37_C     46   51   51     33   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     K    38_C     K    38_C     46   51   51     33   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     A    39_C     A    39_C     46   51   51     33   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     C    40_C     C    40_C     46   51   51     33   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     Q    41_C     Q    41_C     46   51   51     33   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     R    42_C     R    42_C     46   51   51     33   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     Y    43_C     Y    43_C     46   51   51     33   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     W    44_C     W    44_C     46   51   51     33   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     T    45_C     T    45_C     46   51   51     33   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     S    46_C     S    46_C     46   51   51     33   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     G    47_C     G    47_C     46   51   51     33   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     G    48_C     G    48_C     46   51   51     33   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     T    49_C     T    49_C     46   51   51     10   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     M    50_C     M    50_C     46   51   51      8   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     R    51_C     R    51_C     46   51   51     24   42   43   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     S    52_C     S    52_C     46   51   51      3   18   42   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     V    53_C     V    53_C     46   51   51      3   15   39   45   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     P    54_C     P    54_C     13   51   51      3    5    9   28   42   46   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     I    55_C     I    55_C     13   51   51      3   13   23   38   47   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     G    56_C     G    56_C     13   51   51      3    6   16   28   42   47   49   50   51   51   51   51   51   51   51   51   51   51   51   51 
LCS_AVERAGE  LCS_A:  95.46  (  86.39  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     33     42     43     45     47     47     49     50     51     51     51     51     51     51     51     51     51     51     51     51 
GDT PERCENT_AT  64.71  82.35  84.31  88.24  92.16  92.16  96.08  98.04 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.31   0.52   0.55   0.74   1.03   1.03   1.30   1.45   1.58   1.58   1.58   1.58   1.58   1.58   1.58   1.58   1.58   1.58   1.58   1.58
GDT RMS_ALL_AT   1.80   1.74   1.75   1.70   1.62   1.62   1.59   1.59   1.58   1.58   1.58   1.58   1.58   1.58   1.58   1.58   1.58   1.58   1.58   1.58

# Checking swapping
#   possible swapping detected:  F    22_C      F    22_C
#   possible swapping detected:  F    36_C      F    36_C

