
#######################################################
#                                                     #
#                        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        1.14     1.14
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    34       1_A - 34_A        1.14     1.14
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    28       7_A - 34_A        0.95     1.18
  LCS_AVERAGE:     72.32

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   34   34     19   28   30   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G     2_B     G     2_A      4   34   34     19   28   30   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     P     3_B     P     3_A      4   34   34     12   28   30   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     N     4_B     N     4_A      4   34   34      4   28   30   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G     5_B     G     5_A     13   34   34      3    9   24   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G     6_B     G     6_A     23   34   34      3    9   24   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     V     7_B     V     7_A     28   34   34      3    9   24   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C     8_B     C     8_A     28   34   34      7   27   30   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     P     9_B     P     9_A     28   34   34     10   28   30   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     V    10_B     V    10_A     28   34   34      8   28   30   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     L    11_B     L    11_A     28   34   34     11   26   30   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     I    12_B     I    12_A     28   34   34      3   28   30   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     Y    13_B     Y    13_A     28   34   34     19   28   30   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     L    14_B     L    14_A     28   34   34     19   28   30   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    15_B     C    15_A     28   34   34     19   28   30   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     R    16_B     R    16_A     28   34   34     19   28   30   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     R    17_B     R    17_A     28   34   34     19   28   30   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     D    18_B     D    18_A     28   34   34     19   28   30   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     S    19_B     S    19_A     28   34   34     19   28   30   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     D    20_B     D    20_A     28   34   34     19   28   30   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    21_B     C    21_A     28   34   34     19   28   30   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     P    22_B     P    22_A     28   34   34     19   28   30   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    23_B     G    23_A     28   34   34     19   28   30   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     E    24_B     E    24_A     28   34   34     16   28   30   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    25_B     C    25_A     28   34   34     19   28   30   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     I    26_B     I    26_A     28   34   34     19   28   30   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    27_B     C    27_A     28   34   34     19   28   30   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     L    28_B     L    28_A     28   34   34     19   28   30   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    29_B     G    29_A     28   34   34      4   28   30   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     N    30_B     N    30_A     28   34   34      6   16   26   31   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    31_B     G    31_A     28   34   34      6   28   30   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     Y    32_B     Y    32_A     28   34   34     19   28   30   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    33_B     C    33_A     28   34   34     19   28   30   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    34_B     G    34_A     28   34   34     19   28   30   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_AVERAGE  LCS_A:  90.77  (  72.32  100.00  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     19     28     30     33     34     34     34     34     34     34     34     34     34     34     34     34     34     34     34     34 
GDT PERCENT_AT  55.88  82.35  88.24  97.06 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.29   0.59   0.67   1.08   1.14   1.14   1.14   1.14   1.14   1.14   1.14   1.14   1.14   1.14   1.14   1.14   1.14   1.14   1.14   1.14
GDT RMS_ALL_AT   1.44   1.24   1.22   1.15   1.14   1.14   1.14   1.14   1.14   1.14   1.14   1.14   1.14   1.14   1.14   1.14   1.14   1.14   1.14   1.14

