
#######################################################
#                                                     #
#                        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   23 (  157),  selected   23 , name one
# Molecule2: number of CA atoms   33 (  231),  selected   23 , 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:    16       7_A - 22_A        4.97    11.37
  LONGEST_CONTINUOUS_SEGMENT:    16       8_A - 23_A        4.15    11.95
  LCS_AVERAGE:     47.04

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13      11_A - 23_A        1.76    12.77
  LCS_AVERAGE:     31.09

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7      17_A - 23_A        0.72    13.01
  LCS_AVERAGE:     15.81

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   23
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      3    4   11      0    3    3    3    3    4    5    5    8    8    9    9   12   13   14   15   15   15   15   16 
LCS_GDT     R     2_A     R     2_A      3    7   14      3    3    4    5    7    7    7    8    8    8    9   11   11   13   14   15   15   15   15   16 
LCS_GDT     Q     3_A     Q     3_A      3    7   15      3    3    4    4    7    7    7    8    8   10   11   11   13   13   14   15   15   15   15   16 
LCS_GDT     S     4_A     S     4_A      5    7   15      3    4    5    5    7    7    9   11   12   12   13   13   14   14   15   15   15   15   16   17 
LCS_GDT     S     5_A     S     5_A      5    7   15      3    4    5    6    8    9   10   11   12   12   13   13   14   14   15   15   15   15   16   17 
LCS_GDT     A     6_A     A     6_A      5    7   15      3    4    5    5    7    9   10   11   12   12   13   13   14   14   15   15   15   15   16   17 
LCS_GDT     T     7_A     T     7_A      5    7   16      3    4    5    6    8    9   10   11   12   12   13   13   14   14   15   15   16   16   17   17 
LCS_GDT     S     8_A     S     8_A      5    7   16      3    4    5    5    8    9   10   11   12   12   13   14   15   15   16   16   16   16   17   17 
LCS_GDT     S     9_A     S     9_A      3    7   16      3    3    4    6    7    8   10   11   12   12   13   14   15   15   16   16   16   16   17   17 
LCS_GDT     F    10_A     F    10_A      4    7   16      3    3    5    6    8    9   10   11   12   12   13   14   15   15   16   16   16   16   17   17 
LCS_GDT     G    11_A     G    11_A      5   13   16      3    4    8   10   12   13   13   13   13   13   13   14   15   15   16   16   16   16   17   17 
LCS_GDT     G    12_A     G    12_A      5   13   16      3    4    5    9   12   13   13   13   13   13   13   14   15   15   16   16   16   16   17   17 
LCS_GDT     L    13_A     L    13_A      5   13   16      3    4    5   10   12   13   13   13   13   13   13   14   15   15   16   16   16   16   17   17 
LCS_GDT     G    14_A     G    14_A      5   13   16      2    6    8   10   12   13   13   13   13   13   13   14   15   15   16   16   16   16   17   17 
LCS_GDT     G    15_A     G    15_A      5   13   16      0    4    8    9   10   13   13   13   13   13   13   14   15   15   16   16   16   16   17   17 
LCS_GDT     G    16_A     G    16_A      5   13   16      3    3    5   10   12   13   13   13   13   13   13   14   15   15   16   16   16   16   17   17 
LCS_GDT     S    17_A     S    17_A      7   13   16      4    6    8   10   12   13   13   13   13   13   13   14   15   15   16   16   16   16   17   17 
LCS_GDT     V    18_A     V    18_A      7   13   16      4    6    8   10   12   13   13   13   13   13   13   14   15   15   16   16   16   16   17   17 
LCS_GDT     R    19_A     R    19_A      7   13   16      4    6    8   10   12   13   13   13   13   13   13   14   15   15   16   16   16   16   17   17 
LCS_GDT     F    20_A     F    20_A      7   13   16      4    6    8   10   12   13   13   13   13   13   13   14   15   15   16   16   16   16   17   17 
LCS_GDT     G    21_A     G    21_A      7   13   16      4    6    8   10   12   13   13   13   13   13   13   14   15   15   16   16   16   16   17   17 
LCS_GDT     P    22_A     P    22_A      7   13   16      3    6    8   10   12   13   13   13   13   13   13   14   15   15   16   16   16   16   17   17 
LCS_GDT     G    23_A     G    23_A      7   13   16      4    6    8   10   12   13   13   13   13   13   13   14   14   15   16   16   16   16   17   17 
LCS_AVERAGE  LCS_A:  31.31  (  15.81   31.09   47.04 )

