
#######################################################
#                                                     #
#                        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        2.60     2.60
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       2_A - 34_A        1.92     2.63
  LCS_AVERAGE:     94.64

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      11_A - 34_A        0.79     3.14
  LCS_AVERAGE:     56.40

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      0    5   34      0    0    0    3    5    5    5    5    7    8    8   16   23   25   31   32   34   34   34   34 
LCS_GDT     G     2_B     G     2_A      4   33   34      0    3    5    6    6   19   31   33   33   33   33   33   33   33   33   33   34   34   34   34 
LCS_GDT     P     3_B     P     3_A      9   33   34      4   15   23   25   28   30   31   33   33   33   33   33   33   33   33   33   34   34   34   34 
LCS_GDT     N     4_B     N     4_A      9   33   34      4    6   23   26   28   30   31   33   33   33   33   33   33   33   33   33   34   34   34   34 
LCS_GDT     G     5_B     G     5_A      9   33   34      4    6   19   26   28   30   31   33   33   33   33   33   33   33   33   33   34   34   34   34 
LCS_GDT     G     6_B     G     6_A      9   33   34      3    6   14   26   28   30   31   33   33   33   33   33   33   33   33   33   34   34   34   34 
LCS_GDT     V     7_B     V     7_A      9   33   34      3    6    9   17   25   30   31   33   33   33   33   33   33   33   33   33   34   34   34   34 
LCS_GDT     C     8_B     C     8_A      9   33   34      4   10   20   26   28   30   31   33   33   33   33   33   33   33   33   33   34   34   34   34 
LCS_GDT     P     9_B     P     9_A      9   33   34      3    6   12   21   28   30   31   33   33   33   33   33   33   33   33   33   34   34   34   34 
LCS_GDT     V    10_B     V    10_A      9   33   34      3    6    9   16   28   30   31   33   33   33   33   33   33   33   33   33   34   34   34   34 
LCS_GDT     L    11_B     L    11_A     24   33   34      3    5    8   25   28   30   31   33   33   33   33   33   33   33   33   33   34   34   34   34 
LCS_GDT     I    12_B     I    12_A     24   33   34      6   22   23   26   28   30   31   33   33   33   33   33   33   33   33   33   34   34   34   34 
LCS_GDT     Y    13_B     Y    13_A     24   33   34     18   22   23   26   28   30   31   33   33   33   33   33   33   33   33   33   34   34   34   34 
LCS_GDT     L    14_B     L    14_A     24   33   34     18   22   23   26   28   30   31   33   33   33   33   33   33   33   33   33   34   34   34   34 
LCS_GDT     C    15_B     C    15_A     24   33   34     18   22   23   26   28   30   31   33   33   33   33   33   33   33   33   33   34   34   34   34 
LCS_GDT     R    16_B     R    16_A     24   33   34     18   22   23   26   28   30   31   33   33   33   33   33   33   33   33   33   34   34   34   34 
LCS_GDT     R    17_B     R    17_A     24   33   34     18   22   23   26   28   30   31   33   33   33   33   33   33   33   33   33   34   34   34   34 
LCS_GDT     D    18_B     D    18_A     24   33   34     18   22   23   26   28   30   31   33   33   33   33   33   33   33   33   33   34   34   34   34 
LCS_GDT     S    19_B     S    19_A     24   33   34     18   22   23   26   28   30   31   33   33   33   33   33   33   33   33   33   34   34   34   34 
LCS_GDT     D    20_B     D    20_A     24   33   34     18   22   23   26   28   30   31   33   33   33   33   33   33   33   33   33   34   34   34   34 
LCS_GDT     C    21_B     C    21_A     24   33   34     18   22   23   26   28   30   31   33   33   33   33   33   33   33   33   33   34   34   34   34 
LCS_GDT     P    22_B     P    22_A     24   33   34     18   22   23   26   28   30   31   33   33   33   33   33   33   33   33   33   34   34   34   34 
LCS_GDT     G    23_B     G    23_A     24   33   34     18   22   23   26   28   30   31   33   33   33   33   33   33   33   33   33   34   34   34   34 
LCS_GDT     E    24_B     E    24_A     24   33   34     18   22   23   26   28   30   31   33   33   33   33   33   33   33   33   33   34   34   34   34 
LCS_GDT     C    25_B     C    25_A     24   33   34     18   22   23   26   28   30   31   33   33   33   33   33   33   33   33   33   34   34   34   34 
LCS_GDT     I    26_B     I    26_A     24   33   34     17   22   23   26   28   30   31   33   33   33   33   33   33   33   33   33   34   34   34   34 
LCS_GDT     C    27_B     C    27_A     24   33   34     18   22   23   26   28   30   31   33   33   33   33   33   33   33   33   33   34   34   34   34 
LCS_GDT     L    28_B     L    28_A     24   33   34     18   22   23   26   28   30   31   33   33   33   33   33   33   33   33   33   34   34   34   34 
LCS_GDT     G    29_B     G    29_A     24   33   34      7   22   23   26   28   30   31   33   33   33   33   33   33   33   33   33   34   34   34   34 
LCS_GDT     N    30_B     N    30_A     24   33   34      5   10   23   25   27   29   31   33   33   33   33   33   33   33   33   33   34   34   34   34 
LCS_GDT     G    31_B     G    31_A     24   33   34      5   22   23   26   28   30   31   33   33   33   33   33   33   33   33   33   34   34   34   34 
LCS_GDT     Y    32_B     Y    32_A     24   33   34     18   22   23   26   28   30   31   33   33   33   33   33   33   33   33   33   34   34   34   34 
LCS_GDT     C    33_B     C    33_A     24   33   34     18   22   23   26   28   30   31   33   33   33   33   33   33   33   33   33   34   34   34   34 
LCS_GDT     G    34_B     G    34_A     24   33   34     18   22   23   26   28   30   31   33   33   33   33   33   33   33   33   33   34   34   34   34 
LCS_AVERAGE  LCS_A:  83.68  (  56.40   94.64  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     18     22     23     26     28     30     31     33     33     33     33     33     33     33     33     33     34     34     34     34 
GDT PERCENT_AT  52.94  64.71  67.65  76.47  82.35  88.24  91.18  97.06  97.06  97.06  97.06  97.06  97.06  97.06  97.06  97.06 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.35   0.46   0.56   1.15   1.31   1.57   1.64   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92   1.92   2.60   2.60   2.60   2.60
GDT RMS_ALL_AT   3.09   3.14   3.07   2.83   2.76   2.67   2.68   2.63   2.63   2.63   2.63   2.63   2.63   2.63   2.63   2.63   2.60   2.60   2.60   2.60

