
#######################################################
#                                                     #
#                        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        4.76     4.76
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    30       5_A - 34_A        1.61     5.39
  LCS_AVERAGE:     79.76

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29       6_A - 34_A        0.74     5.72
  LCS_AVERAGE:     74.39

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      4    5   34      3    3    4    4    4    5    5    6    7    7    9    9   10   11   11   12   12   13   14   16 
LCS_GDT     G     2_B     G     2_A      4    5   34      3    3    4    4    4    5    5    6    7    9   10   11   11   12   14   14   15   21   31   32 
LCS_GDT     P     3_B     P     3_A      4    5   34      3    3    4    4    4    8    8   10   12   17   21   27   29   32   32   32   32   32   32   32 
LCS_GDT     N     4_B     N     4_A      4    7   34      3    3    4    5    6    7    8   10   14   21   29   29   31   32   32   32   32   32   32   32 
LCS_GDT     G     5_B     G     5_A      3   30   34      1    3    4    7   14   20   26   29   30   30   30   30   31   32   32   32   32   32   32   32 
LCS_GDT     G     6_B     G     6_A     29   30   34      7   21   29   29   29   29   29   29   30   30   30   30   31   32   32   32   32   32   32   32 
LCS_GDT     V     7_B     V     7_A     29   30   34      4    4   29   29   29   29   29   29   30   30   30   30   31   32   32   32   32   32   32   32 
LCS_GDT     C     8_B     C     8_A     29   30   34     12   25   29   29   29   29   29   29   30   30   30   30   31   32   32   32   32   32   32   32 
LCS_GDT     P     9_B     P     9_A     29   30   34     14   25   29   29   29   29   29   29   30   30   30   30   31   32   32   32   32   32   32   32 
LCS_GDT     V    10_B     V    10_A     29   30   34     14   25   29   29   29   29   29   29   30   30   30   30   31   32   32   32   32   32   32   32 
LCS_GDT     L    11_B     L    11_A     29   30   34      5   18   29   29   29   29   29   29   30   30   30   30   31   32   32   32   32   32   32   32 
LCS_GDT     I    12_B     I    12_A     29   30   34     16   25   29   29   29   29   29   29   30   30   30   30   31   32   32   32   32   32   32   32 
LCS_GDT     Y    13_B     Y    13_A     29   30   34     16   25   29   29   29   29   29   29   30   30   30   30   31   32   32   32   32   32   32   32 
LCS_GDT     L    14_B     L    14_A     29   30   34     16   25   29   29   29   29   29   29   30   30   30   30   31   32   32   32   32   32   32   32 
LCS_GDT     C    15_B     C    15_A     29   30   34     16   25   29   29   29   29   29   29   30   30   30   30   31   32   32   32   32   32   32   32 
LCS_GDT     R    16_B     R    16_A     29   30   34     16   25   29   29   29   29   29   29   30   30   30   30   31   32   32   32   32   32   32   32 
LCS_GDT     R    17_B     R    17_A     29   30   34     13   25   29   29   29   29   29   29   30   30   30   30   31   32   32   32   32   32   32   32 
LCS_GDT     D    18_B     D    18_A     29   30   34     16   25   29   29   29   29   29   29   30   30   30   30   31   32   32   32   32   32   32   32 
LCS_GDT     S    19_B     S    19_A     29   30   34     16   25   29   29   29   29   29   29   30   30   30   30   31   32   32   32   32   32   32   32 
LCS_GDT     D    20_B     D    20_A     29   30   34     16   25   29   29   29   29   29   29   30   30   30   30   31   32   32   32   32   32   32   32 
LCS_GDT     C    21_B     C    21_A     29   30   34     16   25   29   29   29   29   29   29   30   30   30   30   31   32   32   32   32   32   32   32 
LCS_GDT     P    22_B     P    22_A     29   30   34     16   25   29   29   29   29   29   29   30   30   30   30   31   32   32   32   32   32   32   32 
LCS_GDT     G    23_B     G    23_A     29   30   34     15   25   29   29   29   29   29   29   30   30   30   30   31   32   32   32   32   32   32   32 
LCS_GDT     E    24_B     E    24_A     29   30   34     16   25   29   29   29   29   29   29   30   30   30   30   31   32   32   32   32   32   32   32 
LCS_GDT     C    25_B     C    25_A     29   30   34     16   25   29   29   29   29   29   29   30   30   30   30   31   32   32   32   32   32   32   32 
LCS_GDT     I    26_B     I    26_A     29   30   34     16   25   29   29   29   29   29   29   30   30   30   30   31   32   32   32   32   32   32   32 
LCS_GDT     C    27_B     C    27_A     29   30   34     16   25   29   29   29   29   29   29   30   30   30   30   31   32   32   32   32   32   32   32 
LCS_GDT     L    28_B     L    28_A     29   30   34     16   25   29   29   29   29   29   29   30   30   30   30   31   32   32   32   32   32   32   32 
LCS_GDT     G    29_B     G    29_A     29   30   34     16   25   29   29   29   29   29   29   30   30   30   30   31   32   32   32   32   32   32   32 
LCS_GDT     N    30_B     N    30_A     29   30   34      4   22   29   29   29   29   29   29   30   30   30   30   31   32   32   32   32   32   32   32 
LCS_GDT     G    31_B     G    31_A     29   30   34     16   25   29   29   29   29   29   29   30   30   30   30   31   32   32   32   32   32   32   32 
LCS_GDT     Y    32_B     Y    32_A     29   30   34     16   25   29   29   29   29   29   29   30   30   30   30   31   32   32   32   32   32   32   32 
LCS_GDT     C    33_B     C    33_A     29   30   34     16   25   29   29   29   29   29   29   30   30   30   30   31   32   32   32   32   32   32   32 
LCS_GDT     G    34_B     G    34_A     29   30   34     16   25   29   29   29   29   29   29   30   30   30   30   31   32   32   32   32   32   32   32 
LCS_AVERAGE  LCS_A:  84.72  (  74.39   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     16     25     29     29     29     29     29     29     30     30     30     30     31     32     32     32     32     32     32     32 
GDT PERCENT_AT  47.06  73.53  85.29  85.29  85.29  85.29  85.29  85.29  88.24  88.24  88.24  88.24  91.18  94.12  94.12  94.12  94.12  94.12  94.12  94.12
GDT RMS_LOCAL    0.32   0.50   0.74   0.74   0.74   0.74   0.74   0.74   1.61   1.61   1.61   1.61   2.47   3.18   3.18   3.18   3.18   3.18   3.18   3.18
GDT RMS_ALL_AT   5.80   5.82   5.72   5.72   5.72   5.72   5.72   5.72   5.39   5.39   5.39   5.39   5.13   4.91   4.91   4.91   4.91   4.91   4.91   4.91

