
#######################################################
#                                                     #
#                        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:    26      10_A - 35_A        4.97     8.95
  LCS_AVERAGE:     72.08

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16       1_A - 16_A        1.39    11.99
  LCS_AVERAGE:     33.14

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14       2_A - 15_A        0.95    12.37
  LCS_AVERAGE:     25.14

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     11   16   23      3    6   11   15   16   17   17   18   21   23   24   25   26   27   29   29   30   30   32   32 
LCS_GDT     D     2_A     D     2_A     14   16   23      4    9   14   15   16   17   17   18   19   20   24   25   26   27   29   29   30   30   32   32 
LCS_GDT     E     3_A     E     3_A     14   16   23      4    9   14   15   16   17   17   18   21   23   24   25   26   27   29   29   30   30   32   32 
LCS_GDT     M     4_A     M     4_A     14   16   23      4   12   14   15   16   17   18   19   21   23   24   25   26   27   29   29   30   30   32   32 
LCS_GDT     W     5_A     W     5_A     14   16   23      4   12   14   15   16   17   18   19   21   23   24   25   26   27   29   29   30   30   32   32 
LCS_GDT     F     6_A     F     6_A     14   16   23      6   12   14   15   16   17   18   19   21   23   24   25   26   27   29   29   30   30   32   32 
LCS_GDT     C     7_A     C     7_A     14   16   23      7   12   14   15   16   17   18   19   21   23   24   25   26   27   29   29   30   30   32   32 
LCS_GDT     E     8_A     E     8_A     14   16   23      7   12   14   15   16   17   18   19   21   23   24   25   26   27   29   29   30   30   32   32 
LCS_GDT     T     9_A     T     9_A     14   16   23      7   12   14   15   16   17   18   19   21   23   24   25   26   27   29   29   30   30   32   32 
LCS_GDT     L    10_A     L    10_A     14   16   26      7   12   14   15   16   17   18   19   21   23   24   25   26   27   29   29   30   30   32   32 
LCS_GDT     R    11_A     R    11_A     14   16   26      7   12   14   15   16   17   18   19   21   23   24   25   26   27   29   29   30   30   32   32 
LCS_GDT     R    12_A     R    12_A     14   16   26      7   12   14   15   16   17   18   19   21   23   24   25   26   27   29   29   30   30   32   32 
LCS_GDT     L    13_A     L    13_A     14   16   26      7   12   14   15   16   17   18   19   21   23   24   25   26   27   29   29   30   30   32   32 
LCS_GDT     L    14_A     L    14_A     14   16   26      4   12   14   15   16   17   17   18   21   23   24   25   26   26   29   29   30   30   31   32 
LCS_GDT     C    15_A     C    15_A     14   16   26      4   12   14   15   16   17   17   18   19   23   24   25   26   26   29   29   30   30   31   32 
LCS_GDT     P    16_A     P    16_A      5   16   26      3    4    7   14   15   17   17   18   21   23   24   25   26   27   29   29   30   30   32   32 