# 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    10.717     0    0.131   0.671    12.605    3.571    2.381
LGA    G     2_B      G     2_A     4.329     0    0.708   0.708     6.929   47.024   47.024
LGA    P     3_B      P     3_A     2.400     0    0.414   0.554     3.385   63.095   60.612
LGA    N     4_B      N     4_A     1.442     0    0.218   1.158     5.822   77.262   57.976
LGA    G     5_B      G     5_A     1.886     0    0.666   0.666     3.662   65.476   65.476
LGA    G     6_B      G     6_A     2.388     0    0.092   0.092     2.438   64.762   64.762
LGA    V     7_B      V     7_A     3.961     0    0.075   0.376     6.516   46.667   36.803
LGA    C     8_B      C     8_A     1.332     0    0.034   0.088     2.693   67.024   73.333
LGA    P     9_B      P     9_A     2.901     0    0.050   0.076     3.383   67.024   60.748
LGA    V    10_B      V    10_A     3.349     0    0.093   0.103     5.349   53.571   42.585
LGA    L    11_B      L    11_A     2.486     3    0.063   0.077     3.017   62.857   37.679
LGA    I    12_B      I    12_A     1.368     0    0.228   0.685     4.285   79.286   70.595
LGA    Y    13_B      Y    13_A     1.103     0    0.053   0.296     2.462   85.952   75.913
LGA    L    14_B      L    14_A     0.567     0    0.048   0.164     1.021   88.214   89.345
LGA    C    15_B      C    15_A     0.421     0    0.013   0.074     0.662   95.238   96.825
LGA    R    16_B      R    16_A     0.977     0    0.097   0.462     5.556   88.214   61.039
LGA    R    17_B      R    17_A     0.417     0    0.054   0.345     1.341  100.000   90.649
LGA    D    18_B      D    18_A     0.418     0    0.011   0.062     0.618   97.619   97.619
LGA    S    19_B      S    19_A     0.795     0    0.022   0.095     0.999   90.476   90.476
LGA    D    20_B      D    20_A     0.694     0    0.027   0.145     0.825   90.476   90.476
LGA    C    21_B      C    21_A     0.597     0    0.012   0.055     1.027   88.214   90.556
LGA    P    22_B      P    22_A     1.372     0    0.048   0.112     1.587   81.429   81.497
LGA    G    23_B      G    23_A     1.821     0    0.018   0.018     1.821   75.000   75.000
LGA    E    24_B      E    24_A     1.466     0    0.008   0.407     1.601   79.286   78.571
LGA    C    25_B      C    25_A     1.409     0    0.035   0.122     1.546   79.286   80.000
LGA    I    26_B      I    26_A     1.228     0    0.018   0.036     1.887   85.952   81.548
LGA    C    27_B      C    27_A     0.632     0    0.021   0.026     0.901   90.476   93.651
LGA    L    28_B      L    28_A     1.385     0    0.029   0.062     2.631   79.286   72.083
LGA    G    29_B      G    29_A     2.087     0    0.026   0.026     3.169   61.190   61.190
LGA    N    30_B      N    30_A     3.195     0    0.077   0.196     4.421   55.357   50.298
LGA    G    31_B      G    31_A     1.527     0    0.059   0.059     1.944   79.405   79.405
LGA    Y    32_B      Y    32_A     1.168     0    0.022   0.120     2.283   81.429   73.016
LGA    C    33_B      C    33_A     1.169     0    0.019   0.045     1.963   77.143   78.571
LGA    G    34_B      G    34_A     1.697     0    0.038   0.038     1.697   81.548   81.548

# 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):     2.600          2.478                  2.698           74.377   70.272

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   34    4.0     33    1.92    83.824    88.494     1.637

LGA_LOCAL      RMSD:   1.916  Number of atoms:   33  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.635  Number of assigned atoms:   34 
Std_ASGN_ATOMS RMSD:   2.600  Standard rmsd on all 34 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.024960 * X  +  -0.435799 * Y  +  -0.899698 * Z  +  -9.061698
  Y_new =   0.719177 * X  +   0.617292 * Y  +  -0.318958 * Z  +  -8.099425
  Z_new =   0.694378 * X  +  -0.655004 * Y  +   0.298009 * Z  + -20.705284 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.605489 -0.767555 -1.143815   [DEG:   91.9877  -43.9777  -65.5358 ]
ZXZ: -1.230103  1.268190  2.327023   [DEG:  -70.4797   72.6619  133.3286 ]
 
# END of job
