
#######################################################
#                                                     #
#                        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:    35       1_A - 35_A        4.19     4.19
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16       1_A - 16_A        1.35     6.67
  LCS_AVERAGE:     34.20

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14       2_A - 15_A        0.90     6.87
  LONGEST_CONTINUOUS_SEGMENT:    14       3_A - 16_A        0.87     6.42
  LCS_AVERAGE:     26.53

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     10   16   35      4    6    9   11   14   17   18   21   26   26   28   30   32   33   33   34   34   35   35   35 
LCS_GDT     D     2_A     D     2_A     14   16   35      4    9   13   15   18   24   25   25   28   30   31   31   32   33   33   34   34   35   35   35 
LCS_GDT     E     3_A     E     3_A     14   16   35      4   11   13   15   18   24   25   27   28   30   31   31   32   33   33   34   34   35   35   35 
LCS_GDT     M     4_A     M     4_A     14   16   35      7   12   15   19   21   24   25   27   29   30   31   31   32   33   33   34   34   35   35   35 
LCS_GDT     W     5_A     W     5_A     14   16   35      9   12   15   19   21   24   25   27   29   30   31   31   32   33   33   34   34   35   35   35 
LCS_GDT     F     6_A     F     6_A     14   16   35     10   12   15   19   21   24   25   27   29   30   31   31   32   33   33   34   34   35   35   35 
LCS_GDT     C     7_A     C     7_A     14   16   35     10   12   15   19   21   24   25   27   29   30   31   31   32   33   33   34   34   35   35   35 
LCS_GDT     E     8_A     E     8_A     14   16   35     10   12   15   19   21   24   25   27   29   30   31   31   32   33   33   34   34   35   35   35 
LCS_GDT     T     9_A     T     9_A     14   16   35     10   12   15   19   21   24   25   27   29   30   31   31   32   33   33   34   34   35   35   35 
LCS_GDT     L    10_A     L    10_A     14   16   35     10   12   15   19   21   24   25   27   29   30   31   31   32   33   33   34   34   35   35   35 
LCS_GDT     R    11_A     R    11_A     14   16   35     10   12   15   19   21   24   25   27   29   30   31   31   32   33   33   34   34   35   35   35 
LCS_GDT     R    12_A     R    12_A     14   16   35     10   12   15   19   21   24   25   27   29   30   31   31   32   33   33   34   34   35   35   35 
LCS_GDT     L    13_A     L    13_A     14   16   35     10   12   15   19   21   24   25   27   29   30   31   31   32   33   33   34   34   35   35   35 
LCS_GDT     L    14_A     L    14_A     14   16   35     10   12   15   19   21   24   25   27   29   30   31   31   32   33   33   34   34   35   35   35 
LCS_GDT     C    15_A     C    15_A     14   16   35     10   12   15   19   21   24   25   27   29   30   31   31   32   33   33   34   34   35   35   35 
LCS_GDT     P    16_A     P    16_A     14   16   35      3    7   14   16   21   24   25   27   29   30   31   31   32   33   33   34   34   35   35   35 
LCS_GDT     K    17_A     K    17_A      5    7   35      3    4    7    7    9   13   21   23   29   30   31   31   32   33   33   34   34   35   35   35 
LCS_GDT     S    18_A     S    18_A      5    7   35      3    4    7    7    9   13   21   23   29   30   31   31   32   33   33   34   34   35   35   35 
