
#######################################################
#                                                     #
#                        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   33 (  231),  selected   33 , name one
# Molecule2: number of CA atoms   33 (  231),  selected   33 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15      12_A - 26_A        4.85    19.56
  LONGEST_CONTINUOUS_SEGMENT:    15      13_A - 27_A        4.84    19.85
  LONGEST_CONTINUOUS_SEGMENT:    15      14_A - 28_A        5.00    20.05
  LCS_AVERAGE:     41.60

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9      15_A - 23_A        1.91    21.53
  LONGEST_CONTINUOUS_SEGMENT:     9      25_A - 33_A        1.93    28.02
  LCS_AVERAGE:     23.05

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7      26_A - 32_A        0.92    27.17
  LCS_AVERAGE:     14.69

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   33
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     Y     1_A     Y     1_A      6    7   11      3    5    6    6    6    7    8    8    8    8    9    9   10   11   11   11   11   12   12   12 
LCS_GDT     R     2_A     R     2_A      6    7   11      3    5    6    6    6    7    8    8    8    8    9    9   10   11   11   11   11   12   12   12 
LCS_GDT     Q     3_A     Q     3_A      6    7   11      3    5    6    6    6    7    8    8    8    8    9    9   10   11   11   11   11   12   12   12 
LCS_GDT     S     4_A     S     4_A      6    7   11      3    5    6    6    6    7    8    8    8    8    9    9   10   11   11   11   11   12   12   12 
LCS_GDT     S     5_A     S     5_A      6    7   12      3    5    6    6    6    7    8    8    8    8    9   10   11   11   11   12   12   12   12   13 
LCS_GDT     A     6_A     A     6_A      6    7   12      3    4    6    6    6    7    8    9    9   10   11   11   11   12   12   12   12   12   12   13 
LCS_GDT     T     7_A     T     7_A      4    7   12      3    4    4    4    6    7    8    9    9   10   11   11   11   12   12   12   12   12   13   13 
LCS_GDT     S     8_A     S     8_A      4    5   12      3    4    4    4    4    7    8    9    9   10   11   11   11   12   12   12   13   13   14   15 
LCS_GDT     S     9_A     S     9_A      3    4   12      3    3    3    3    4    5    7    8    9   10   11   11   11   12   12   12   12   12   14   14 
LCS_GDT     F    10_A     F    10_A      3    5   12      3    3    3    5    5    6    7    9    9   10   11   11   11   12   12   12   12   12   14   14 
LCS_GDT     G    11_A     G    11_A      4    5   12      3    3    4    5    5    6    7    9    9   10   11   11   11   12   12   12   13   13   15   16 
LCS_GDT     G    12_A     G    12_A      4    5   15      3    3    4    4    5    5    7    9    9   10   11   11   12   14   15   15   16   17   17   18 
LCS_GDT     L    13_A     L    13_A      4    5   15      3    4    4    4    5    7    9    9   10   10   11   11   13   14   15   15   16   17   17   18 
LCS_GDT     G    14_A     G    14_A      4    5   15      3    4    4    6    7    9   10   11   11   12   13   13   13   14   15   15   16   17   17   18 
