
#######################################################
#                                                     #
#                        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        4.68     4.68
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    42       6_C - 47_C        1.96     5.68
  LONGEST_CONTINUOUS_SEGMENT:    42       7_C - 48_C        1.85     5.67
  LCS_AVERAGE:     72.43

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18       7_C - 24_C        0.60     6.02
  LCS_AVERAGE:     26.07

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      3   42   51      3    3    3    3    5    6    7   38   40   43   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     T     7_C     T     7_C     18   42   51      3   30   34   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     K     8_C     K     8_C     18   42   51     21   30   34   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     I     9_C     I     9_C     18   42   51     21   30   34   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     L    10_C     L    10_C     18   42   51     21   30   34   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     P    11_C     P    11_C     18   42   51     21   30   34   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     C    12_C     C    12_C     18   42   51     21   30   34   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     P    13_C     P    13_C     18   42   51     19   30   34   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     R    14_C     R    14_C     18   42   51     19   30   34   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     C    15_C     C    15_C     18   42   51     17   30   34   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     N    16_C     N    16_C     18   42   51     21   30   34   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     S    17_C     S    17_C     18   42   51     21   30   34   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     M    18_C     M    18_C     18   42   51     21   30   34   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     E    19_C     E    19_C     18   42   51     21   30   34   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     T    20_C     T    20_C     18   42   51     21   30   34   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     K    21_C     K    21_C     18   42   51     12   30   34   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     F    22_C     F    22_C     18   42   51     21   30   34   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     C    23_C     C    23_C     18   42   51     20   30   34   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     Y    24_C     Y    24_C     18   42   51      3   30   34   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     Y    25_C     Y    25_C      3   42   51      3    3    4    5    7    7   29   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     N    26_C     N    26_C      3   42   51      3    4    6   21   29   37   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     N    27_C     N    27_C      3   42   51      3    3    4    4    6   36   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     Y    28_C     Y    28_C      3   42   51      4   22   34   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     N    29_C     N    29_C      7   42   51      0    4   14   29   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     V    30_C     V    30_C      7   42   51      3    4   14   26   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     N    31_C     N    31_C      7   42   51      4    7   15   28   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     Q    32_C     Q    32_C     17   42   51      4   12   28   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     P    33_C     P    33_C     17   42   51      5   29   34   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     R    34_C     R    34_C     17   42   51     21   30   34   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     H    35_C     H    35_C     17   42   51     21   30   34   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     F    36_C     F    36_C     17   42   51     21   30   34   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     C    37_C     C    37_C     17   42   51     21   30   34   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     K    38_C     K    38_C     17   42   51     21   30   34   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     A    39_C     A    39_C     17   42   51     21   30   34   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     C    40_C     C    40_C     17   42   51     21   30   34   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     Q    41_C     Q    41_C     17   42   51     21   30   34   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     R    42_C     R    42_C     17   42   51     21   30   34   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     Y    43_C     Y    43_C     17   42   51     21   30   34   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     W    44_C     W    44_C     17   42   51     21   30   34   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     T    45_C     T    45_C     17   42   51     12   30   34   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     S    46_C     S    46_C     17   42   51     15   30   34   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     G    47_C     G    47_C     17   42   51     20   30   34   35   38   38   40   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     G    48_C     G    48_C     17   42   51      3   10   23   34   36   37   39   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     T    49_C     T    49_C      3   22   51      3    3    6   18   25   31   38   41   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     M    50_C     M    50_C      3    8   51      3    3    3    7   11   16   19   28   36   43   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     R    51_C     R    51_C      3    8   51      3    3    4    6   13   25   33   40   43   44   45   47   47   48   49   49   49   49   50   51 
LCS_GDT     S    52_C     S    52_C      4    8   51      3    3    4    5   11   12   16   25   29   36   44   47   47   48   49   49   49   49   50   51 
LCS_GDT     V    53_C     V    53_C      4    8   51      3    4    4    6   11   12   14   18   22   26   35   38   44   48   49   49   49   49   50   51 
LCS_GDT     P    54_C     P    54_C      4    8   51      3    4    4    5   11   12   14   18   19   25   35   38   42   46   49   49   49   49   50   51 
LCS_GDT     I    55_C     I    55_C      4    8   51      3    4    4    5    8    8   14   18   18   19   22   26   28   30   32   35   43   47   50   51 
LCS_GDT     G    56_C     G    56_C      4    8   51      3    4    4    5    8   10   14   18   18   19   22   23   27   29   32   37   43   47   50   51 
LCS_AVERAGE  LCS_A:  66.17  (  26.07   72.43  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     21     30     34     35     38     38     40     41     43     44     45     47     47     48     49     49     49     49     50     51 
GDT PERCENT_AT  41.18  58.82  66.67  68.63  74.51  74.51  78.43  80.39  84.31  86.27  88.24  92.16  92.16  94.12  96.08  96.08  96.08  96.08  98.04 100.00
GDT RMS_LOCAL    0.33   0.49   0.71   0.83   1.27   1.27   1.58   1.77   2.14   2.27   2.39   2.98   2.98   3.36   3.72   3.72   3.72   3.72   4.22   4.68
GDT RMS_ALL_AT   5.83   5.89   5.83   5.74   5.68   5.68   5.69   5.71   5.36   5.37   5.36   5.07   5.07   4.92   4.80   4.80   4.80   4.80   4.71   4.68

