
#######################################################
#                                                     #
#                        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   38 (  302),  selected   37 , name one
# Molecule2: number of CA atoms   37 (  291),  selected   37 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:C  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    37       2_B - 38_B        3.36     3.36
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       5_B - 37_B        1.80     3.70
  LONGEST_CONTINUOUS_SEGMENT:    33       6_B - 38_B        1.66     4.02
  LCS_AVERAGE:     82.62

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    31       7_B - 37_B        0.41     4.20
  LCS_AVERAGE:     71.51

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   37
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     A     2_C     A     2_B      3    3   37      0    3    3    3    3    4    4    8    9    9   11   13   14   17   22   23   28   32   36   36 
LCS_GDT     E     3_C     E     3_B      3    3   37      0    3    3    3    3    4    5   16   22   29   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     A     4_C     A     4_B      3    3   37      3    3    3    3    6    7    8   31   33   34   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     E     5_C     E     5_B      3   33   37      3    3    3    4    6   11   17   26   33   34   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     Q     6_C     Q     6_B      3   33   37      3    3    3    3   10   22   28   32   33   34   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     E     7_C     E     7_B     31   33   37     21   31   31   31   31   31   31   32   33   34   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     K     8_C     K     8_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     D     9_C     D     9_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     Q    10_C     Q    10_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     L    11_C     L    11_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     R    12_C     R    12_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     T    13_C     T    13_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     Q    14_C     Q    14_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     V    15_C     V    15_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     V    16_C     V    16_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     R    17_C     R    17_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     L    18_C     L    18_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     Q    19_C     Q    19_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     A    20_C     A    20_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     E    21_C     E    21_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     K    22_C     K    22_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     A    23_C     A    23_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     D    24_C     D    24_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     L    25_C     L    25_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     L    26_C     L    26_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     G    27_C     G    27_B     31   33   37     23   31   31   31   31   31   31   32   33   34   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     I    28_C     I    28_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     V    29_C     V    29_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     S    30_C     S    30_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     E    31_C     E    31_B     31   33   37     23   31   31   31   31   31   31   32   33   34   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     L    32_C     L    32_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     Q    33_C     Q    33_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     L    34_C     L    34_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     K    35_C     K    35_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     L    36_C     L    36_B     31   33   37     23   31   31   31   31   31   31   32   33   34   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     N    37_C     N    37_B     31   33   37     24   31   31   31   31   31   31   32   33   34   35   35   35   35   36   36   36   36   36   36 
LCS_GDT     S    38_C     S    38_B      3   33   37      3    3    3    3    4    4    6    9   14   32   32   32   34   35   36   36   36   36   36   36 
LCS_AVERAGE  LCS_A:  84.71  (  71.51   82.62  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     24     31     31     31     31     31     31     32     33     34     35     35     35     35     36     36     36     36     36     36 
GDT PERCENT_AT  64.86  83.78  83.78  83.78  83.78  83.78  83.78  86.49  89.19  91.89  94.59  94.59  94.59  94.59  97.30  97.30  97.30  97.30  97.30  97.30
GDT RMS_LOCAL    0.29   0.41   0.41   0.41   0.41   0.41   0.41   1.15   2.02   2.06   2.46   2.46   2.46   2.36   2.72   2.72   2.72   2.72   2.72   2.72
GDT RMS_ALL_AT   4.24   4.20   4.20   4.20   4.20   4.20   4.20   3.99   3.50   3.55   3.43   3.43   3.43   3.57   3.43   3.43   3.43   3.43   3.43   3.43

