
#######################################################
#                                                     #
#                        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        1.45     1.45
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    34       1_A - 34_A        1.45     1.45
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    30       5_A - 34_A        0.72     1.67
  LCS_AVERAGE:     80.62

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      8   34   34      3    6   14   22   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G     2_B     G     2_A      8   34   34      3    8   15   28   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     P     3_B     P     3_A      8   34   34      3    8   14   16   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     N     4_B     N     4_A      8   34   34      3    8   12   19   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G     5_B     G     5_A     30   34   34      3   22   29   30   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G     6_B     G     6_A     30   34   34      3   27   29   30   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     V     7_B     V     7_A     30   34   34      5   13   29   30   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C     8_B     C     8_A     30   34   34     12   27   29   30   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     P     9_B     P     9_A     30   34   34     20   27   29   30   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     V    10_B     V    10_A     30   34   34     20   27   29   30   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     L    11_B     L    11_A     30   34   34      7   27   29   30   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     I    12_B     I    12_A     30   34   34     20   27   29   30   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     Y    13_B     Y    13_A     30   34   34     20   27   29   30   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     L    14_B     L    14_A     30   34   34     20   27   29   30   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    15_B     C    15_A     30   34   34     20   27   29   30   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     R    16_B     R    16_A     30   34   34     20   27   29   30   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     R    17_B     R    17_A     30   34   34     20   27   29   30   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     D    18_B     D    18_A     30   34   34     20   27   29   30   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     S    19_B     S    19_A     30   34   34     20   27   29   30   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     D    20_B     D    20_A     30   34   34     20   27   29   30   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    21_B     C    21_A     30   34   34     20   27   29   30   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     P    22_B     P    22_A     30   34   34     19   27   29   30   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    23_B     G    23_A     30   34   34     20   27   29   30   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     E    24_B     E    24_A     30   34   34     16   27   29   30   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    25_B     C    25_A     30   34   34     20   27   29   30   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     I    26_B     I    26_A     30   34   34     20   27   29   30   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    27_B     C    27_A     30   34   34     20   27   29   30   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     L    28_B     L    28_A     30   34   34     20   27   29   30   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    29_B     G    29_A     30   34   34      8   27   29   30   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     N    30_B     N    30_A     30   34   34      6   15   29   30   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    31_B     G    31_A     30   34   34     14   27   29   30   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     Y    32_B     Y    32_A     30   34   34     20   27   29   30   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    33_B     C    33_A     30   34   34     20   27   29   30   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    34_B     G    34_A     30   34   34     20   27   29   30   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_AVERAGE  LCS_A:  93.54  (  80.62  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     20     27     29     30     31     34     34     34     34     34     34     34     34     34     34     34     34     34     34     34 
GDT PERCENT_AT  58.82  79.41  85.29  88.24  91.18 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.34   0.54   0.64   0.72   0.98   1.45   1.45   1.45   1.45   1.45   1.45   1.45   1.45   1.45   1.45   1.45   1.45   1.45   1.45   1.45
GDT RMS_ALL_AT   1.68   1.71   1.74   1.67   1.57   1.45   1.45   1.45   1.45   1.45   1.45   1.45   1.45   1.45   1.45   1.45   1.45   1.45   1.45   1.45

# 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     2.894     0    0.297   0.639     4.373   48.571   52.857
LGA    G     2_B      G     2_A     2.700     0    0.072   0.072     2.968   59.048   59.048
LGA    P     3_B      P     3_A     3.736     0    0.297   0.335     4.482   43.333   41.565
LGA    N     4_B      N     4_A     3.331     0    0.676   1.191     5.963   45.357   40.893
LGA    G     5_B      G     5_A     1.159     0    0.679   0.679     3.507   69.762   69.762
LGA    G     6_B      G     6_A     1.080     0    0.140   0.140     1.885   81.548   81.548
LGA    V     7_B      V     7_A     2.093     0    0.044   0.057     3.478   70.833   61.905
LGA    C     8_B      C     8_A     1.362     0    0.009   0.043     1.675   79.286   80.000
LGA    P     9_B      P     9_A     0.395     0    0.052   0.087     0.802   95.238   94.558
LGA    V    10_B      V    10_A     0.860     0    0.127   0.117     1.241   90.476   86.599
LGA    L    11_B      L    11_A     1.444     3    0.140   0.178     1.942   79.286   49.821
LGA    I    12_B      I    12_A     0.855     0    0.087   0.620     2.086   88.214   87.321
LGA    Y    13_B      Y    13_A     0.829     0    0.044   0.891     5.015   90.476   70.198
LGA    L    14_B      L    14_A     0.730     0    0.047   0.131     1.202   90.476   89.345
LGA    C    15_B      C    15_A     0.415     0    0.024   0.051     0.717   97.619   96.825
LGA    R    16_B      R    16_A     0.411     0    0.035   1.228     7.032  100.000   70.519
LGA    R    17_B      R    17_A     0.390     0    0.056   0.222     0.823  100.000   94.805
LGA    D    18_B      D    18_A     0.266     0    0.019   0.101     1.078  100.000   94.107
LGA    S    19_B      S    19_A     0.182     0    0.029   0.034     0.253  100.000  100.000
LGA    D    20_B      D    20_A     0.168     0    0.065   0.168     0.694  100.000   98.810
LGA    C    21_B      C    21_A     0.527     0    0.027   0.076     0.672   92.857   92.063
LGA    P    22_B      P    22_A     0.903     0    0.111   0.174     1.138   88.214   89.184
LGA    G    23_B      G    23_A     1.194     0    0.046   0.046     1.438   81.429   81.429
LGA    E    24_B      E    24_A     1.631     0    0.027   0.356     3.712   77.143   64.603
LGA    C    25_B      C    25_A     0.973     0    0.034   0.039     1.132   88.214   88.968
LGA    I    26_B      I    26_A     0.793     0    0.018   0.086     0.890   90.476   90.476
LGA    C    27_B      C    27_A     0.795     0    0.035   0.035     0.872   90.476   90.476
LGA    L    28_B      L    28_A     0.850     0    0.025   0.043     1.274   85.952   91.786
LGA    G    29_B      G    29_A     1.736     0    0.018   0.018     2.317   72.976   72.976
LGA    N    30_B      N    30_A     1.895     0    0.055   0.070     2.484   77.143   74.048
LGA    G    31_B      G    31_A     0.918     0    0.030   0.030     1.180   88.214   88.214
LGA    Y    32_B      Y    32_A     0.786     0    0.031   0.126     2.444   90.476   78.135
LGA    C    33_B      C    33_A     0.523     0    0.061   0.071     0.911   90.476   90.476
LGA    G    34_B      G    34_A     0.513     0    0.039   0.039     1.386   88.214   88.214

# 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):     1.453          1.539                  1.852           83.288   79.457

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   34    4.0     34    1.45    91.912    95.872     2.190

LGA_LOCAL      RMSD:   1.453  Number of atoms:   34  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.453  Number of assigned atoms:   34 
Std_ASGN_ATOMS RMSD:   1.453  Standard rmsd on all 34 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.226890 * X  +   0.967759 * Y  +  -0.109380 * Z  +  -9.882873
  Y_new =   0.856798 * X  +  -0.251740 * Y  +  -0.450027 * Z  +  -6.347914
  Z_new =  -0.463053 * X  +   0.008390 * Y  +  -0.886291 * Z  + -16.348682 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.311926  0.481437  3.132126   [DEG:   75.1678   27.5843  179.4576 ]
ZXZ: -0.238429  2.660070 -1.552679   [DEG:  -13.6610  152.4108  -88.9620 ]
 
# END of job
