
#######################################################
#                                                     #
#                        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        3.62     3.62
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       5_B - 37_B        1.99     3.97
  LONGEST_CONTINUOUS_SEGMENT:    33       6_B - 38_B        1.79     4.32
  LCS_AVERAGE:     82.62

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    31       7_B - 37_B        0.52     4.54
  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    4    9   10   10   12   13   17   18   23   25   28   32   35 
LCS_GDT     E     3_C     E     3_B      3    3   37      0    3    3    3    3    4    4   15   21   26   30   35   35   35   35   36   36   36   36   36 
LCS_GDT     A     4_C     A     4_B      3    3   37      3    3    3    3    6    6    7   26   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     E     5_C     E     5_B      3   33   37      3    3    3    4    6    8   12   22   28   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     Q     6_C     Q     6_B      3   33   37      3    3    3    4   11   18   27   30   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     E     7_C     E     7_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     K     8_C     K     8_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     D     9_C     D     9_B     31   33   37     22   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     Q    10_C     Q    10_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     L    11_C     L    11_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     R    12_C     R    12_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     T    13_C     T    13_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     Q    14_C     Q    14_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     V    15_C     V    15_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     V    16_C     V    16_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     R    17_C     R    17_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     L    18_C     L    18_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     Q    19_C     Q    19_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     A    20_C     A    20_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     E    21_C     E    21_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     K    22_C     K    22_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     A    23_C     A    23_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     D    24_C     D    24_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     L    25_C     L    25_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     L    26_C     L    26_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     G    27_C     G    27_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     I    28_C     I    28_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     V    29_C     V    29_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     S    30_C     S    30_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     E    31_C     E    31_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     L    32_C     L    32_B     31   33   37     22   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     Q    33_C     Q    33_B     31   33   37     18   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     L    34_C     L    34_B     31   33   37     17   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     K    35_C     K    35_B     31   33   37     21   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     L    36_C     L    36_B     31   33   37     17   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     N    37_C     N    37_B     31   33   37     15   31   31   31   31   31   31   31   33   34   34   35   35   35   35   36   36   36   36   36 
LCS_GDT     S    38_C     S    38_B      3   33   37      3    3    3    3    3    4    5    7    9   21   32   32   32   34   35   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     23     31     31     31     31     31     31     31     33     34     34     35     35     35     35     36     36     36     36     36 
GDT PERCENT_AT  62.16  83.78  83.78  83.78  83.78  83.78  83.78  83.78  89.19  91.89  91.89  94.59  94.59  94.59  94.59  97.30  97.30  97.30  97.30  97.30
GDT RMS_LOCAL    0.30   0.52   0.52   0.52   0.52   0.52   0.52   0.52   1.88   2.26   2.26   2.69   2.69   2.69   2.53   2.93   2.93   2.93   2.93   2.93
GDT RMS_ALL_AT   4.50   4.54   4.54   4.54   4.54   4.54   4.54   4.54   3.99   3.82   3.82   3.69   3.69   3.69   3.84   3.69   3.69   3.69   3.69   3.69