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    P     6_C      P     6_C     3.576     2    0.154   0.153     4.769   38.810   30.340
LGA    T     7_C      T     7_C     4.899     0    0.154   0.449     6.898   32.976   27.551
LGA    K     8_C      K     8_C     2.522     4    0.200   0.197     2.878   65.000   36.085
LGA    I     9_C      I     9_C     1.134     0    0.049   0.717     3.495   81.429   77.560
LGA    L    10_C      L    10_C     0.850     0    0.047   0.219     2.021   90.476   86.131
LGA    P    11_C      P    11_C     0.566     0    0.023   0.063     0.960   90.476   90.476
LGA    C    12_C      C    12_C     0.746     0    0.044   0.117     1.229   88.214   87.460
LGA    P    13_C      P    13_C     1.052     0    0.088   0.303     1.747   83.690   82.789
LGA    R    14_C      R    14_C     1.297     0    0.153   0.587     3.608   77.262   71.948
LGA    C    15_C      C    15_C     0.902     0    0.058   0.160     1.133   88.214   87.460
LGA    N    16_C      N    16_C     0.549     0    0.054   0.261     1.413   90.476   88.274
LGA    S    17_C      S    17_C     0.579     0    0.096   0.142     0.817   92.857   92.063
LGA    M    18_C      M    18_C     0.372     0    0.040   0.611     1.601   95.238   91.845
LGA    E    19_C      E    19_C     0.673     4    0.048   0.047     0.853   90.476   50.265
LGA    T    20_C      T    20_C     0.765     0    0.085   0.105     0.953   90.476   90.476
LGA    K    21_C      K    21_C     0.586     0    0.012   0.457     3.773   90.476   77.778
LGA    F    22_C      F    22_C     0.546     0    0.015   0.054     0.652   90.476   92.208
LGA    C    23_C      C    23_C     0.611     0    0.031   0.049     0.696   90.476   90.476
LGA    Y    24_C      Y    24_C     0.640     0    0.017   0.062     0.920   90.476   90.476
LGA    Y    25_C      Y    25_C     0.505     0    0.067   0.085     0.996   90.476   92.857
LGA    N    26_C      N    26_C     1.058     0    0.066   0.262     2.363   83.690   78.333
LGA    N    27_C      N    27_C     1.741     0    0.022   0.358     3.291   75.000   69.048
LGA    Y    28_C      Y    28_C     1.390     0    0.075   0.087     3.415   81.429   65.992
LGA    N    29_C      N    29_C     0.531     0    0.070   0.214     0.773   95.238   97.619
LGA    V    30_C      V    30_C     0.370     0    0.046   1.147     2.978  100.000   87.483
LGA    N    31_C      N    31_C     0.238     0    0.029   0.410     1.516  100.000   94.226
LGA    Q    32_C      Q    32_C     0.371     0    0.015   0.329     1.159   97.619   93.704
LGA    P    33_C      P    33_C     0.505     0    0.033   0.060     0.769   92.857   94.558
LGA    R    34_C      R    34_C     0.687     0    0.031   0.931     4.059   90.476   78.658
LGA    H    35_C      H    35_C     0.531     0    0.065   1.067     2.710   90.476   84.571
LGA    F    36_C      F    36_C     0.985     0    0.016   0.128     1.778   90.476   82.381
LGA    C    37_C      C    37_C     0.986     0    0.070   0.127     1.383   85.952   87.460
LGA    K    38_C      K    38_C     0.826     0    0.098   0.477     1.541   90.476   84.550
LGA    A    39_C      A    39_C     0.839     0    0.101   0.099     0.898   90.476   90.476
LGA    C    40_C      C    40_C     1.379     0    0.023   0.032     1.471   81.429   81.429
LGA    Q    41_C      Q    41_C     1.521     0    0.039   0.086     1.717   77.143   74.762
LGA    R    42_C      R    42_C     1.426     0    0.018   1.325     6.681   81.429   60.996
LGA    Y    43_C      Y    43_C     1.100     0    0.053   0.110     1.287   81.429   81.429
LGA    W    44_C      W    44_C     0.791     0    0.034   0.194     1.094   90.476   88.537
LGA    T    45_C      T    45_C     0.436     0    0.057   0.118     0.665   95.238   94.558
LGA    S    46_C      S    46_C     0.523     0    0.035   0.185     0.979   92.857   93.651
LGA    G    47_C      G    47_C     0.771     0    0.035   0.035     1.104   88.214   88.214
LGA    G    48_C      G    48_C     0.971     0    0.103   0.103     0.971   90.476   90.476
LGA    T    49_C      T    49_C     0.703     0    0.110   0.193     1.233   88.214   87.891
LGA    M    50_C      M    50_C     0.707     0    0.126   0.691     4.256   92.857   73.036
LGA    R    51_C      R    51_C     0.522     0    0.133   0.507     3.741   92.857   73.506
LGA    S    52_C      S    52_C     1.454     0    0.060   0.159     2.575   79.405   74.603
LGA    V    53_C      V    53_C     2.041     0    0.140   1.156     3.636   68.810   61.905
LGA    P    54_C      P    54_C     4.397     0    0.088   0.173     5.728   41.786   35.306
LGA    I    55_C      I    55_C     3.160     0    0.116   1.366     4.126   45.000   45.952
LGA    G    56_C      G    56_C     4.171     0    0.654   0.654     5.094   34.524   34.524

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       51     204    204  100.00     404    404  100.00                51
SUMMARY(RMSD_GDC):     1.577          1.610                  1.804           83.035   77.732

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   65   51    4.0     50    1.45    92.157    95.287     3.235

LGA_LOCAL      RMSD:   1.446  Number of atoms:   50  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.587  Number of assigned atoms:   51 
Std_ASGN_ATOMS RMSD:   1.577  Standard rmsd on all 51 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.296795 * X  +   0.435409 * Y  +  -0.849901 * Z  + -28.534933
  Y_new =  -0.915326 * X  +   0.383397 * Y  +  -0.123226 * Z  +  -7.915598
  Z_new =   0.272195 * X  +   0.814510 * Y  +   0.512332 * Z  +   5.271176 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.257242 -0.275674  1.009321   [DEG:  -72.0347  -15.7949   57.8298 ]
ZXZ: -1.426811  1.032899  0.322515   [DEG:  -81.7502   59.1807   18.4788 ]
 
# END of job