LCS_GDT     C    19_A     C    19_A      5    7   35      3    4    7    9   15   19   22   27   29   30   31   31   32   33   33   34   34   35   35   35 
LCS_GDT     S    20_A     S    20_A      5    7   35      3    4    5    6    8   11   13   13   19   23   24   27   29   31   32   34   34   35   35   35 
LCS_GDT     I    21_A     I    21_A      5    7   35      3    4    5    6    8   11   13   15   23   23   28   30   31   32   33   34   34   35   35   35 
LCS_GDT     E    22_A     E    22_A      4    7   35      3    4    4    5   12   16   21   24   29   30   31   31   32   33   33   34   34   35   35   35 
LCS_GDT     G    23_A     G    23_A      4    6   35      3    4    4    7   14   19   23   27   29   30   31   31   32   33   33   34   34   35   35   35 
LCS_GDT     G    24_A     G    24_A      4    6   35      3    4    7    7    9   19   23   27   29   30   31   31   32   33   33   34   34   35   35   35 
LCS_GDT     C    25_A     C    25_A      4   10   35      3    4    7   11   20   24   25   27   29   30   31   31   32   33   33   34   34   35   35   35 
LCS_GDT     P    26_A     P    26_A      7   10   35      4    4    7    8    9   16   19   22   26   27   28   30   30   33   33   33   34   35   35   35 
LCS_GDT     E    27_A     E    27_A      7   10   35      6    7   13   19   21   24   25   27   29   30   31   31   32   33   33   34   34   35   35   35 
LCS_GDT     V    28_A     V    28_A      7   10   35      6   11   15   19   21   24   25   27   29   30   31   31   32   33   33   34   34   35   35   35 
LCS_GDT     C    29_A     C    29_A      7   10   35      6    6   12   19   21   24   25   27   29   30   31   31   32   33   33   34   34   35   35   35 
LCS_GDT     S    30_A     S    30_A      7   10   35      6    6   12   19   21   24   25   27   29   30   31   31   32   33   33   34   34   35   35   35 
LCS_GDT     H    31_A     H    31_A      7   10   35      6    6   12   19   21   24   25   27   29   30   31   31   32   33   33   34   34   35   35   35 
LCS_GDT     M    32_A     M    32_A      7   10   35      6    6    9   17   21   24   25   27   29   30   31   31   32   33   33   34   34   35   35   35 
LCS_GDT     C    33_A     C    33_A      5   10   35      4   10   15   19   21   24   25   27   29   30   31   31   32   33   33   34   34   35   35   35 
LCS_GDT     P    34_A     P    34_A      5   10   35      4   11   15   19   21   24   25   27   29   30   31   31   32   33   33   34   34   35   35   35 
LCS_GDT     L    35_A     L    35_A      5    9   35     10   12   14   15   18   24   25   27   29   30   31   31   32   33   33   34   34   35   35   35 
LCS_AVERAGE  LCS_A:  53.58  (  26.53   34.20  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     10     12     15     19     21     24     25     27     29     30     31     31     32     33     33     34     34     35     35     35 
GDT PERCENT_AT  28.57  34.29  42.86  54.29  60.00  68.57  71.43  77.14  82.86  85.71  88.57  88.57  91.43  94.29  94.29  97.14  97.14 100.00 100.00 100.00
GDT RMS_LOCAL    0.31   0.42   0.88   1.32   1.51   1.84   1.96   2.44   2.93   3.03   3.13   3.13   3.33   3.53   3.53   3.99   3.99   4.19   4.19   4.19
GDT RMS_ALL_AT   6.30   6.52   5.51   5.37   5.14   5.17   5.08   4.49   4.31   4.25   4.23   4.23   4.25   4.30   4.30   4.20   4.20   4.19   4.19   4.19

