
#######################################################
#                                                     #
#                        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        2.04     2.04
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       2_A - 34_A        1.87     2.05
  LCS_AVERAGE:     94.98

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    30       5_A - 34_A        0.94     2.35
  LCS_AVERAGE:     79.58

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      4    9   34      4    4    4    4    8   17   20   31   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G     2_B     G     2_A      4   33   34      4    4    4   10   15   30   31   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     P     3_B     P     3_A      6   33   34      4    6    8   12   18   30   31   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     N     4_B     N     4_A      6   33   34      4    4    8   12   22   30   31   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G     5_B     G     5_A     30   33   34      3    9   22   29   30   30   31   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G     6_B     G     6_A     30   33   34      3    5   28   29   30   30   31   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     V     7_B     V     7_A     30   33   34      4   12   28   29   30   30   31   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C     8_B     C     8_A     30   33   34     20   26   28   29   30   30   31   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     P     9_B     P     9_A     30   33   34     20   26   28   29   30   30   31   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     V    10_B     V    10_A     30   33   34     20   26   28   29   30   30   31   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     L    11_B     L    11_A     30   33   34     14   26   28   29   30   30   31   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     I    12_B     I    12_A     30   33   34     12   26   28   29   30   30   31   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     Y    13_B     Y    13_A     30   33   34     20   26   28   29   30   30   31   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     L    14_B     L    14_A     30   33   34     20   26   28   29   30   30   31   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    15_B     C    15_A     30   33   34     20   26   28   29   30   30   31   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     R    16_B     R    16_A     30   33   34     20   26   28   29   30   30   31   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     R    17_B     R    17_A     30   33   34     20   26   28   29   30   30   31   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     D    18_B     D    18_A     30   33   34     20   26   28   29   30   30   31   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     S    19_B     S    19_A     30   33   34     20   26   28   29   30   30   31   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     D    20_B     D    20_A     30   33   34     20   26   28   29   30   30   31   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    21_B     C    21_A     30   33   34     20   26   28   29   30   30   31   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     P    22_B     P    22_A     30   33   34     20   26   28   29   30   30   31   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    23_B     G    23_A     30   33   34     20   26   28   29   30   30   31   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     E    24_B     E    24_A     30   33   34     18   26   28   29   30   30   31   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    25_B     C    25_A     30   33   34     20   26   28   29   30   30   31   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     I    26_B     I    26_A     30   33   34     20   26   28   29   30   30   31   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    27_B     C    27_A     30   33   34     20   26   28   29   30   30   31   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     L    28_B     L    28_A     30   33   34     20   26   28   29   30   30   31   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    29_B     G    29_A     30   33   34     14   26   28   29   30   30   30   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     N    30_B     N    30_A     30   33   34      6   15   28   29   30   30   30   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    31_B     G    31_A     30   33   34     18   26   28   29   30   30   31   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     Y    32_B     Y    32_A     30   33   34     20   26   28   29   30   30   31   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    33_B     C    33_A     30   33   34     20   26   28   29   30   30   31   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    34_B     G    34_A     30   33   34     20   26   28   29   30   30   31   33   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_AVERAGE  LCS_A:  91.52  (  79.58   94.98  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     26     28     29     30     30     31     33     34     34     34     34     34     34     34     34     34     34     34     34 
GDT PERCENT_AT  58.82  76.47  82.35  85.29  88.24  88.24  91.18  97.06 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.31   0.45   0.57   0.71   0.94   0.94   1.83   1.87   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04
GDT RMS_ALL_AT   2.64   2.64   2.61   2.51   2.35   2.35   2.06   2.05   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04

