
#######################################################
#                                                     #
#                        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        2.64     2.64
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       2_A - 34_A        1.89     2.67
  LCS_AVERAGE:     94.64

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      11_A - 34_A        0.77     3.17
  LCS_AVERAGE:     56.40

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      0    5   34      0    0    3    4    5    6    6    6    6    6    7   15   16   25   30   32   32   34   34   34 
LCS_GDT     G     2_B     G     2_A      4   33   34      0    3    5    7    9   19   31   33   33   33   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     P     3_B     P     3_A      9   33   34      4   18   23   25   28   30   32   33   33   33   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     N     4_B     N     4_A      9   33   34      4    7   23   26   28   30   32   33   33   33   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     G     5_B     G     5_A      9   33   34      4    8   20   26   28   30   32   33   33   33   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     G     6_B     G     6_A      9   33   34      3    8   14   26   28   30   32   33   33   33   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     V     7_B     V     7_A      9   33   34      3    7   10   17   27   30   32   33   33   33   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     C     8_B     C     8_A      9   33   34      4   10   20   26   28   30   32   33   33   33   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     P     9_B     P     9_A      9   33   34      3    7   12   20   28   30   32   33   33   33   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     V    10_B     V    10_A      9   33   34      4    7   10   15   28   30   32   33   33   33   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     L    11_B     L    11_A     24   33   34      3    4    8   25   28   30   32   33   33   33   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     I    12_B     I    12_A     24   33   34     18   22   23   26   28   30   32   33   33   33   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     Y    13_B     Y    13_A     24   33   34     19   22   23   26   28   30   32   33   33   33   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     L    14_B     L    14_A     24   33   34     19   22   23   26   28   30   32   33   33   33   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     C    15_B     C    15_A     24   33   34     19   22   23   26   28   30   32   33   33   33   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     R    16_B     R    16_A     24   33   34     19   22   23   26   28   30   32   33   33   33   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     R    17_B     R    17_A     24   33   34     19   22   23   26   28   30   32   33   33   33   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     D    18_B     D    18_A     24   33   34     19   22   23   26   28   30   32   33   33   33   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     S    19_B     S    19_A     24   33   34     19   22   23   26   28   30   32   33   33   33   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     D    20_B     D    20_A     24   33   34     19   22   23   26   28   30   32   33   33   33   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     C    21_B     C    21_A     24   33   34     19   22   23   26   28   30   32   33   33   33   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     P    22_B     P    22_A     24   33   34     19   22   23   26   28   30   32   33   33   33   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     G    23_B     G    23_A     24   33   34     19   22   23   26   28   30   32   33   33   33   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     E    24_B     E    24_A     24   33   34     19   22   23   26   28   30   32   33   33   33   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     C    25_B     C    25_A     24   33   34     19   22   23   26   28   30   32   33   33   33   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     I    26_B     I    26_A     24   33   34     19   22   23   26   28   30   32   33   33   33   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     C    27_B     C    27_A     24   33   34     19   22   23   26   28   30   32   33   33   33   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     L    28_B     L    28_A     24   33   34     19   22   23   26   28   30   32   33   33   33   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     G    29_B     G    29_A     24   33   34      9   22   23   26   28   30   32   33   33   33   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     N    30_B     N    30_A     24   33   34      6   13   23   25   27   29   32   33   33   33   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     G    31_B     G    31_A     24   33   34      6   22   23   26   28   30   32   33   33   33   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     Y    32_B     Y    32_A     24   33   34     19   22   23   26   28   30   32   33   33   33   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     C    33_B     C    33_A     24   33   34     19   22   23   26   28   30   32   33   33   33   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     G    34_B     G    34_A     24   33   34     19   22   23   26   28   30   32   33   33   33   33   33   33   33   33   33   33   34   34   34 
LCS_AVERAGE  LCS_A:  83.68  (  56.40   94.64  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     19     22     23     26     28     30     32     33     33     33     33     33     33     33     33     33     33     34     34     34 
GDT PERCENT_AT  55.88  64.71  67.65  76.47  82.35  88.24  94.12  97.06  97.06  97.06  97.06  97.06  97.06  97.06  97.06  97.06  97.06 100.00 100.00 100.00
GDT RMS_LOCAL    0.33   0.43   0.55   1.13   1.29   1.56   1.77   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   2.64   2.64   2.64
GDT RMS_ALL_AT   3.13   3.17   3.10   2.87   2.80   2.71   2.70   2.67   2.67   2.67   2.67   2.67   2.67   2.67   2.67   2.67   2.67   2.64   2.64   2.64