# Checking swapping
#   possible swapping detected:  D     2_A      D     2_A
#   possible swapping detected:  E     3_A      E     3_A
#   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     7.161     0    0.120   0.166    10.861   20.952   14.048
LGA    D     2_A      D     2_A     4.909     0    0.025   1.179     6.103   37.262   30.536
LGA    E     3_A      E     3_A     4.077     0    0.101   0.802     6.628   47.143   35.291
LGA    M     4_A      M     4_A     1.412     0    0.063   0.875     3.608   77.619   67.798
LGA    W     5_A      W     5_A     1.696     0    0.091   0.251     4.990   77.143   52.993
LGA    F     6_A      F     6_A     1.596     0    0.011   0.186     3.238   79.405   66.667
LGA    C     7_A      C     7_A     1.212     0    0.033   0.144     2.723   81.548   77.460
LGA    E     8_A      E     8_A     1.435     0    0.060   0.087     3.703   83.690   70.000
LGA    T     9_A      T     9_A     0.686     0    0.056   0.292     1.867   92.857   88.027
LGA    L    10_A      L    10_A     1.069     0    0.039   0.229     2.590   81.548   75.298
LGA    R    11_A      R    11_A     1.653     0    0.017   0.643     5.022   75.000   54.848
LGA    R    12_A      R    12_A     1.419     0    0.023   1.066     3.665   81.429   73.333
LGA    L    13_A      L    13_A     0.884     0    0.011   1.107     4.482   83.690   76.071
LGA    L    14_A      L    14_A     2.133     0    0.094   0.119     2.695   64.881   63.869
LGA    C    15_A      C    15_A     2.573     0    0.622   0.828     3.435   59.167   59.921
LGA    P    16_A      P    16_A     2.514     0    0.652   0.589     6.331   44.762   37.007
LGA    K    17_A      K    17_A     7.430     0    0.045   0.662    15.951   11.548    5.450
LGA    S    18_A      S    18_A     7.291     0    0.071   0.075     8.980   13.452   10.635
LGA    C    19_A      C    19_A     4.844     0    0.197   0.492     7.780   20.000   22.063
LGA    S    20_A      S    20_A    11.650     0    0.093   0.694    14.909    0.357    0.238
LGA    I    21_A      I    21_A    11.485     0    0.569   0.540    15.070    0.238    0.119
LGA    E    22_A      E    22_A     6.686     0    0.630   0.708     8.301   12.143   10.476
LGA    G    23_A      G    23_A     4.220     0    0.628   0.628     5.949   31.786   31.786
LGA    G    24_A      G    24_A     4.223     0    0.336   0.336     5.431   39.167   39.167
LGA    C    25_A      C    25_A     2.975     0    0.614   0.805     5.361   44.405   47.619
LGA    P    26_A      P    26_A     6.907     0    0.605   0.648     9.058   22.976   16.463
LGA    E    27_A      E    27_A     2.823     0    0.172   1.007     4.418   60.119   67.566
LGA    V    28_A      V    28_A     2.033     0    0.055   1.140     3.954   75.357   66.667
LGA    C    29_A      C    29_A     2.402     0    0.077   0.756     3.512   62.857   61.270
LGA    S    30_A      S    30_A     2.317     0    0.081   0.586     2.529   64.881   67.619
LGA    H    31_A      H    31_A     1.378     0    0.285   1.420     3.467   83.690   70.333
LGA    M    32_A      M    32_A     1.906     0    0.032   1.210     4.543   75.000   64.821
LGA    C    33_A      C    33_A     0.800     0    0.012   0.162     1.845   85.952   83.016
LGA    P    34_A      P    34_A     0.990     0    0.489   0.441     2.903   80.119   80.748
LGA    L    35_A      L    35_A     3.203     0    0.384   0.548     9.607   69.762   39.226

# 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):     4.188          4.063                  4.774           55.483   49.384

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   35   35    4.0     27    2.44    65.714    60.569     1.063

LGA_LOCAL      RMSD:   2.440  Number of atoms:   27  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.487  Number of assigned atoms:   35 
Std_ASGN_ATOMS RMSD:   4.188  Standard rmsd on all 35 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.457835 * X  +   0.721681 * Y  +  -0.519195 * Z  +  -2.332985
  Y_new =   0.283433 * X  +   0.435038 * Y  +   0.854639 * Z  +  -2.767316
  Z_new =   0.842646 * X  +  -0.538441 * Y  +  -0.005373 * Z  +  -2.877991 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.554326 -1.002179 -1.580775   [DEG:   31.7605  -57.4206  -90.5717 ]
ZXZ: -2.595675  1.576169  2.139391   [DEG: -148.7212   90.3078  122.5781 ]
 
# END of job