# Checking swapping
#   possible swapping detected:  Y    24_C      Y    24_C
#   possible swapping detected:  Y    25_C      Y    25_C
#   possible swapping detected:  Y    28_C      Y    28_C
#   possible swapping detected:  Y    43_C      Y    43_C

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    P     6_C      P     6_C     5.851     2    0.674   0.606     6.952   22.262   14.626
LGA    T     7_C      T     7_C     1.740     0    0.633   0.971     4.110   72.976   63.401
LGA    K     8_C      K     8_C     0.772     4    0.049   0.045     1.018   88.214   49.259
LGA    I     9_C      I     9_C     0.496     0    0.030   0.160     0.690   95.238   95.238
LGA    L    10_C      L    10_C     0.752     0    0.033   0.083     1.441   92.857   87.143
LGA    P    11_C      P    11_C     0.777     0    0.018   0.068     1.099   90.476   89.184
LGA    C    12_C      C    12_C     0.861     0    0.080   0.111     1.291   85.952   87.460
LGA    P    13_C      P    13_C     1.298     0    0.011   0.085     1.474   81.429   81.429
LGA    R    14_C      R    14_C     1.520     0    0.192   0.991     2.528   72.976   72.294
LGA    C    15_C      C    15_C     1.272     0    0.022   0.206     1.287   81.429   82.937
LGA    N    16_C      N    16_C     0.976     0    0.151   0.259     1.451   83.690   87.083
LGA    S    17_C      S    17_C     0.685     0    0.041   0.122     0.985   90.476   90.476
LGA    M    18_C      M    18_C     0.378     0    0.030   0.669     1.673   97.619   90.714
LGA    E    19_C      E    19_C     0.527     4    0.062   0.060     0.840   92.857   51.323
LGA    T    20_C      T    20_C     0.432     0    0.006   0.069     0.709   95.238   97.279
LGA    K    21_C      K    21_C     0.724     0    0.044   0.446     1.380   90.476   86.455
LGA    F    22_C      F    22_C     0.597     0    0.029   0.113     2.542   88.333   78.788
LGA    C    23_C      C    23_C     2.005     0    0.568   0.600     4.683   58.690   62.063
LGA    Y    24_C      Y    24_C     1.332     0    0.694   0.521    11.424   67.738   32.143
LGA    Y    25_C      Y    25_C     5.194     0    0.609   1.458    15.412   37.976   13.730
LGA    N    26_C      N    26_C     4.102     0    0.609   0.613     6.922   40.476   30.536
LGA    N    27_C      N    27_C     3.715     0    0.222   0.278     7.490   48.452   31.488
LGA    Y    28_C      Y    28_C     1.603     0    0.651   0.478     3.855   67.857   69.365
LGA    N    29_C      N    29_C     2.399     0    0.252   0.587     3.633   62.857   62.143
LGA    V    30_C      V    30_C     2.850     0    0.645   0.883     5.290   52.143   50.136
LGA    N    31_C      N    31_C     3.331     0    0.119   0.429     6.930   51.905   36.369
LGA    Q    32_C      Q    32_C     2.119     0    0.099   0.817     6.021   70.952   51.217
LGA    P    33_C      P    33_C     0.739     0    0.152   0.182     1.727   83.810   86.735
LGA    R    34_C      R    34_C     1.331     0    0.177   1.064     7.697   81.548   53.506
