
#######################################################
#                                                     #
#                        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   35 (  269),  selected   35 , name one
# Molecule2: number of CA atoms   35 (  269),  selected   35 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      11_A - 35_A        4.88     7.80
  LCS_AVERAGE:     64.16

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9      25_A - 33_A        1.97     7.81
  LONGEST_CONTINUOUS_SEGMENT:     9      26_A - 34_A        1.89     8.52
  LONGEST_CONTINUOUS_SEGMENT:     9      27_A - 35_A        1.68     9.50
  LCS_AVERAGE:     19.10

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7      29_A - 35_A        0.78     9.35
  LCS_AVERAGE:     12.41

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   35
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_A     S     1_A      3    4   12      3    3    3    3    4    4    4    6    7   17   22   22   23   25   27   29   30   31   32   32 
LCS_GDT     D     2_A     D     2_A      3    4   12      3    3    3    3    4    5    5    6    7   10   22   22   23   25   27   29   30   31   32   32 
LCS_GDT     E     3_A     E     3_A      3    4   12      3    3    3    3    4    5    5    6    8   13   15   20   23   25   27   29   30   31   32   32 
LCS_GDT     M     4_A     M     4_A      3    4   12      3    3    3    3    4    5    5    7    9   13   15   18   22   25   27   29   30   31   32   32 
LCS_GDT     W     5_A     W     5_A      3    3   17      3    3    3    4    4    5    5    7    8   10   12   14   17   23   26   29   30   31   32   32 
LCS_GDT     F     6_A     F     6_A      3    3   18      3    3    3    4    4    5    5    7   10   11   14   18   21   24   27   29   30   31   32   32 
LCS_GDT     C     7_A     C     7_A      4    5   18      4    4    4    5    5    5    6    9   11   13   14   18   20   23   26   29   30   31   32   32 
LCS_GDT     E     8_A     E     8_A      4    5   18      4    4    4    5    6    6    7    9   11   13   14   16   18   20   22   23   25   28   29   31 
LCS_GDT     T     9_A     T     9_A      4    5   18      4    4    4    5    5    5    5    7    9   11   12   16   17   17   19   22   23   27   28   30 
LCS_GDT     L    10_A     L    10_A      4    5   24      4    4    4    5    6    6    7    9   11   13   14   18   21   23   26   29   30   31   32   32 
LCS_GDT     R    11_A     R    11_A      4    5   25      3    3    4    5    5    5    5    7    9   10   14   16   18   22   24   27   29   31   32   32 
LCS_GDT     R    12_A     R    12_A      3    4   25      3    3    3    3    4    5    6    7   13   14   16   19   21   25   27   29   30   31   32   32 
LCS_GDT     L    13_A     L    13_A      3    7   25      3    5    7    8   11   12   17   18   19   20   22   22   23   25   27   29   30   31   32   32 
LCS_GDT     L    14_A     L    14_A      3    7   25      3    3    4    5    8   10   17   18   19   20   22   22   23   25   27   29   30   31   32   32 
LCS_GDT     C    15_A     C    15_A      3    7   25      0    3    6    8    9   14   17   18   19   20   22   22   23   25   27   29   30   31   32   32 
