
#######################################################
#                                                     #
#                        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   34 (  238),  selected   34 , name one
# Molecule2: number of CA atoms   34 (  235),  selected   34 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    34       1_A - 34_A        4.48     4.48
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    30       5_A - 34_A        1.59     5.06
  LCS_AVERAGE:     79.76

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29       6_A - 34_A        0.79     5.37
  LCS_AVERAGE:     74.05

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   34
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     S     1_B     S     1_A      3    5   34      3    3    4    4    4    5    5    6    6    8    8    9    9   11   11   12   12   15   15   17 
LCS_GDT     G     2_B     G     2_A      3    5   34      3    3    4    4    4    5    5    6    7    8   11   11   13   15   18   18   31   32   33   33 
LCS_GDT     P     3_B     P     3_A      3    5   34      3    3    4    4    6    6    9   11   16   18   25   28   32   32   32   32   32   32   33   33 
LCS_GDT     N     4_B     N     4_A      3    7   34      3    3    4    4    6    8    8    8   16   20   26   30   32   32   32   32   32   32   33   33 
LCS_GDT     G     5_B     G     5_A      3   30   34      0    3    3    4   11   20   27   29   30   30   30   30   32   32   32   32   32   32   33   33 
LCS_GDT     G     6_B     G     6_A     29   30   34      8   25   28   29   29   29   29   29   30   30   30   30   32   32   32   32   32   32   33   33 
LCS_GDT     V     7_B     V     7_A     29   30   34      3    5   28   29   29   29   29   29   30   30   30   30   32   32   32   32   32   32   33   33 
LCS_GDT     C     8_B     C     8_A     29   30   34     14   25   28   29   29   29   29   29   30   30   30   30   32   32   32   32   32   32   33   33 
LCS_GDT     P     9_B     P     9_A     29   30   34     17   25   28   29   29   29   29   29   30   30   30   30   32   32   32   32   32   32   33   33 
LCS_GDT     V    10_B     V    10_A     29   30   34      8   25   28   29   29   29   29   29   30   30   30   30   32   32   32   32   32   32   33   33 
LCS_GDT     L    11_B     L    11_A     29   30   34      4   25   28   29   29   29   29   29   30   30   30   30   32   32   32   32   32   32   33   33 
LCS_GDT     I    12_B     I    12_A     29   30   34     17   25   28   29   29   29   29   29   30   30   30   30   32   32   32   32   32   32   33   33 
LCS_GDT     Y    13_B     Y    13_A     29   30   34     17   25   28   29   29   29   29   29   30   30   30   30   32   32   32   32   32   32   33   33 
LCS_GDT     L    14_B     L    14_A     29   30   34     17   25   28   29   29   29   29   29   30   30   30   30   32   32   32   32   32   32   33   33 
LCS_GDT     C    15_B     C    15_A     29   30   34     17   25   28   29   29   29   29   29   30   30   30   30   32   32   32   32   32   32   33   33 
LCS_GDT     R    16_B     R    16_A     29   30   34     17   25   28   29   29   29   29   29   30   30   30   30   32   32   32   32   32   32   33   33 
LCS_GDT     R    17_B     R    17_A     29   30   34      8   25   28   29   29   29   29   29   30   30   30   30   32   32   32   32   32   32   33   33 