LCS_GDT     K    17_A     K    17_A      4    6   26      3    4    4    5   12   14   16   19   21   22   24   25   26   27   29   29   30   30   32   32 
LCS_GDT     S    18_A     S    18_A      4    6   26      3    5    7   12   13   14   16   19   21   22   23   25   26   27   29   29   30   30   32   32 
LCS_GDT     C    19_A     C    19_A      3    6   26      3    3    4    5    6   15   16   19   21   22   23   24   25   26   28   29   30   30   32   32 
LCS_GDT     S    20_A     S    20_A      3    6   26      3    3    4    5    7   11   13   14   20   20   22   23   23   25   27   29   29   29   32   32 
LCS_GDT     I    21_A     I    21_A      3    5   26      3    3    4    4    6    8   10   13   16   19   21   23   23   24   25   28   29   29   30   30 
LCS_GDT     E    22_A     E    22_A      3    5   26      3    3    4    8   10   11   13   19   21   22   23   23   24   26   27   29   29   29   32   32 
LCS_GDT     G    23_A     G    23_A      4    5   26      3    4    4    8   10   15   16   19   21   22   23   24   25   26   27   29   29   30   32   32 
LCS_GDT     G    24_A     G    24_A      4    5   26      3    4    4    5    6   15   16   19   21   22   23   24   25   26   27   29   29   30   32   32 
LCS_GDT     C    25_A     C    25_A      4   10   26      3    5    7   12   13   15   16   19   21   22   23   25   26   27   29   29   30   30   32   32 
LCS_GDT     P    26_A     P    26_A      7   10   26      4    4    7    7   13   16   18   19   21   23   24   25   26   27   29   29   30   30   32   32 
LCS_GDT     E    27_A     E    27_A      7   10   26      4    6    9   12   13   16   18   19   21   23   24   25   26   27   29   29   30   30   32   32 
LCS_GDT     V    28_A     V    28_A      7   10   26      5    6    9   12   13   16   18   19   21   23   24   25   26   27   29   29   30   30   32   32 
LCS_GDT     C    29_A     C    29_A      7   10   26      5    6    9   12   13   16   18   19   21   23   24   25   26   27   29   29   30   30   32   32 
LCS_GDT     S    30_A     S    30_A      7   10   26      5    6    9   12   13   16   18   19   21   23   24   25   26   27   29   29   30   30   32   32 
LCS_GDT     H    31_A     H    31_A      7   10   26      5    6    9   12   13   16   18   19   21   23   24   25   26   27   29   29   30   30   32   32 
LCS_GDT     M    32_A     M    32_A      7   10   26      5    6    9   12   13   16   18   19   21   23   24   25   26   27   29   29   30   30   32   32 
LCS_GDT     C    33_A     C    33_A      7   10   26      3    4    9   12   13   16   18   19   21   23   24   25   26   27   29   29   30   30   32   32 
LCS_GDT     P    34_A     P    34_A      4   10   26      3    4    7   12   13   15   16   19   21   22   24   25   26   27   29   29   30   30   32   32 
LCS_GDT     L    35_A     L    35_A      4    6   26      3    3   11   11   16   17   17   19   21   22   23   24   26   27   29   29   30   30   32   32 
LCS_AVERAGE  LCS_A:  43.46  (  25.14   33.14   72.08 )