LCS_GDT     P    16_A     P    16_A      3    7   25      3    3    4    8    9   14   17   18   19   20   22   22   23   25   27   29   30   31   32   32 
LCS_GDT     K    17_A     K    17_A      3    7   25      3    3    4    6    9   14   16   18   19   20   22   22   23   25   27   29   30   31   32   32 
LCS_GDT     S    18_A     S    18_A      4    7   25      3    3    5    5    8   10   11   12   15   18   20   20   23   24   27   29   30   31   32   32 
LCS_GDT     C    19_A     C    19_A      4    7   25      3    3    5    5    9   14   17   18   19   20   22   22   23   25   27   29   30   31   32   32 
LCS_GDT     S    20_A     S    20_A      4    7   25      3    4    5    6    9   10   17   18   19   20   22   22   23   25   27   29   30   31   32   32 
LCS_GDT     I    21_A     I    21_A      4    7   25      3    4    5    6   11   14   17   18   19   20   22   22   23   25   27   29   30   31   32   32 
LCS_GDT     E    22_A     E    22_A      4    7   25      3    4    7    8   11   14   17   18   19   20   22   22   23   25   27   29   30   31   32   32 
LCS_GDT     G    23_A     G    23_A      4    7   25      3    5    7    8   11   14   17   18   19   20   22   22   23   25   27   29   30   31   32   32 
LCS_GDT     G    24_A     G    24_A      3    7   25      3    3    3    5    8   12   17   18   19   20   22   22   23   25   27   29   30   31   32   32 
LCS_GDT     C    25_A     C    25_A      5    9   25      1    4    6    8   11   14   17   18   19   20   22   22   23   25   27   29   30   31   32   32 
LCS_GDT     P    26_A     P    26_A      5    9   25      3    5    7    8   11   14   17   18   19   20   22   22   23   25   27   29   30   31   32   32 
LCS_GDT     E    27_A     E    27_A      5    9   25      3    4    6    8   11   14   17   18   19   20   22   22   23   25   27   29   30   31   32   32 
LCS_GDT     V    28_A     V    28_A      5    9   25      3    4    6    7    9   12   15   17   19   20   22   22   23   25   27   29   30   31   32   32 
LCS_GDT     C    29_A     C    29_A      7    9   25      3    5    7    8   11   14   17   18   19   20   22   22   23   25   27   29   30   31   32   32 
LCS_GDT     S    30_A     S    30_A      7    9   25      3    5    7    8   11   14   17   18   19   20   22   22   23   25   27   29   30   31   32   32 
LCS_GDT     H    31_A     H    31_A      7    9   25      3    5    7    8   11   14   17   18   19   20   22   22   23   25   27   29   30   31   32   32 
LCS_GDT     M    32_A     M    32_A      7    9   25      4    5    7    8   11   14   17   18   19   20   22   22   23   25   27   29   30   31   32   32 
LCS_GDT     C    33_A     C    33_A      7    9   25      4    5    7    7    9   10   14   16   19   20   22   22   23   25   27   29   30   31   32   32 
LCS_GDT     P    34_A     P    34_A      7    9   25      4    5    7    7    9    9   13   15   17   19   21   21   22   23   25   27   29   30   32   32 
LCS_GDT     L    35_A     L    35_A      7    9   25      4    5    7    7    9    9   10   10   13   14   16   20   21   21   22   24   27   30   31   32 
LCS_AVERAGE  LCS_A:  31.89  (  12.41   19.10   64.16 )