LCS_GDT     D    18_B     D    18_A     29   30   34      9   25   28   29   29   29   29   29   30   30   30   30   32   32   32   32   32   32   33   33 
LCS_GDT     S    19_B     S    19_A     29   30   34     13   25   28   29   29   29   29   29   30   30   30   30   32   32   32   32   32   32   33   33 
LCS_GDT     D    20_B     D    20_A     29   30   34     17   25   28   29   29   29   29   29   30   30   30   30   32   32   32   32   32   32   33   33 
LCS_GDT     C    21_B     C    21_A     29   30   34     17   25   28   29   29   29   29   29   30   30   30   30   32   32   32   32   32   32   33   33 
LCS_GDT     P    22_B     P    22_A     29   30   34     17   25   28   29   29   29   29   29   30   30   30   30   32   32   32   32   32   32   33   33 
LCS_GDT     G    23_B     G    23_A     29   30   34     17   25   28   29   29   29   29   29   30   30   30   30   32   32   32   32   32   32   33   33 
LCS_GDT     E    24_B     E    24_A     29   30   34     17   25   28   29   29   29   29   29   30   30   30   30   32   32   32   32   32   32   33   33 
LCS_GDT     C    25_B     C    25_A     29   30   34     17   25   28   29   29   29   29   29   30   30   30   30   32   32   32   32   32   32   33   33 
LCS_GDT     I    26_B     I    26_A     29   30   34     17   25   28   29   29   29   29   29   30   30   30   30   32   32   32   32   32   32   33   33 
LCS_GDT     C    27_B     C    27_A     29   30   34     17   25   28   29   29   29   29   29   30   30   30   30   32   32   32   32   32   32   33   33 
LCS_GDT     L    28_B     L    28_A     29   30   34     17   25   28   29   29   29   29   29   30   30   30   30   32   32   32   32   32   32   33   33 
LCS_GDT     G    29_B     G    29_A     29   30   34     16   25   28   29   29   29   29   29   30   30   30   30   32   32   32   32   32   32   33   33 
LCS_GDT     N    30_B     N    30_A     29   30   34      4   21   28   29   29   29   29   29   30   30   30   30   32   32   32   32   32   32   33   33 
LCS_GDT     G    31_B     G    31_A     29   30   34     12   25   28   29   29   29   29   29   30   30   30   30   32   32   32   32   32   32   33   33 
LCS_GDT     Y    32_B     Y    32_A     29   30   34     17   25   28   29   29   29   29   29   30   30   30   30   32   32   32   32   32   32   33   33 
LCS_GDT     C    33_B     C    33_A     29   30   34     17   25   28   29   29   29   29   29   30   30   30   30   32   32   32   32   32   32   33   33 
LCS_GDT     G    34_B     G    34_A     29   30   34      0    5    8   29   29   29   29   29   30   30   30   30   32   32   32   32   32   32   33   33 
LCS_AVERAGE  LCS_A:  84.60  (  74.05   79.76  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     17     25     28     29     29     29     29     29     30     30     30     30     32     32     32     32     32     32     33     33 
GDT PERCENT_AT  50.00  73.53  82.35  85.29  85.29  85.29  85.29  85.29  88.24  88.24  88.24  88.24  94.12  94.12  94.12  94.12  94.12  94.12  97.06  97.06
GDT RMS_LOCAL    0.32   0.56   0.72   0.79   0.79   0.79   0.79   0.79   1.59   1.59   1.59   1.59   3.05   3.05   3.05   3.05   3.05   3.05   3.83   3.83
GDT RMS_ALL_AT   5.44   5.37   5.36   5.37   5.37   5.37   5.37   5.37   5.06   5.06   5.06   5.06   4.62   4.62   4.62   4.62   4.62   4.62   4.51   4.51