# 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    17.820     0    0.456   0.555    19.953    0.000    0.000
LGA    G     2_B      G     2_A    18.391     0    0.037   0.037    18.391    0.000    0.000
LGA    P     3_B      P     3_A    14.689     0    0.368   0.579    18.774    0.000    0.000
LGA    N     4_B      N     4_A    12.325     0    0.631   1.216    16.075    0.119    0.060
LGA    G     5_B      G     5_A     8.584     0    0.570   0.570     9.809    9.405    9.405
LGA    G     6_B      G     6_A     1.377     0    0.663   0.663     3.805   74.167   74.167
LGA    V     7_B      V     7_A     1.745     0    0.072   0.110     3.574   68.929   59.864
LGA    C     8_B      C     8_A     0.794     0    0.065   0.100     1.072   90.595   92.143
LGA    P     9_B      P     9_A     0.528     0    0.021   0.305     0.952   92.857   91.837
LGA    V    10_B      V    10_A     0.625     0    0.496   1.000     3.672   84.048   75.102
LGA    L    11_B      L    11_A     1.327     3    0.173   0.232     1.630   79.286   49.821
LGA    I    12_B      I    12_A     0.565     0    0.141   0.139     2.298   92.976   84.048
LGA    Y    13_B      Y    13_A     0.198     0    0.054   0.496     2.567   97.619   85.040
LGA    L    14_B      L    14_A     0.326     0    0.037   0.060     0.855  100.000   96.429
LGA    C    15_B      C    15_A     0.278     0    0.042   0.072     0.547  100.000   98.413
LGA    R    16_B      R    16_A     0.463     0    0.114   1.625     9.598  100.000   58.442
LGA    R    17_B      R    17_A     0.888     0    0.092   1.349     8.191   90.476   56.970
LGA    D    18_B      D    18_A     0.805     0    0.019   0.066     0.992   90.476   90.476
LGA    S    19_B      S    19_A     0.935     0    0.011   0.012     1.154   90.476   87.460
LGA    D    20_B      D    20_A     0.186     0    0.040   0.123     0.398  100.000  100.000
LGA    C    21_B      C    21_A     0.609     0    0.026   0.052     1.035   97.619   93.730
LGA    P    22_B      P    22_A     0.428     0    0.030   0.120     1.149   97.619   93.265
LGA    G    23_B      G    23_A     0.448     0    0.048   0.048     0.664   97.619   97.619
LGA    E    24_B      E    24_A     0.183     0    0.027   0.894     3.987  100.000   83.386
LGA    C    25_B      C    25_A     0.318     0    0.011   0.042     0.580  100.000   98.413
LGA    I    26_B      I    26_A     0.389     0    0.075   1.436     4.611   95.238   79.286
LGA    C    27_B      C    27_A     0.526     0    0.039   0.062     0.625   97.619   95.238
LGA    L    28_B      L    28_A     0.465     0    0.069   0.090     1.697   95.238   87.321
LGA    G    29_B      G    29_A     0.565     0    0.027   0.027     1.348   90.595   90.595
LGA    N    30_B      N    30_A     1.346     0    0.059   1.224     3.408   83.690   75.417
LGA    G    31_B      G    31_A     0.563     0    0.027   0.027     0.646   95.238   95.238
LGA    Y    32_B      Y    32_A     0.278     0    0.028   0.069     1.301  100.000   92.937
LGA    C    33_B      C    33_A     0.607     0    0.024   0.038     1.082   92.857   90.556
LGA    G    34_B      G    34_A     0.737     0    0.254   0.254     1.379   85.952   85.952

# 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):     4.764          4.641                  4.782           79.139   72.607

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   34    4.0     29    0.74    84.559    84.465     3.434

LGA_LOCAL      RMSD:   0.744  Number of atoms:   29  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.722  Number of assigned atoms:   34 
Std_ASGN_ATOMS RMSD:   4.764  Standard rmsd on all 34 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.900456 * X  +  -0.195671 * Y  +   0.388448 * Z  +   2.156521
  Y_new =  -0.206633 * X  +   0.978321 * Y  +   0.013812 * Z  +   9.285061
  Z_new =  -0.382729 * X  +  -0.067829 * Y  +  -0.921367 * Z  + -11.439792 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.916022  0.392749 -3.068108   [DEG: -167.0758   22.5028 -175.7896 ]
ZXZ:  1.606339  2.742380 -1.746199   [DEG:   92.0364  157.1268 -100.0498 ]
 
# END of job