# 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     5.238     0    0.056   0.743     7.774   15.476   26.984
LGA    G     2_B      G     2_A     4.430     0    0.176   0.176     4.665   34.286   34.286
LGA    P     3_B      P     3_A     4.990     0    0.342   0.386     5.647   30.119   28.503
LGA    N     4_B      N     4_A     4.474     0    0.676   1.153     6.479   31.786   31.250
LGA    G     5_B      G     5_A     1.610     0    0.680   0.680     3.586   65.476   65.476
LGA    G     6_B      G     6_A     1.237     0    0.195   0.195     2.106   79.524   79.524
LGA    V     7_B      V     7_A     2.318     0    0.028   1.033     3.762   70.833   61.973
LGA    C     8_B      C     8_A     1.866     0    0.020   0.044     2.125   70.833   71.508
LGA    P     9_B      P     9_A     0.958     0    0.041   0.076     1.367   88.214   86.599
LGA    V    10_B      V    10_A     0.760     0    0.286   0.238     1.341   88.214   89.184
LGA    L    11_B      L    11_A     1.118     3    0.135   0.165     1.830   81.548   50.952
LGA    I    12_B      I    12_A     0.937     0    0.077   0.611     1.578   90.476   87.143
LGA    Y    13_B      Y    13_A     0.963     0    0.045   0.918     5.412   88.214   66.706
LGA    L    14_B      L    14_A     0.888     0    0.046   0.133     1.398   90.476   85.952
LGA    C    15_B      C    15_A     0.474     0    0.026   0.053     0.840   92.857   93.651
LGA    R    16_B      R    16_A     0.409     0    0.048   0.967     5.093  100.000   75.498
LGA    R    17_B      R    17_A     0.432     0    0.057   0.277     1.647   97.619   89.913
LGA    D    18_B      D    18_A     0.679     0    0.014   0.201     1.933   90.476   84.881
LGA    S    19_B      S    19_A     0.688     0    0.031   0.038     0.732   90.476   90.476
LGA    D    20_B      D    20_A     0.509     0    0.069   0.206     1.082   90.476   91.726
LGA    C    21_B      C    21_A     0.895     0    0.029   0.070     1.204   85.952   87.460
LGA    P    22_B      P    22_A     1.396     0    0.101   0.173     1.508   79.286   80.204
LGA    G    23_B      G    23_A     1.875     0    0.070   0.070     2.092   70.833   70.833
LGA    E    24_B      E    24_A     2.243     0    0.033   0.571     4.792   64.762   53.915
LGA    C    25_B      C    25_A     1.516     0    0.031   0.038     1.728   77.143   78.571
LGA    I    26_B      I    26_A     1.244     0    0.014   0.082     1.613   81.429   80.357
LGA    C    27_B      C    27_A     1.068     0    0.059   0.061     1.440   81.429   84.444
LGA    L    28_B      L    28_A     1.287     0    0.037   0.061     1.671   77.143   82.679
LGA    G    29_B      G    29_A     2.165     0    0.041   0.041     2.661   64.881   64.881
LGA    N    30_B      N    30_A     2.116     0    0.062   0.106     2.711   70.833   67.857
LGA    G    31_B      G    31_A     1.253     0    0.026   0.026     1.517   81.548   81.548
LGA    Y    32_B      Y    32_A     0.972     0    0.033   0.126     2.928   88.214   74.048
LGA    C    33_B      C    33_A     0.473     0    0.062   0.080     0.850   92.857   93.651
LGA    G    34_B      G    34_A     0.890     0    0.031   0.031     1.827   83.810   83.810

# 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):     2.041          2.193                  2.295           76.103   72.837

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   34    4.0     33    1.87    89.706    92.386     1.676

LGA_LOCAL      RMSD:   1.869  Number of atoms:   33  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.049  Number of assigned atoms:   34 
Std_ASGN_ATOMS RMSD:   2.041  Standard rmsd on all 34 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.239819 * X  +   0.946137 * Y  +  -0.217512 * Z  +  -9.734916
  Y_new =   0.950763 * X  +  -0.274199 * Y  +  -0.144448 * Z  +  -5.566394
  Z_new =  -0.196309 * X  +  -0.172161 * Y  +  -0.965310 * Z  + -18.518167 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.323712  0.197592 -2.965100   [DEG:   75.8431   11.3212 -169.8877 ]
ZXZ: -0.984579  2.877424 -2.290752   [DEG:  -56.4122  164.8643 -131.2504 ]
 
# END of job