LCS_GDT     G    15_A     G    15_A      4    9   15      3    4    4    5    8    9   10   11   11   12   13   13   13   14   15   15   16   17   17   18 
LCS_GDT     G    16_A     G    16_A      4    9   15      0    4    4    5    8    9   10   11   11   12   13   13   13   14   15   15   16   17   17   18 
LCS_GDT     S    17_A     S    17_A      4    9   15      3    4    5    5    8    9   10   11   11   12   13   13   13   14   15   15   16   17   17   18 
LCS_GDT     V    18_A     V    18_A      4    9   15      3    4    5    6    8    9   10   11   11   12   13   13   13   14   15   15   16   17   17   18 
LCS_GDT     R    19_A     R    19_A      4    9   15      3    4    5    5    8    9   10   11   11   12   13   13   13   14   15   15   16   17   17   18 
LCS_GDT     F    20_A     F    20_A      4    9   15      3    4    5    6    8    9   10   11   11   12   13   13   13   14   15   15   16   17   17   18 
LCS_GDT     G    21_A     G    21_A      4    9   15      3    4    5    6    8    9   10   11   12   12   13   13   13   14   15   15   16   17   17   18 
LCS_GDT     P    22_A     P    22_A      4    9   15      3    4    4    6    8    9   11   11   12   12   13   13   13   14   15   15   16   17   17   18 
LCS_GDT     G    23_A     G    23_A      4    9   15      0    4    4    6    8    9   11   11   12   12   13   13   13   14   15   15   16   17   17   18 
LCS_GDT     V    24_A     V    24_A      3    6   15      4    4    5    6    9    9   11   11   12   12   13   13   13   14   15   15   16   17   17   18 
LCS_GDT     A    25_A     A    25_A      3    9   15      4    4    5    7    9    9   11   11   12   12   13   13   13   14   15   15   16   17   17   18 
LCS_GDT     F    26_A     F    26_A      7    9   15      4    6    6    7    9    9   11   11   12   12   13   13   13   14   15   15   16   17   17   18 
LCS_GDT     R    27_A     R    27_A      7    9   15      4    6    6    7    9    9   11   11   12   12   12   12   13   13   14   15   16   17   17   18 
LCS_GDT     A    28_A     A    28_A      7    9   15      4    6    6    7    9    9   11   11   12   12   12   12   13   13   14   15   16   17   17   18 
LCS_GDT     P    29_A     P    29_A      7    9   14      4    6    6    7    9    9   11   11   12   12   12   12   13   13   14   14   14   15   15   18 
LCS_GDT     S    30_A     S    30_A      7    9   14      4    6    6    7    9    9   11   11   12   12   12   12   13   13   14   14   14   15   15   18 
LCS_GDT     I    31_A     I    31_A      7    9   14      4    6    6    7    9    9   11   11   12   12   12   12   13   13   14   14   14   15   15   18 
LCS_GDT     H    32_A     H    32_A      7    9   14      3    4    6    7    9    9   11   11   12   12   12   12   13   13   14   14   14   15   15   15 
LCS_GDT     G    33_A     G    33_A      3    9   14      3    3    3    7    8    9    9    9   10   10   12   12   13   13   13   13   14   15   15   15 
LCS_AVERAGE  LCS_A:  26.45  (  14.69   23.05   41.60 )

