
#######################################################
#                                                     #
#                        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   47 (  370),  selected   44 , name one
# Molecule2: number of CA atoms   61 (  480),  selected   44 , 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:    44      33_A - 76_A        4.12     4.12
  LCS_AVERAGE:     72.13

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20      57_A - 76_A        1.73     6.16
  LCS_AVERAGE:     28.46

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17      57_A - 73_A        0.95     5.42
  LCS_AVERAGE:     21.50

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   44
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     T    33_A     T    33_A     14   18   44      6   12   14   17   30   31   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     M    34_A     M    34_A     14   18   44      6   12   14   17   30   31   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     A    35_A     A    35_A     14   18   44      6   12   14   26   30   31   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     D    36_A     D    36_A     14   18   44      6   12   20   26   30   31   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     L    37_A     L    37_A     14   18   44      6   12   20   26   30   31   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     K    38_A     K    38_A     14   18   44      6   12   14   26   30   31   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     M    39_A     M    39_A     14   18   44      5   12   20   26   30   31   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     Q    40_A     Q    40_A     14   18   44      5   13   20   26   30   31   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     A    41_A     A    41_A     14   18   44      5   13   20   26   30   31   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     V    42_A     V    42_A     14   18   44      5   12   20   26   30   31   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     K    43_A     K    43_A     14   18   44      5   13   20   26   30   31   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     E    44_A     E    44_A     14   18   44      5   12   20   26   30   31   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     I    45_A     I    45_A     14   18   44      5   12   14   26   30   31   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     C    46_A     C    46_A     14   18   44      4    9   19   26   30   31   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     Y    47_A     Y    47_A     10   18   44      4    8   14   22   29   31   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     E    48_A     E    48_A     10   18   44      4    8   12   17   23   29   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     V    49_A     V    49_A     10   18   44      4    8   12   17   24   30   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     A    50_A     A    50_A      4   18   44      4    4    5    6   15   24   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     L    51_A     L    51_A      4    4   44      4    4    4    5    7   11   16   25   30   36   37   40   40   41   41   43   44   44   44   44 
LCS_GDT     A    52_A     A    52_A      4    5   44      4    4    5    5    7    9   13   23   30   33   37   38   39   41   41   42   44   44   44   44 
LCS_GDT     D    53_A     D    53_A      4    5   44      4    4    4    4    7   17   26   35   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     F    54_A     F    54_A      3    5   44      3    4    5   13   19   30   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     R    55_A     R    55_A      3    5   44      3    4    5    5    7   11   23   27   30   36   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     H    56_A     H    56_A      3   16   44      3    3    5    5   13   23   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     G    57_A     G    57_A     17   20   44      7   13   20   26   30   31   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     R    58_A     R    58_A     17   20   44      7   13   20   26   30   31   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     A    59_A     A    59_A     17   20   44      8   13   20   26   30   31   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     E    60_A     E    60_A     17   20   44      8   13   20   26   30   31   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     I    61_A     I    61_A     17   20   44      8   13   20   26   30   31   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     E    62_A     E    62_A     17   20   44      8   13   20   26   30   31   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     A    63_A     A    63_A     17   20   44      8   13   20   26   30   31   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     L    64_A     L    64_A     17   20   44      8   13   20   26   30   31   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     A    65_A     A    65_A     17   20   44      7   13   20   26   30   31   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     A    66_A     A    66_A     17   20   44      6   13   20   26   30   31   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     L    67_A     L    67_A     17   20   44      8   13   20   26   30   31   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     K    68_A     K    68_A     17   20   44      7   13   16   26   30   31   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     M    69_A     M    69_A     17   20   44      8   13   20   26   30   31   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     R    70_A     R    70_A     17   20   44      6   13   18   26   30   31   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     E    71_A     E    71_A     17   20   44      6   13   16   23   30   31   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     L    72_A     L    72_A     17   20   44      5   13   15   19   27   31   33   35   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     C    73_A     C    73_A     17   20   44      6   13   15   21   30   31   33   36   38   38   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     R    74_A     R    74_A     15   20   44      4   10   14   18   24   29   32   32   34   37   39   40   40   41   42   43   44   44   44   44 
LCS_GDT     T    75_A     T    75_A     12   20   44      3    4   11   14   16   20   26   29   32   34   35   36   38   40   42   43   44   44   44   44 
LCS_GDT     Y    76_A     Y    76_A     10   20   44      3    4   10   13   15   19   22   27   31   34   35   36   38   41   42   43   44   44   44   44 
LCS_AVERAGE  LCS_A:  40.70  (  21.50   28.46   72.13 )

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      8     13     20     26     30     31     33     36     38     38     39     40     40     41     42     43     44     44     44     44 
GDT PERCENT_AT  13.11  21.31  32.79  42.62  49.18  50.82  54.10  59.02  62.30  62.30  63.93  65.57  65.57  67.21  68.85  70.49  72.13  72.13  72.13  72.13
GDT RMS_LOCAL    0.30   0.59   1.05   1.35   1.66   1.73   1.97   2.48   2.70   2.70   2.88   3.25   3.10   3.48   3.57   3.89   4.12   4.12   4.12   4.12
GDT RMS_ALL_AT   5.26   5.10   5.02   4.95   4.99   5.05   4.74   4.37   4.30   4.30   4.26   4.28   4.20   4.33   4.21   4.14   4.12   4.12   4.12   4.12