# Checking swapping
#   possible swapping detected:  E     5_C      E     5_B
#   possible swapping detected:  D     9_C      D     9_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     2_C      A     2_B    17.747     0    0.447   0.441    19.308    0.000    0.000
LGA    E     3_C      E     3_B    12.131     0    0.589   1.022    13.958    0.000    0.000
LGA    A     4_C      A     4_B     9.271     0    0.596   0.588    10.340    0.595    0.571
LGA    E     5_C      E     5_B    10.111     0    0.588   1.060    12.015    1.548    0.688
LGA    Q     6_C      Q     6_B     7.311     0    0.616   1.068    12.603   16.429    7.989
LGA    E     7_C      E     7_B     0.559     0    0.575   0.969     8.545   84.524   50.317
LGA    K     8_C      K     8_B     0.386     0    0.079   1.075     5.793   95.238   73.228
LGA    D     9_C      D     9_B     0.903     0    0.025   0.178     2.361   90.476   81.726
LGA    Q    10_C      Q    10_B     0.633     0    0.031   0.661     2.140   92.857   85.714
LGA    L    11_C      L    11_B     0.489     0    0.019   0.042     0.911  100.000   95.238
LGA    R    12_C      R    12_B     0.659     0    0.037   0.166     2.765   92.857   79.697
LGA    T    13_C      T    13_B     0.391     0    0.019   0.966     2.710  100.000   88.639
LGA    Q    14_C      Q    14_B     0.509     0    0.017   1.035     3.493   97.619   78.889
LGA    V    15_C      V    15_B     0.417     0    0.016   0.034     0.758  100.000   95.918
LGA    V    16_C      V    16_B     0.372     0    0.014   0.061     0.642  100.000   97.279
LGA    R    17_C      R    17_B     0.318     0    0.031   1.637     9.101  100.000   61.342
LGA    L    18_C      L    18_B     0.290     0    0.015   0.088     0.894  100.000   96.429
LGA    Q    19_C      Q    19_B     0.303     0    0.027   0.272     0.894  100.000   96.825
LGA    A    20_C      A    20_B     0.274     0    0.055   0.061     0.384  100.000  100.000
LGA    E    21_C      E    21_B     0.207     0    0.011   0.865     3.028  100.000   83.598
LGA    K    22_C      K    22_B     0.468     0    0.014   0.104     0.548   97.619   96.825
LGA    A    23_C      A    23_B     0.461     0    0.027   0.030     0.475  100.000  100.000
LGA    D    24_C      D    24_B     0.330     0    0.021   0.231     1.339  100.000   96.488
LGA    L    25_C      L    25_B     0.365     0    0.025   0.055     0.489  100.000  100.000
LGA    L    26_C      L    26_B     0.361     0    0.022   0.106     0.731  100.000   96.429
LGA    G    27_C      G    27_B     0.591     0    0.068   0.068     0.591   97.619   97.619
LGA    I    28_C      I    28_B     0.461     0    0.030   0.116     0.676   97.619   95.238
LGA    V    29_C      V    29_B     0.276     0    0.012   0.041     0.408  100.000  100.000
LGA    S    30_C      S    30_B     0.370     0    0.028   0.056     0.545  100.000   98.413
LGA    E    31_C      E    31_B     0.521     0    0.025   1.052     5.927   97.619   68.571
LGA    L    32_C      L    32_B     0.257     0    0.014   0.024     0.546  100.000   98.810
LGA    Q    33_C      Q    33_B     0.630     0    0.046   1.056     3.096   92.857   84.074
LGA    L    34_C      L    34_B     0.777     0    0.041   0.220     1.176   90.476   88.214
LGA    K    35_C      K    35_B     0.514     0    0.031   0.544     2.359   90.476   89.788
LGA    L    36_C      L    36_B     0.822     0    0.080   0.094     0.909   90.476   90.476
LGA    N    37_C      N    37_B     1.016     0    0.367   0.852     7.489   67.500   47.619
LGA    S    38_C      S    38_B     7.130     0    0.136   0.629     9.304   14.762   10.556

# 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):     3.617          3.518                  4.064           81.329   73.871

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   38   37    4.0     31    0.52    87.162    86.254     5.006

LGA_LOCAL      RMSD:   0.519  Number of atoms:   31  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.541  Number of assigned atoms:   37 
Std_ASGN_ATOMS RMSD:   3.617  Standard rmsd on all 37 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.050109 * X  +  -0.988232 * Y  +  -0.144522 * Z  + -39.524246
  Y_new =   0.821210 * X  +  -0.041588 * Y  +   0.569108 * Z  +  50.717205
  Z_new =  -0.568421 * X  +  -0.147201 * Y  +   0.809462 * Z  + -108.095383 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.509853  0.604586 -0.179884   [DEG:   86.5082   34.6402  -10.3066 ]
ZXZ: -2.892905  0.627560 -1.824193   [DEG: -165.7512   35.9566 -104.5186 ]
 
# END of job