# Checking swapping
#   possible swapping detected:  Y    13_B      Y    13_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     1_B      S     1_A    16.956     0    0.687   0.898    18.620    0.000    0.000
LGA    G     2_B      G     2_A    16.541     0    0.158   0.158    16.541    0.000    0.000
LGA    P     3_B      P     3_A    13.743     0    0.343   0.557    17.522    0.000    0.000
LGA    N     4_B      N     4_A    12.055     0    0.560   1.234    15.760    0.119    0.060
LGA    G     5_B      G     5_A     8.293     0    0.501   0.501     9.490   12.262   12.262
LGA    G     6_B      G     6_A     0.916     0    0.674   0.674     3.480   80.476   80.476
LGA    V     7_B      V     7_A     1.663     0    0.060   0.108     3.596   75.119   64.422
LGA    C     8_B      C     8_A     0.863     0    0.054   0.088     1.192   90.595   92.143
LGA    P     9_B      P     9_A     0.532     0    0.025   0.302     1.507   95.238   89.388
LGA    V    10_B      V    10_A     1.019     0    0.268   1.159     4.110   79.524   69.320
LGA    L    11_B      L    11_A     0.848     3    0.061   0.071     1.244   85.952   53.155
LGA    I    12_B      I    12_A     0.337     0    0.040   0.106     1.515  100.000   91.905
LGA    Y    13_B      Y    13_A     0.367     0    0.058   0.523     2.610  100.000   83.730
LGA    L    14_B      L    14_A     0.379     0    0.055   0.095     1.075  100.000   92.976
LGA    C    15_B      C    15_A     0.316     0    0.038   0.060     0.673  100.000   98.413
LGA    R    16_B      R    16_A     0.339     0    0.110   1.626     9.446  100.000   59.091
LGA    R    17_B      R    17_A     1.063     0    0.091   1.345     7.743   88.214   57.576
LGA    D    18_B      D    18_A     0.890     0    0.021   0.064     1.044   90.476   89.345
LGA    S    19_B      S    19_A     0.937     0    0.012   0.013     1.122   90.476   87.460
LGA    D    20_B      D    20_A     0.284     0    0.037   0.127     0.452  100.000  100.000
LGA    C    21_B      C    21_A     0.510     0    0.021   0.045     0.932   97.619   95.238
LGA    P    22_B      P    22_A     0.459     0    0.028   0.115     1.147  100.000   94.626
LGA    G    23_B      G    23_A     0.436     0    0.046   0.046     0.594   97.619   97.619
LGA    E    24_B      E    24_A     0.296     0    0.030   0.892     3.730  100.000   84.233
LGA    C    25_B      C    25_A     0.311     0    0.019   0.041     0.579  100.000   98.413
LGA    I    26_B      I    26_A     0.454     0    0.098   1.436     4.854   92.976   78.155
LGA    C    27_B      C    27_A     0.650     0    0.041   0.063     0.786   90.476   90.476
LGA    L    28_B      L    28_A     0.650     0    0.026   0.047     1.551   95.238   87.321
LGA    G    29_B      G    29_A     0.291     0    0.032   0.032     1.186   92.976   92.976
LGA    N    30_B      N    30_A     1.454     0    0.046   0.108     2.441   83.690   78.333
LGA    G    31_B      G    31_A     0.656     0    0.101   0.101     0.682   95.238   95.238
LGA    Y    32_B      Y    32_A     0.246     0    0.038   0.057     1.063  100.000   93.690
LGA    C    33_B      C    33_A     0.563     0    0.657   0.606     2.766   84.524   86.508
LGA    G    34_B      G    34_A     1.836     0    0.440   0.440     6.190   50.000   50.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       34     136    136  100.00     235    235  100.00                34
SUMMARY(RMSD_GDC):     4.478          4.374                  4.519           78.494   71.898

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   34    4.0     29    0.79    84.559    84.349     3.254

LGA_LOCAL      RMSD:   0.791  Number of atoms:   29  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.375  Number of assigned atoms:   34 
Std_ASGN_ATOMS RMSD:   4.478  Standard rmsd on all 34 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.905887 * X  +  -0.325297 * Y  +  -0.271201 * Z  +   1.973817
  Y_new =  -0.398268 * X  +   0.436507 * Y  +   0.806749 * Z  +   6.631867
  Z_new =  -0.144052 * X  +   0.838835 * Y  +  -0.524981 * Z  + -11.788089 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.727384  0.144555  2.130004   [DEG: -156.2676    8.2824  122.0402 ]
ZXZ: -2.817295  2.123489 -0.170070   [DEG: -161.4191  121.6670   -9.7443 ]
 
# END of job