# Checking swapping
#   possible swapping detected:  E    44_A      E    44_A
#   possible swapping detected:  D    53_A      D    53_A
#   possible swapping detected:  E    62_A      E    62_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    T    33_A      T    33_A     2.544     0    0.541   1.176     6.124   55.952   43.469
LGA    M    34_A      M    34_A     2.584     0    0.040   0.816     4.203   59.048   53.095
LGA    A    35_A      A    35_A     2.357     0    0.138   0.159     2.659   66.905   64.952
LGA    D    36_A      D    36_A     0.721     0    0.102   0.160     2.752   88.214   76.548
LGA    L    37_A      L    37_A     0.866     0    0.086   0.151     1.333   85.952   87.143
LGA    K    38_A      K    38_A     1.833     0    0.080   0.881     6.564   72.857   51.217
LGA    M    39_A      M    39_A     1.489     0    0.055   0.853     1.983   79.286   78.214
LGA    Q    40_A      Q    40_A     1.342     0    0.022   0.446     1.816   77.143   79.577
LGA    A    41_A      A    41_A     1.956     0    0.035   0.048     2.469   68.810   69.619
LGA    V    42_A      V    42_A     2.216     0    0.119   0.161     2.783   68.810   64.898
LGA    K    43_A      K    43_A     1.373     0    0.055   0.919     5.120   75.000   59.312
LGA    E    44_A      E    44_A     1.912     0    0.188   0.424     2.611   66.905   75.132
LGA    I    45_A      I    45_A     2.348     0    0.049   0.442     4.436   68.810   58.750
LGA    C    46_A      C    46_A     0.317     0    0.173   0.824     1.887   86.190   86.111
LGA    Y    47_A      Y    47_A     1.737     0    0.080   0.089     5.690   67.619   51.746
LGA    E    48_A      E    48_A     3.623     0    0.570   0.679     5.604   55.595   40.529
LGA    V    49_A      V    49_A     2.863     0    0.636   0.799     3.606   51.905   53.197
LGA    A    50_A      A    50_A     4.469     0    0.598   0.604     6.551   28.690   25.619
LGA    L    51_A      L    51_A    10.673     0    0.207   1.330    16.280    1.190    0.595
LGA    A    52_A      A    52_A    10.802     0    0.324   0.337    11.312    1.071    0.857
LGA    D    53_A      D    53_A     6.268     0    0.366   1.143     7.695   16.429   16.607
LGA    F    54_A      F    54_A     4.531     0    0.406   1.491     8.372   25.357   19.177
LGA    R    55_A      R    55_A     8.466     0    0.062   1.595    19.279    9.524    3.463
LGA    H    56_A      H    56_A     5.149     0    0.582   1.441    10.413   35.476   17.286
LGA    G    57_A      G    57_A     1.580     0    0.513   0.513     1.618   77.143   77.143
LGA    R    58_A      R    58_A     1.237     0    0.031   1.299     6.019   81.429   65.022
LGA    A    59_A      A    59_A     1.702     0    0.037   0.033     1.885   72.857   72.857
LGA    E    60_A      E    60_A     2.060     0    0.025   1.021     5.793   70.833   50.370
LGA    I    61_A      I    61_A     1.856     0    0.020   0.171     1.997   72.857   75.000
LGA    E    62_A      E    62_A     1.487     0    0.047   0.223     1.699   79.286   78.571
LGA    A    63_A      A    63_A     1.359     0    0.059   0.065     1.550   77.143   78.000
LGA    L    64_A      L    64_A     2.079     0    0.189   0.446     2.739   64.881   71.131
LGA    A    65_A      A    65_A     2.045     0    0.049   0.058     2.268   73.095   71.429
LGA    A    66_A      A    66_A     0.676     0    0.023   0.036     1.394   83.690   85.048
LGA    L    67_A      L    67_A     1.689     0    0.043   1.070     4.908   69.048   63.810
LGA    K    68_A      K    68_A     2.497     0    0.024   0.798     5.984   62.857   49.418
LGA    M    69_A      M    69_A     1.839     0    0.062   1.347     3.849   70.833   69.226
LGA    R    70_A      R    70_A     2.475     0    0.072   0.597     3.814   55.714   65.195
LGA    E    71_A      E    71_A     3.900     0    0.035   1.339     8.676   39.167   27.143
LGA    L    72_A      L    72_A     4.626     0    0.135   0.271     5.285   31.548   32.262
LGA    C    73_A      C    73_A     4.545     0    0.014   0.204     6.591   25.833   33.968
LGA    R    74_A      R    74_A     7.241     0    0.268   0.751    10.493    8.571   18.571
LGA    T    75_A      T    75_A     9.765     0    0.116   0.191    11.245    1.310    1.020
LGA    Y    76_A      Y    76_A    10.347     0    0.664   0.662    10.874    0.119    0.357

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       44     176    176  100.00     350    350  100.00                61
SUMMARY(RMSD_GDC):     4.116          4.132                  5.020           39.852   37.093

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   47   61    4.0     36    2.48    48.361    45.770     1.398

LGA_LOCAL      RMSD:   2.476  Number of atoms:   36  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.365  Number of assigned atoms:   44 
Std_ASGN_ATOMS RMSD:   4.116  Standard rmsd on all 44 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.497658 * X  +  -0.240203 * Y  +  -0.833450 * Z  +   9.188720
  Y_new =  -0.212701 * X  +   0.897754 * Y  +  -0.385740 * Z  +  24.563885
  Z_new =   0.840889 * X  +   0.369242 * Y  +   0.395683 * Z  +  -6.027582 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.403904 -0.998924  0.750845   [DEG:  -23.1420  -57.2341   43.0202 ]
ZXZ: -1.137330  1.163984  1.157036   [DEG:  -65.1642   66.6914   66.2933 ]
 
# END of job
