
#######################################################
#                                                     #
#                        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        0.86     0.86
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    34       1_A - 34_A        0.86     0.86
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    34       1_A - 34_A        0.86     0.86
  LCS_AVERAGE:    100.00

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     34   34   34     18   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G     2_B     G     2_A     34   34   34     18   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     P     3_B     P     3_A     34   34   34     18   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     N     4_B     N     4_A     34   34   34      6   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G     5_B     G     5_A     34   34   34      3   12   30   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G     6_B     G     6_A     34   34   34      3   12   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     V     7_B     V     7_A     34   34   34     18   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C     8_B     C     8_A     34   34   34     18   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     P     9_B     P     9_A     34   34   34     11   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     V    10_B     V    10_A     34   34   34     14   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     L    11_B     L    11_A     34   34   34      5   14   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     I    12_B     I    12_A     34   34   34     12   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     Y    13_B     Y    13_A     34   34   34     14   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     L    14_B     L    14_A     34   34   34     18   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    15_B     C    15_A     34   34   34     14   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     R    16_B     R    16_A     34   34   34     15   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     R    17_B     R    17_A     34   34   34     18   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     D    18_B     D    18_A     34   34   34     18   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     S    19_B     S    19_A     34   34   34     18   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     D    20_B     D    20_A     34   34   34     18   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    21_B     C    21_A     34   34   34     18   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     P    22_B     P    22_A     34   34   34     18   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    23_B     G    23_A     34   34   34     18   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     E    24_B     E    24_A     34   34   34     18   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    25_B     C    25_A     34   34   34     18   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     I    26_B     I    26_A     34   34   34     18   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    27_B     C    27_A     34   34   34     18   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     L    28_B     L    28_A     34   34   34     14   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    29_B     G    29_A     34   34   34     11   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     N    30_B     N    30_A     34   34   34     10   17   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    31_B     G    31_A     34   34   34     14   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     Y    32_B     Y    32_A     34   34   34     18   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    33_B     C    33_A     34   34   34     18   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    34_B     G    34_A     34   34   34     18   30   32   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_AVERAGE  LCS_A: 100.00  ( 100.00  100.00  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     18     30     32     34     34     34     34     34     34     34     34     34     34     34     34     34     34     34     34     34 
GDT PERCENT_AT  52.94  88.24  94.12 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.30   0.57   0.69   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86
GDT RMS_ALL_AT   1.03   0.90   0.90   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86

# 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     0.668     0    0.068   0.584     2.721   90.476   84.921
LGA    G     2_B      G     2_A     0.833     0    0.080   0.080     0.833   92.857   92.857
LGA    P     3_B      P     3_A     0.312     0    0.229   0.203     1.441   90.595   87.959
LGA    N     4_B      N     4_A     0.791     0    0.704   1.190     5.347   82.143   68.155
LGA    G     5_B      G     5_A     2.238     0    0.673   0.673     2.779   66.905   66.905
LGA    G     6_B      G     6_A     1.765     0    0.050   0.050     2.375   72.976   72.976
LGA    V     7_B      V     7_A     0.484     0    0.113   0.152     0.746   97.619   94.558
LGA    C     8_B      C     8_A     0.540     0    0.058   0.051     0.589   95.238   95.238
LGA    P     9_B      P     9_A     0.600     0    0.016   0.287     1.492   92.857   90.544
LGA    V    10_B      V    10_A     0.882     0    0.320   1.008     3.331   88.214   78.435
LGA    L    11_B      L    11_A     1.752     3    0.075   0.089     1.834   77.143   47.679
LGA    I    12_B      I    12_A     0.599     0    0.013   0.638     2.266   95.238   88.512
LGA    Y    13_B      Y    13_A     0.589     0    0.048   0.445     3.726   95.238   74.762
LGA    L    14_B      L    14_A     0.787     0    0.019   1.392     3.986   90.476   75.357
LGA    C    15_B      C    15_A     0.586     0    0.012   0.059     0.665   90.476   93.651
LGA    R    16_B      R    16_A     0.408     0    0.120   1.080     5.517   97.619   68.312
LGA    R    17_B      R    17_A     0.565     0    0.053   0.995     2.663   92.857   85.152
LGA    D    18_B      D    18_A     0.753     0    0.018   0.063     0.892   90.476   90.476
LGA    S    19_B      S    19_A     1.056     0    0.011   0.012     1.286   85.952   84.444
LGA    D    20_B      D    20_A     0.769     0    0.069   0.065     1.122   88.214   90.536
LGA    C    21_B      C    21_A     0.251     0    0.019   0.044     0.416  100.000  100.000
LGA    P    22_B      P    22_A     0.610     0    0.047   0.097     0.837   92.857   91.837
LGA    G    23_B      G    23_A     0.439     0    0.026   0.026     0.475  100.000  100.000
LGA    E    24_B      E    24_A     0.534     0    0.078   0.298     1.475   95.238   91.587
LGA    C    25_B      C    25_A     0.306     0    0.018   0.099     0.611   97.619   96.825
LGA    I    26_B      I    26_A     0.724     0    0.046   0.057     1.412   92.857   87.143
LGA    C    27_B      C    27_A     0.472     0    0.024   0.097     0.597   95.238   96.825
LGA    L    28_B      L    28_A     0.732     0    0.030   0.105     1.748   92.857   86.071
LGA    G    29_B      G    29_A     0.800     0    0.038   0.038     1.210   85.952   85.952
LGA    N    30_B      N    30_A     1.557     0    0.050   1.194     3.722   79.286   70.357
LGA    G    31_B      G    31_A     0.775     0    0.035   0.035     0.886   90.476   90.476
LGA    Y    32_B      Y    32_A     0.132     0    0.025   0.041     0.385  100.000  100.000
LGA    C    33_B      C    33_A     0.198     0    0.014   0.037     0.328  100.000  100.000
LGA    G    34_B      G    34_A     0.315     0    0.018   0.018     0.442  100.000  100.000

# 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):     0.862          0.876                  1.369           91.057   86.132

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   34    4.0     34    0.86    97.059    98.633     3.535

LGA_LOCAL      RMSD:   0.862  Number of atoms:   34  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.862  Number of assigned atoms:   34 
Std_ASGN_ATOMS RMSD:   0.862  Standard rmsd on all 34 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.334974 * X  +   0.766704 * Y  +   0.547683 * Z  + -36.052990
  Y_new =   0.560804 * X  +  -0.629329 * Y  +   0.538000 * Z  + -30.913315
  Z_new =   0.757160 * X  +   0.126927 * Y  +  -0.640780 * Z  + -23.243547 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.032357 -0.858954  2.946043   [DEG:   59.1497  -49.2145  168.7958 ]
ZXZ:  2.347276  2.266310  1.404705   [DEG:  134.4890  129.8500   80.4837 ]
 
# END of job