LGA    H    35_C      H    35_C     1.113     0    0.081   1.051     2.607   81.429   75.619
LGA    F    36_C      F    36_C     0.728     0    0.023   0.075     0.940   90.476   90.476
LGA    C    37_C      C    37_C     0.585     0    0.023   0.803     3.011   90.476   83.730
LGA    K    38_C      K    38_C     0.671     0    0.083   0.448     1.762   90.476   89.577
LGA    A    39_C      A    39_C     0.468     0    0.194   0.206     0.569   97.619   96.190
LGA    C    40_C      C    40_C     0.845     0    0.031   0.033     0.943   90.476   90.476
LGA    Q    41_C      Q    41_C     0.775     0    0.061   0.078     1.418   90.476   85.450
LGA    R    42_C      R    42_C     0.342     0    0.076   1.495     6.612  100.000   70.866
LGA    Y    43_C      Y    43_C     1.108     0    0.043   0.085     1.482   83.690   82.183
LGA    W    44_C      W    44_C     1.264     0    0.062   0.107     1.492   81.429   84.660
LGA    T    45_C      T    45_C     2.126     0    0.065   0.135     3.090   66.786   61.633
LGA    S    46_C      S    46_C     1.470     0    0.663   0.802     4.385   64.048   67.063
LGA    G    47_C      G    47_C     1.441     0    0.708   0.708     2.355   77.381   77.381
LGA    G    48_C      G    48_C     4.026     0    0.679   0.679     4.273   40.238   40.238
LGA    T    49_C      T    49_C     6.393     0    0.110   0.132    10.177   20.833   13.265
LGA    M    50_C      M    50_C     9.031     0    0.585   0.619    13.818    3.929    1.964
LGA    R    51_C      R    51_C     7.848     0    0.674   0.906    12.063    4.881    3.247
LGA    S    52_C      S    52_C    11.969     0    0.548   0.765    16.316    0.000    0.000
LGA    V    53_C      V    53_C    13.981     0    0.143   1.212    15.648    0.000    0.000
LGA    P    54_C      P    54_C    15.292     0    0.614   0.508    16.427    0.000    0.000
LGA    I    55_C      I    55_C    18.237     0    0.579   1.156    21.399    0.000    0.000
LGA    G    56_C      G    56_C    19.895     0    0.084   0.084    20.331    0.000    0.000

# 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):     4.680          4.716                  5.220           65.128   58.795

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   65   51    4.0     41    1.77    75.980    76.923     2.197

LGA_LOCAL      RMSD:   1.766  Number of atoms:   41  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.711  Number of assigned atoms:   51 
Std_ASGN_ATOMS RMSD:   4.680  Standard rmsd on all 51 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.820662 * X  +  -0.075737 * Y  +   0.566372 * Z  + -19.457649
  Y_new =   0.570411 * X  +  -0.167262 * Y  +   0.804148 * Z  + -36.201351
  Z_new =   0.033829 * X  +   0.982999 * Y  +   0.180467 * Z  +  -2.279539 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.534189 -0.033835  1.389230   [DEG:  145.1983   -1.9386   79.5970 ]
ZXZ:  2.527978  1.389335  0.034400   [DEG:  144.8425   79.6030    1.9710 ]
 
# END of job