# Checking swapping
#   possible swapping detected:  E    24_B      E    24_A
#   possible swapping detected:  Y    32_B      Y    32_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     1_B      S     1_A    11.177     0    0.045   0.618    13.116    2.381    1.587
LGA    G     2_B      G     2_A     4.191     0    0.396   0.396     6.813   45.000   45.000
LGA    P     3_B      P     3_A     2.523     0    0.292   0.290     3.998   59.524   57.755
LGA    N     4_B      N     4_A     1.531     0    0.477   1.225     5.859   73.333   56.012
LGA    G     5_B      G     5_A     1.837     0    0.676   0.676     3.881   63.452   63.452
LGA    G     6_B      G     6_A     2.338     0    0.195   0.195     2.540   62.976   62.976
LGA    V     7_B      V     7_A     3.855     0    0.171   0.283     6.452   46.786   36.667
LGA    C     8_B      C     8_A     1.344     0    0.023   0.076     2.599   67.024   74.841
LGA    P     9_B      P     9_A     2.934     0    0.027   0.111     3.456   67.024   60.748
LGA    V    10_B      V    10_A     3.380     0    0.057   0.076     5.452   53.571   42.585
LGA    L    11_B      L    11_A     2.438     3    0.121   0.148     3.059   66.786   39.643
LGA    I    12_B      I    12_A     1.383     0    0.258   0.684     4.244   79.286   70.595
LGA    Y    13_B      Y    13_A     1.163     0    0.041   0.270     2.434   85.952   75.913
LGA    L    14_B      L    14_A     0.628     0    0.078   0.156     1.185   88.214   89.345
LGA    C    15_B      C    15_A     0.421     0    0.014   0.056     0.556   95.238   96.825
LGA    R    16_B      R    16_A     0.992     0    0.038   0.388     5.399   88.214   61.472
LGA    R    17_B      R    17_A     0.310     0    0.059   0.365     0.967   97.619   93.074
LGA    D    18_B      D    18_A     0.385     0    0.018   0.156     0.803   97.619   95.238
LGA    S    19_B      S    19_A     0.815     0    0.044   0.141     1.311   88.214   88.968
LGA    D    20_B      D    20_A     0.784     0    0.052   0.145     1.036   90.476   89.345
LGA    C    21_B      C    21_A     0.673     0    0.017   0.076     1.115   88.214   88.968
LGA    P    22_B      P    22_A     1.325     0    0.103   0.172     1.542   81.429   81.497
LGA    G    23_B      G    23_A     1.830     0    0.018   0.018     1.830   75.000   75.000
LGA    E    24_B      E    24_A     1.382     0    0.024   0.370     1.581   79.286   79.524
LGA    C    25_B      C    25_A     1.341     0    0.013   0.106     1.383   81.429   81.429
LGA    I    26_B      I    26_A     1.116     0    0.013   0.085     1.756   85.952   81.548
LGA    C    27_B      C    27_A     0.564     0    0.046   0.064     0.754   90.476   93.651
LGA    L    28_B      L    28_A     1.358     0    0.043   0.058     2.604   79.286   72.083
LGA    G    29_B      G    29_A     2.048     0    0.050   0.050     3.168   61.190   61.190
LGA    N    30_B      N    30_A     3.189     0    0.073   0.103     4.384   57.262   51.250
LGA    G    31_B      G    31_A     1.402     0    0.051   0.051     1.828   83.810   83.810
LGA    Y    32_B      Y    32_A     1.109     0    0.025   0.104     2.214   81.429   73.016
LGA    C    33_B      C    33_A     1.146     0    0.051   0.059     1.909   79.286   81.508
LGA    G    34_B      G    34_A     1.618     0    0.061   0.061     1.618   81.548   81.548

# 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):     2.638          2.540                  2.739           74.244   70.237

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   34    4.0     33    1.89    83.824    88.623     1.656

LGA_LOCAL      RMSD:   1.893  Number of atoms:   33  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.674  Number of assigned atoms:   34 
Std_ASGN_ATOMS RMSD:   2.638  Standard rmsd on all 34 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.028601 * X  +  -0.438504 * Y  +  -0.898274 * Z  +  -9.085118
  Y_new =   0.719413 * X  +   0.614877 * Y  +  -0.323066 * Z  +  -8.084579
  Z_new =   0.693994 * X  +  -0.655470 * Y  +   0.297879 * Z  + -20.708591 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.610531 -0.767022 -1.144246   [DEG:   92.2766  -43.9471  -65.5605 ]
ZXZ: -1.225549  1.268326  2.327654   [DEG:  -70.2188   72.6697  133.3648 ]
 
# END of job