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      4      5      7      8     11     14     17     18     19     20     22     22     23     25     27     29     30     31     32     32 
GDT PERCENT_AT  11.43  14.29  20.00  22.86  31.43  40.00  48.57  51.43  54.29  57.14  62.86  62.86  65.71  71.43  77.14  82.86  85.71  88.57  91.43  91.43
GDT RMS_LOCAL    0.21   0.51   0.78   1.20   1.73   2.23   2.59   2.67   2.82   2.99   3.53   3.53   3.72   4.40   4.86   5.58   5.63   5.82   6.00   6.00
GDT RMS_ALL_AT  10.68   9.07   9.35   7.84   7.75   9.35   8.51   8.62   8.58   8.47   7.93   7.93   8.03   7.37   7.25   6.97   7.00   6.98   6.90   6.90

# Checking swapping
#   possible swapping detected:  E     8_A      E     8_A
#   possible swapping detected:  E    22_A      E    22_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     1_A      S     1_A     9.060     0    0.375   0.415    11.611    2.262    1.508
LGA    D     2_A      D     2_A     6.789     0    0.252   1.391     7.496   10.833   17.440
LGA    E     3_A      E     3_A     9.364     0    0.547   1.164    10.582    3.095    2.169
LGA    M     4_A      M     4_A    11.253     0    0.614   0.968    16.789    0.000    0.000
LGA    W     5_A      W     5_A    13.433     0    0.556   0.352    19.589    0.000    0.000
LGA    F     6_A      F     6_A    13.808     0    0.610   1.340    14.368    0.000    0.823
LGA    C     7_A      C     7_A    15.303     0    0.557   1.028    16.913    0.000    0.000
LGA    E     8_A      E     8_A    17.987     0    0.095   0.788    21.423    0.000    0.000
LGA    T     9_A      T     9_A    19.486     0    0.026   0.301    22.626    0.000    0.000
LGA    L    10_A      L    10_A    15.188     0    0.631   0.575    19.110    0.000    0.000
LGA    R    11_A      R    11_A    13.447     0    0.302   0.974    24.842    0.000    0.000
LGA    R    12_A      R    12_A    10.498     0    0.652   0.945    16.303    3.571    1.299
LGA    L    13_A      L    13_A     3.544     0    0.634   1.089     6.113   51.548   47.262
LGA    L    14_A      L    14_A     3.627     0    0.631   1.371    10.460   55.595   30.714
LGA    C    15_A      C    15_A     2.231     0    0.655   0.589     3.040   61.190   59.841
LGA    P    16_A      P    16_A     2.806     0    0.536   0.789     5.116   47.619   43.129
LGA    K    17_A      K    17_A     3.598     0    0.069   1.052     5.986   37.024   43.862
LGA    S    18_A      S    18_A     6.649     0    0.665   0.817     9.813   24.286   17.063
LGA    C    19_A      C    19_A     3.007     0    0.646   0.642     4.515   52.738   58.254
LGA    S    20_A      S    20_A     3.623     0    0.043   0.492     4.898   46.905   42.698
LGA    I    21_A      I    21_A     2.647     0    0.566   0.531     5.445   47.619   50.595
LGA    E    22_A      E    22_A     1.572     0    0.306   0.542     3.339   69.286   68.677
LGA    G    23_A      G    23_A     1.484     0    0.135   0.135     1.995   79.286   79.286
LGA    G    24_A      G    24_A     3.419     0    0.604   0.604     3.419   65.119   65.119
LGA    C    25_A      C    25_A     1.616     0    0.467   0.522     4.363   59.881   60.397
LGA    P    26_A      P    26_A     1.234     0    0.197   0.249     2.988   79.405   72.041
LGA    E    27_A      E    27_A     3.186     0    0.699   0.650     4.389   51.786   44.339
LGA    V    28_A      V    28_A     5.104     0    0.088   1.156     8.524   34.524   25.034
LGA    C    29_A      C    29_A     2.704     0    0.099   0.757     6.801   67.143   55.317
LGA    S    30_A      S    30_A     1.744     0    0.103   0.569     2.734   71.310   69.206
LGA    H    31_A      H    31_A     2.321     0    0.161   1.117     8.201   64.881   39.476
LGA    M    32_A      M    32_A     1.145     0    0.078   0.236     3.257   67.500   66.190
LGA    C    33_A      C    33_A     5.406     0    0.109   0.126     7.207   24.167   21.190
LGA    P    34_A      P    34_A     8.080     0    0.202   0.181    10.884    4.643    7.823
LGA    L    35_A      L    35_A    11.648     0    0.109   1.184    13.362    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       35     140    140  100.00     269    269  100.00                35
SUMMARY(RMSD_GDC):     6.801          6.635                  7.989           33.806   31.164

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   35   35    4.0     18    2.67    42.857    38.159     0.650

LGA_LOCAL      RMSD:   2.671  Number of atoms:   18  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   8.621  Number of assigned atoms:   35 
Std_ASGN_ATOMS RMSD:   6.801  Standard rmsd on all 35 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.350837 * X  +  -0.809076 * Y  +   0.471496 * Z  +  11.402640
  Y_new =   0.747866 * X  +  -0.545100 * Y  +  -0.378897 * Z  +   0.027655
  Z_new =   0.563569 * X  +   0.219685 * Y  +   0.796322 * Z  +  -1.024433 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.009435 -0.598700  0.269179   [DEG:  115.1321  -34.3030   15.4228 ]
ZXZ:  0.893861  0.649606  1.199105   [DEG:   51.2145   37.2197   68.7037 ]
 
# END of job