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      8     10     12     13     13     13     13     13     13     14     15     15     16     16     16     16     17     17 
GDT PERCENT_AT  12.12  18.18  24.24  30.30  36.36  39.39  39.39  39.39  39.39  39.39  39.39  42.42  45.45  45.45  48.48  48.48  48.48  48.48  51.52  51.52
GDT RMS_LOCAL    0.29   0.51   0.88   1.26   1.57   1.76   1.76   1.76   1.76   1.76   1.76   2.60   4.11   3.54   4.15   4.15   4.15   4.15   5.08   5.08
GDT RMS_ALL_AT  12.59  13.02  13.12  13.10  12.83  12.77  12.77  12.77  12.77  12.77  12.77  12.67  11.84  12.30  11.95  11.95  11.95  11.95  11.47  11.47

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

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    Y     1_A      Y     1_A    24.667     0    0.219   0.346    31.704    0.000    0.000
LGA    R     2_A      R     2_A    24.250     0    0.608   1.336    27.638    0.000    0.000
LGA    Q     3_A      Q     3_A    24.988     0    0.178   0.315    31.796    0.000    0.000
LGA    S     4_A      S     4_A    21.470     0    0.108   0.679    22.895    0.000    0.000
LGA    S     5_A      S     5_A    21.647     0    0.201   0.616    23.071    0.000    0.000
LGA    A     6_A      A     6_A    19.110     0    0.017   0.029    20.184    0.000    0.000
LGA    T     7_A      T     7_A    16.538     0    0.068   1.043    20.092    0.000    0.000
LGA    S     8_A      S     8_A    11.877     0    0.689   0.766    13.480    0.000    0.079
LGA    S     9_A      S     9_A    10.888     0    0.530   0.462    13.296    0.119    0.079
LGA    F    10_A      F    10_A     7.867     0    0.084   1.453     8.691   14.881    9.351
LGA    G    11_A      G    11_A     1.770     0    0.641   0.641     3.495   67.262   67.262
LGA    G    12_A      G    12_A     2.649     0    0.327   0.327     3.705   59.524   59.524
LGA    L    13_A      L    13_A     2.276     0    0.574   1.003     7.969   67.262   47.321
LGA    G    14_A      G    14_A     1.255     0    0.319   0.319     1.964   83.810   83.810
LGA    G    15_A      G    15_A     2.897     0    0.504   0.504     3.532   61.548   61.548
LGA    G    16_A      G    16_A     2.625     0    0.611   0.611     2.625   66.905   66.905
LGA    S    17_A      S    17_A     1.311     0    0.123   0.682     2.350   85.952   78.889
LGA    V    18_A      V    18_A     1.058     0    0.048   1.065     3.394   83.690   73.742
LGA    R    19_A      R    19_A     0.458     0    0.053   1.440     7.439   90.833   61.342
LGA    F    20_A      F    20_A     1.684     0    0.117   0.278     6.192   83.810   49.567
LGA    G    21_A      G    21_A     0.568     0    0.079   0.079     1.161   88.333   88.333
LGA    P    22_A      P    22_A     0.843     0    0.646   0.865     2.723   84.524   81.973
LGA    G    23_A      G    23_A     1.077     0    0.337   0.337     1.530   79.286   79.286

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       23      92     92  100.00     157    157  100.00                33
SUMMARY(RMSD_GDC):     9.251          9.134                  9.832           30.841   27.546

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   23   33    4.0     13    1.76    34.091    34.740     0.699

LGA_LOCAL      RMSD:   1.760  Number of atoms:   13  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  12.770  Number of assigned atoms:   23 
Std_ASGN_ATOMS RMSD:   9.251  Standard rmsd on all 23 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.003571 * X  +  -0.652165 * Y  +  -0.758069 * Z  +  -6.305583
  Y_new =   0.727406 * X  +   0.518497 * Y  +  -0.449489 * Z  + -11.111411
  Z_new =   0.686198 * X  +  -0.553029 * Y  +   0.472537 * Z  +   3.324256 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.575706 -0.756249 -0.863723   [DEG:   90.2813  -43.3299  -49.4877 ]
ZXZ: -1.035584  1.078629  2.249145   [DEG:  -59.3346   61.8009  128.8665 ]
 
# END of job