# Checking swapping
#   possible swapping detected:  E     3_C      E     3_B
#   possible swapping detected:  E     7_C      E     7_B
#   possible swapping detected:  D     9_C      D     9_B
#   possible swapping detected:  E    31_C      E    31_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     2_C      A     2_B    15.715     0    0.400   0.381    17.267    0.000    0.000
LGA    E     3_C      E     3_B    10.385     0    0.636   1.042    12.060    1.071    0.847
LGA    A     4_C      A     4_B     8.047     0    0.592   0.569     9.047    3.452    3.048
LGA    E     5_C      E     5_B     8.630     0    0.610   0.664    11.629    6.905    3.228
LGA    Q     6_C      Q     6_B     5.741     0    0.594   1.299    13.637   29.643   14.815
LGA    E     7_C      E     7_B     1.374     0    0.590   0.966     9.992   83.690   44.603
LGA    K     8_C      K     8_B     0.879     0    0.068   1.282     4.925   85.952   67.566
LGA    D     9_C      D     9_B     0.867     0    0.044   0.940     3.292   90.476   78.036
LGA    Q    10_C      Q    10_B     0.502     0    0.035   0.287     1.104   92.857   92.646
LGA    L    11_C      L    11_B     0.866     0    0.013   0.061     1.146   90.476   85.952
LGA    R    12_C      R    12_B     0.714     0    0.040   1.420     7.182   90.476   64.762
LGA    T    13_C      T    13_B     0.298     0    0.020   1.001     2.441  100.000   91.088
LGA    Q    14_C      Q    14_B     0.480     0    0.033   1.219     5.218  100.000   72.328
LGA    V    15_C      V    15_B     0.518     0    0.013   0.039     0.743   97.619   94.558
LGA    V    16_C      V    16_B     0.390     0    0.019   0.077     0.455  100.000  100.000
LGA    R    17_C      R    17_B     0.308     0    0.062   1.805    10.452  100.000   56.364
LGA    L    18_C      L    18_B     0.296     0    0.019   0.113     0.397  100.000  100.000
LGA    Q    19_C      Q    19_B     0.273     0    0.016   0.178     0.820  100.000   98.942
LGA    A    20_C      A    20_B     0.290     0    0.019   0.021     0.389  100.000  100.000
LGA    E    21_C      E    21_B     0.240     0    0.018   0.060     0.597  100.000   97.884
LGA    K    22_C      K    22_B     0.237     0    0.034   0.074     0.593  100.000   97.884
LGA    A    23_C      A    23_B     0.209     0    0.000   0.009     0.261  100.000  100.000
LGA    D    24_C      D    24_B     0.251     0    0.009   0.204     1.287  100.000   95.298
LGA    L    25_C      L    25_B     0.105     0    0.013   0.030     0.462  100.000  100.000
LGA    L    26_C      L    26_B     0.433     0    0.036   0.047     0.604   97.619   97.619
LGA    G    27_C      G    27_B     0.682     0    0.083   0.083     0.682   95.238   95.238
LGA    I    28_C      I    28_B     0.287     0    0.015   0.076     0.831  100.000   97.619
LGA    V    29_C      V    29_B     0.370     0    0.019   0.050     0.584  100.000   95.918
LGA    S    30_C      S    30_B     0.650     0    0.027   0.090     0.977   90.476   90.476
LGA    E    31_C      E    31_B     0.678     0    0.033   1.040     6.367   95.238   64.127
LGA    L    32_C      L    32_B     0.335     0    0.006   0.036     0.917  100.000   95.238
LGA    Q    33_C      Q    33_B     0.605     0    0.043   1.069     3.903   97.619   85.450
LGA    L    34_C      L    34_B     0.376     0    0.048   0.181     1.221  100.000   94.107
LGA    K    35_C      K    35_B     0.230     0    0.035   0.554     2.653   97.619   92.116
LGA    L    36_C      L    36_B     0.630     0    0.109   0.131     1.001   95.238   91.726
LGA    N    37_C      N    37_B     0.404     0    0.443   0.854     6.686   74.405   54.405
LGA    S    38_C      S    38_B     7.362     0    0.516   0.806    11.003   10.833    7.698

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       37     148    148  100.00     291    291  100.00                37
SUMMARY(RMSD_GDC):     3.362          3.292                  3.987           81.808   73.556

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   38   37    4.0     32    1.15    87.838    86.562     2.564

LGA_LOCAL      RMSD:   1.148  Number of atoms:   32  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   3.995  Number of assigned atoms:   37 
Std_ASGN_ATOMS RMSD:   3.362  Standard rmsd on all 37 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.475826 * X  +   0.777246 * Y  +  -0.411677 * Z  + -39.080227
  Y_new =   0.787051 * X  +  -0.585201 * Y  +  -0.195166 * Z  +  44.067772
  Z_new =  -0.392606 * X  +  -0.231146 * Y  +  -0.890187 * Z  + -36.553841 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.027025  0.403463 -2.887543   [DEG:   58.8442   23.1167 -165.4440 ]
ZXZ: -1.128102  2.668551 -2.102901   [DEG:  -64.6355  152.8967 -120.4873 ]
 
# END of job