# Checking swapping
#   possible swapping detected:  Y    13_B      Y    13_A
#   possible swapping detected:  D    18_B      D    18_A
#   possible swapping detected:  D    20_B      D    20_A
#   possible swapping detected:  E    24_B      E    24_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     1_B      S     1_A     1.022     0    0.053   0.689     3.191   83.690   77.698
LGA    G     2_B      G     2_A     1.163     0    0.053   0.053     1.163   88.333   88.333
LGA    P     3_B      P     3_A     0.214     0    0.364   0.404     1.922   90.833   89.388
LGA    N     4_B      N     4_A     0.570     0    0.681   1.150     5.812   86.429   66.131
LGA    G     5_B      G     5_A     2.812     0    0.668   0.668     2.812   62.857   62.857
LGA    G     6_B      G     6_A     2.536     0    0.111   0.111     3.254   53.571   53.571
LGA    V     7_B      V     7_A     2.524     0    0.071   0.096     3.872   64.881   57.551
LGA    C     8_B      C     8_A     0.923     0    0.080   0.334     1.475   88.214   85.952
LGA    P     9_B      P     9_A     0.435     0    0.023   0.082     0.578   95.238   97.279
LGA    V    10_B      V    10_A     0.666     0    0.106   0.108     1.092   88.214   86.599
LGA    L    11_B      L    11_A     1.351     3    0.096   0.122     1.942   77.143   48.750
LGA    I    12_B      I    12_A     0.987     0    0.027   0.646     1.586   90.476   84.881
LGA    Y    13_B      Y    13_A     0.531     0    0.044   0.891     5.281   95.238   71.825
LGA    L    14_B      L    14_A     0.521     0    0.038   0.552     1.720   92.857   87.202
LGA    C    15_B      C    15_A     0.391     0    0.016   0.083     0.658   97.619   96.825
LGA    R    16_B      R    16_A     0.413     0    0.095   1.260     7.758  100.000   67.662
LGA    R    17_B      R    17_A     0.635     0    0.056   0.535     3.498   90.476   82.035
LGA    D    18_B      D    18_A     0.841     0    0.020   0.033     0.927   90.476   90.476
LGA    S    19_B      S    19_A     1.091     0    0.025   0.219     1.384   88.214   87.460
LGA    D    20_B      D    20_A     0.532     0    0.038   0.183     1.108   95.238   94.107
LGA    C    21_B      C    21_A     0.304     0    0.019   0.063     0.607   97.619   98.413
LGA    P    22_B      P    22_A     0.353     0    0.038   0.100     0.487  100.000  100.000
LGA    G    23_B      G    23_A     0.782     0    0.052   0.052     0.782   90.476   90.476
LGA    E    24_B      E    24_A     0.556     0    0.020   0.860     3.811   90.476   79.524
LGA    C    25_B      C    25_A     0.797     0    0.025   0.111     0.892   90.476   90.476
LGA    I    26_B      I    26_A     0.954     0    0.024   0.030     1.775   90.476   83.810
LGA    C    27_B      C    27_A     0.548     0    0.020   0.035     0.785   90.476   93.651
LGA    L    28_B      L    28_A     0.895     0    0.034   0.076     2.222   90.476   81.726
LGA    G    29_B      G    29_A     1.149     0    0.047   0.047     1.993   79.405   79.405
LGA    N    30_B      N    30_A     2.345     0    0.037   0.035     3.348   68.810   63.036
LGA    G    31_B      G    31_A     1.032     0    0.099   0.099     1.292   85.952   85.952
LGA    Y    32_B      Y    32_A     0.580     0    0.032   0.085     1.677   90.476   83.770
LGA    C    33_B      C    33_A     0.697     0    0.032   0.064     1.186   88.214   88.968
LGA    G    34_B      G    34_A     0.770     0    0.066   0.066     0.801   90.476   90.476

# 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):     1.142          1.136                  1.644           87.171   81.949

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   34    4.0     34    1.14    94.853    97.523     2.738

LGA_LOCAL      RMSD:   1.142  Number of atoms:   34  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.142  Number of assigned atoms:   34 
Std_ASGN_ATOMS RMSD:   1.142  Standard rmsd on all 34 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.261269 * X  +  -0.782124 * Y  +  -0.565703 * Z  + -10.955890
  Y_new =  -0.076606 * X  +   0.567410 * Y  +  -0.819864 * Z  +  -7.654417
  Z_new =   0.962221 * X  +   0.257541 * Y  +   0.088331 * Z  + -17.200439 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.285215 -1.295047  1.240392   [DEG:  -16.3416  -74.2007   71.0692 ]
ZXZ: -0.603980  1.482350  1.309273   [DEG:  -34.6055   84.9324   75.0158 ]
 
# END of job