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      7     12     14     15     16     17     18     19     21     23     24     25     26     27     29     29     30     30     32     32 
GDT PERCENT_AT  20.00  34.29  40.00  42.86  45.71  48.57  51.43  54.29  60.00  65.71  68.57  71.43  74.29  77.14  82.86  82.86  85.71  85.71  91.43  91.43
GDT RMS_LOCAL    0.24   0.67   0.95   1.14   1.30   1.49   2.23   2.53   2.88   3.19   3.31   3.51   3.71   4.10   4.43   4.43   4.66   4.66   5.39   5.29
GDT RMS_ALL_AT  11.68  12.15  12.37  12.26  12.32  11.94   8.07   7.47   7.02   8.53   8.61   8.55   8.17   6.94   7.34   7.34   7.08   7.08   6.22   6.52

# Checking swapping
#   possible swapping detected:  E     3_A      E     3_A
#   possible swapping detected:  E     8_A      E     8_A
#   possible swapping detected:  E    27_A      E    27_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     1_A      S     1_A     8.412     0    0.603   0.785    11.231    6.667    4.683
LGA    D     2_A      D     2_A     8.318     0    0.206   0.979    10.081   10.595    5.595
LGA    E     3_A      E     3_A     6.641     0    0.058   0.636     9.154   22.976   13.598
LGA    M     4_A      M     4_A     2.350     0    0.086   1.237     4.986   64.286   54.226
LGA    W     5_A      W     5_A     3.536     0    0.071   0.393     7.683   53.810   25.068
LGA    F     6_A      F     6_A     3.552     0    0.040   1.279     5.187   53.810   46.667
LGA    C     7_A      C     7_A     2.347     0    0.072   0.143     4.587   64.881   58.016
LGA    E     8_A      E     8_A     1.928     0    0.112   0.565     7.633   77.143   48.624
LGA    T     9_A      T     9_A     0.737     0    0.031   0.313     3.456   92.857   77.619
LGA    L    10_A      L    10_A     3.014     0    0.052   0.215     5.398   54.048   44.286
LGA    R    11_A      R    11_A     3.687     0    0.053   1.689     6.342   45.119   33.766
LGA    R    12_A      R    12_A     2.264     0    0.102   0.984     4.965   64.762   55.801
LGA    L    13_A      L    13_A     2.453     0    0.019   1.004     4.513   54.524   50.833
LGA    L    14_A      L    14_A     6.274     0    0.105   1.395    11.853   17.976    9.881
LGA    C    15_A      C    15_A     7.052     0    0.587   0.887     8.178   16.429   12.937
LGA    P    16_A      P    16_A     5.185     0    0.577   0.991     8.895   23.095   16.735
LGA    K    17_A      K    17_A     4.773     0    0.159   0.141    15.271   27.143   14.286
LGA    S    18_A      S    18_A     8.996     0    0.451   0.870    12.312    4.048    2.778
LGA    C    19_A      C    19_A    10.218     0    0.060   0.825    14.757    0.714    2.619
LGA    S    20_A      S    20_A    15.924     0    0.314   0.723    20.217    0.000    0.000
LGA    I    21_A      I    21_A    19.119     0    0.116   0.168    21.416    0.000    0.000
LGA    E    22_A      E    22_A    16.638     0    0.490   0.759    17.168    0.000    0.000
LGA    G    23_A      G    23_A    13.198     0    0.606   0.606    15.028    0.000    0.000
LGA    G    24_A      G    24_A    11.146     0    0.183   0.183    11.852    0.476    0.476
LGA    C    25_A      C    25_A     6.126     0    0.572   0.849     7.840   18.214   17.937
LGA    P    26_A      P    26_A     2.710     0    0.616   0.747     3.562   62.857   61.905
LGA    E    27_A      E    27_A     1.684     0    0.122   0.931     5.906   72.857   56.772
LGA    V    28_A      V    28_A     1.643     0    0.090   1.147     4.016   72.857   65.510
LGA    C    29_A      C    29_A     1.843     0    0.080   0.788     2.689   70.833   67.540
LGA    S    30_A      S    30_A     1.093     0    0.081   0.626     2.578   85.952   81.905
LGA    H    31_A      H    31_A     0.628     0    0.344   1.369     5.671   81.786   61.048
LGA    M    32_A      M    32_A     2.037     0    0.107   0.786     3.686   70.952   64.286
LGA    C    33_A      C    33_A     1.492     0    0.213   0.721     2.931   73.929   72.222
LGA    P    34_A      P    34_A     5.273     0    0.327   0.613     8.362   20.357   19.456
LGA    L    35_A      L    35_A     9.239     0    0.294   1.058    14.171    3.095    1.607

# 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):     6.204          6.256                  6.593           39.687   32.819

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   35   35    4.0     19    2.53    53.571    49.614     0.723

LGA_LOCAL      RMSD:   2.526  Number of atoms:   19  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   7.467  Number of assigned atoms:   35 
Std_ASGN_ATOMS RMSD:   6.204  Standard rmsd on all 35 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.404114 * X  +   0.914697 * Y  +   0.004611 * Z  + -19.808666
  Y_new =  -0.867822 * X  +  -0.384988 * Y  +   0.314117 * Z  +  10.086327
  Z_new =   0.289097 * X  +   0.122938 * Y  +   0.949373 * Z  + -39.832653 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.006601 -0.293284  0.128777   [DEG: -114.9697  -16.8039    7.3784 ]
ZXZ:  3.126915  0.319562  1.168716   [DEG:  179.1590   18.3096   66.9625 ]
 
# END of job