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      4      6      6      7      9      9     11     11     12     12     13     13     13     14     15     15     16     17     17     18 
GDT PERCENT_AT  12.12  18.18  18.18  21.21  27.27  27.27  33.33  33.33  36.36  36.36  39.39  39.39  39.39  42.42  45.45  45.45  48.48  51.52  51.52  54.55
GDT RMS_LOCAL    0.11   0.53   0.53   0.92   2.08   1.91   2.45   2.45   2.86   2.86   3.41   3.41   3.37   4.09   4.85   4.85   5.35   5.83   5.83   6.66
GDT RMS_ALL_AT  27.30  26.59  26.59  27.17  29.30  21.53  27.06  27.06  28.29  28.29  20.60  20.60  29.51  20.00  19.56  19.56  19.55  18.98  18.98  18.74

# Checking swapping
#   possible swapping detected:  F    20_A      F    20_A
#   possible swapping detected:  F    26_A      F    26_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    Y     1_A      Y     1_A    56.960     0    0.122   1.098    59.312    0.000    0.000
LGA    R     2_A      R     2_A    51.633     0    0.029   1.405    53.530    0.000    0.000
LGA    Q     3_A      Q     3_A    47.146     0    0.528   0.440    51.732    0.000    0.000
LGA    S     4_A      S     4_A    41.223     0    0.022   0.043    43.449    0.000    0.000
LGA    S     5_A      S     5_A    36.118     0    0.527   0.787    37.834    0.000    0.000
LGA    A     6_A      A     6_A    31.892     0    0.005   0.013    33.918    0.000    0.000
LGA    T     7_A      T     7_A    29.064     0    0.045   1.075    29.429    0.000    0.000
LGA    S     8_A      S     8_A    27.624     0    0.451   0.714    28.648    0.000    0.000
LGA    S     9_A      S     9_A    28.129     0    0.352   0.314    28.722    0.000    0.000
LGA    F    10_A      F    10_A    30.496     0    0.107   0.123    34.874    0.000    0.000
LGA    G    11_A      G    11_A    31.688     0    0.687   0.687    32.224    0.000    0.000
LGA    G    12_A      G    12_A    33.102     0    0.271   0.271    33.190    0.000    0.000
LGA    L    13_A      L    13_A    33.711     0    0.636   0.564    34.227    0.000    0.000
LGA    G    14_A      G    14_A    37.463     0    0.263   0.263    37.463    0.000    0.000
LGA    G    15_A      G    15_A    36.143     0    0.654   0.654    36.475    0.000    0.000
LGA    G    16_A      G    16_A    29.792     0    0.533   0.533    32.314    0.000    0.000
LGA    S    17_A      S    17_A    27.681     0    0.228   0.663    29.212    0.000    0.000
LGA    V    18_A      V    18_A    21.397     0    0.125   1.106    23.689    0.000    0.000
LGA    R    19_A      R    19_A    17.251     0    0.092   1.191    20.188    0.000    0.000
LGA    F    20_A      F    20_A    12.189     0    0.587   1.169    20.627    0.238    0.087
LGA    G    21_A      G    21_A     6.839     0    0.038   0.038     8.672   18.452   18.452
LGA    P    22_A      P    22_A     1.953     0    0.616   0.596     3.917   57.619   54.422
LGA    G    23_A      G    23_A     3.158     0    0.553   0.553     3.158   61.190   61.190
LGA    V    24_A      V    24_A     1.935     0    0.279   0.299     4.686   73.214   62.653
LGA    A    25_A      A    25_A     2.456     0    0.474   0.442     4.152   55.952   56.190
LGA    F    26_A      F    26_A     1.631     0    0.614   1.307     9.740   75.119   38.268
LGA    R    27_A      R    27_A     3.488     0    0.038   1.223    15.063   59.643   23.680
LGA    A    28_A      A    28_A     2.238     0    0.020   0.018     4.921   75.238   66.476
LGA    P    29_A      P    29_A     2.780     0    0.069   0.345     6.704   69.286   49.728
LGA    S    30_A      S    30_A     1.779     0    0.037   0.572     5.263   77.619   62.302
LGA    I    31_A      I    31_A     3.039     0    0.605   0.551     7.492   55.714   37.857
LGA    H    32_A      H    32_A     1.513     0    0.554   0.983     8.410   57.024   33.571
LGA    G    33_A      G    33_A     7.676     0    0.526   0.526    10.200   10.000   10.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       33     132    132  100.00     231    231  100.00                33
SUMMARY(RMSD_GDC):    15.859         15.701                 17.352           22.615   17.421

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   33   33    4.0     11    2.45    29.545    28.888     0.432

LGA_LOCAL      RMSD:   2.446  Number of atoms:   11  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  27.057  Number of assigned atoms:   33 
Std_ASGN_ATOMS RMSD:  15.859  Standard rmsd on all 33 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.119026 * X  +  -0.284130 * Y  +   0.951369 * Z  + -15.997256
  Y_new =   0.858323 * X  +   0.452221 * Y  +   0.242442 * Z  + -50.754974
  Z_new =  -0.499114 * X  +   0.845439 * Y  +   0.190049 * Z  +  -6.335681 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.708590  0.522576  1.349678   [DEG:   97.8950   29.9414   77.3309 ]
ZXZ:  1.820320  1.379584 -0.533302   [DEG:  104.2967   79.0443  -30.5559 ]
 
# END of job
