
#######################################################
#                                                     #
#                        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   25 (  198),  selected   25 , name one
# Molecule2: number of CA atoms  141 ( 1112),  selected   25 , 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:    24     112_A - 135_A       4.32     5.53
  LCS_AVERAGE:     16.99

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20     115_A - 134_A       1.64     6.75
  LCS_AVERAGE:     12.51

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17     115_A - 131_A       0.86     6.62
  LCS_AVERAGE:      9.05

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   25
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     G   111_A     G   111_A      3    6   23      3    4    4    5    7    8    9   11   12   17   18   19   20   21   21   21   21   21   21   22 
LCS_GDT     E   112_A     E   112_A      4    6   24      3    3    4    5    7   11   12   14   16   18   20   20   20   21   21   23   23   24   24   24 
LCS_GDT     E   113_A     E   113_A      4    6   24      3    4    4    6    7   11   13   15   16   18   20   20   22   22   22   23   23   24   24   24 
LCS_GDT     V   114_A     V   114_A      4   18   24      3    4    4    6    7   11   14   18   20   21   21   21   22   22   22   23   23   24   24   24 
LCS_GDT     G   115_A     G   115_A     17   20   24      3    4   13   17   19   19   20   20   20   21   21   21   22   22   22   23   23   24   24   24 
LCS_GDT     P   116_A     P   116_A     17   20   24      8   15   16   17   19   19   20   20   20   21   21   21   22   22   22   23   23   24   24   24 
LCS_GDT     S   117_A     S   117_A     17   20   24     10   15   16   17   19   19   20   20   20   21   21   21   22   22   22   23   23   24   24   24 
LCS_GDT     V   118_A     V   118_A     17   20   24      5   15   16   17   19   19   20   20   20   21   21   21   22   22   22   23   23   24   24   24 
LCS_GDT     Y   119_A     Y   119_A     17   20   24      5   15   16   17   19   19   20   20   20   21   21   21   22   22   22   23   23   24   24   24 
LCS_GDT     L   120_A     L   120_A     17   20   24      4   15   16   17   19   19   20   20   20   21   21   21   22   22   22   23   23   24   24   24 
LCS_GDT     E   121_A     E   121_A     17   20   24     10   15   16   17   19   19   20   20   20   21   21   21   22   22   22   23   23   24   24   24 
LCS_GDT     R   122_A     R   122_A     17   20   24     10   15   16   17   19   19   20   20   20   21   21   21   22   22   22   23   23   24   24   24 
LCS_GDT     L   123_A     L   123_A     17   20   24     10   15   16   17   19   19   20   20   20   21   21   21   22   22   22   23   23   24   24   24 
LCS_GDT     K   124_A     K   124_A     17   20   24     10   15   16   17   19   19   20   20   20   21   21   21   22   22   22   23   23   24   24   24 
LCS_GDT     I   125_A     I   125_A     17   20   24     10   15   16   17   19   19   20   20   20   21   21   21   22   22   22   23   23   24   24   24 
LCS_GDT     L   126_A     L   126_A     17   20   24     10   15   16   17   19   19   20   20   20   21   21   21   22   22   22   23   23   24   24   24 
LCS_GDT     R   127_A     R   127_A     17   20   24     10   15   16   17   19   19   20   20   20   21   21   21   22   22   22   23   23   24   24   24 
LCS_GDT     Q   128_A     Q   128_A     17   20   24     10   15   16   17   19   19   20   20   20   21   21   21   22   22   22   23   23   24   24   24 
LCS_GDT     R   129_A     R   129_A     17   20   24     10   15   16   17   19   19   20   20   20   21   21   21   22   22   22   23   23   24   24   24 
LCS_GDT     C   130_A     C   130_A     17   20   24     10   15   16   17   19   19   20   20   20   21   21   21   22   22   22   23   23   24   24   24 
LCS_GDT     G   131_A     G   131_A     17   20   24      7   15   16   17   19   19   20   20   20   21   21   21   22   22   22   23   23   24   24   24 
LCS_GDT     L   132_A     L   132_A      4   20   24      3    3    4   17   19   19   20   20   20   21   21   21   22   22   22   23   23   24   24   24 
LCS_GDT     D   133_A     D   133_A      4   20   24      3    6    9   17   19   19   20   20   20   21   21   21   22   22   22   23   23   24   24   24 
LCS_GDT     N   134_A     N   134_A      4   20   24      3    3    4    6   16   18   20   20   20   21   21   21   22   22   22   23   23   24   24   24 
LCS_GDT     T   135_A     T   135_A      3    5   24      0    3    4    5    5    5    5    6    6    6   14   18   19   22   22   23   23   24   24   24 
LCS_AVERAGE  LCS_A:  12.85  (   9.05   12.51   16.99 )

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     10     15     16     17     19     19     20     20     20     21     21     21     22     22     22     23     23     24     24     24 
GDT PERCENT_AT   7.09  10.64  11.35  12.06  13.48  13.48  14.18  14.18  14.18  14.89  14.89  14.89  15.60  15.60  15.60  16.31  16.31  17.02  17.02  17.02
GDT RMS_LOCAL    0.33   0.59   0.64   0.86   1.33   1.33   1.64   1.64   1.64   2.29   2.29   2.29   3.25   2.96   2.96   3.97   3.97   4.32   4.32   4.32
GDT RMS_ALL_AT   6.75   6.76   6.77   6.62   6.75   6.75   6.75   6.75   6.75   6.32   6.32   6.32   5.83   6.29   6.29   5.56   5.56   5.53   5.53   5.53

# Checking swapping
#   possible swapping detected:  E   112_A      E   112_A
#   possible swapping detected:  E   113_A      E   113_A
#   possible swapping detected:  E   121_A      E   121_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G   111_A      G   111_A    22.312     0    0.668   0.668    24.204    0.000    0.000
LGA    E   112_A      E   112_A    15.481     0    0.409   1.413    17.946    0.000    0.000
LGA    E   113_A      E   113_A    13.610     0    0.150   1.051    16.327    0.000    0.000
LGA    V   114_A      V   114_A     8.278     0    0.038   0.966    11.240    8.810    5.102
LGA    G   115_A      G   115_A     2.647     0    0.498   0.498     3.961   63.690   63.690
LGA    P   116_A      P   116_A     1.073     0    0.648   0.650     2.970   75.357   78.027
LGA    S   117_A      S   117_A     0.847     0    0.189   0.635     2.463   88.214   84.683
LGA    V   118_A      V   118_A     0.777     0    0.031   1.048     3.174   88.214   79.728
LGA    Y   119_A      Y   119_A     0.733     0    0.040   0.117     1.226   90.476   87.460
LGA    L   120_A      L   120_A     1.042     0    0.044   0.063     2.205   88.214   80.595
LGA    E   121_A      E   121_A     1.080     0    0.041   1.185     4.758   85.952   64.233
LGA    R   122_A      R   122_A     0.908     0    0.031   1.184     7.986   90.476   50.519
LGA    L   123_A      L   123_A     1.219     0    0.040   0.912     2.985   85.952   74.464
LGA    K   124_A      K   124_A     1.158     0    0.028   1.318     5.335   88.214   70.212
LGA    I   125_A      I   125_A     0.408     0    0.039   1.084     4.093   97.619   78.155
LGA    L   126_A      L   126_A     1.276     0    0.033   1.422     5.584   83.690   64.464
LGA    R   127_A      R   127_A     1.579     0    0.046   0.962     8.647   79.286   44.069
LGA    Q   128_A      Q   128_A     1.156     0    0.074   1.130     3.517   88.214   73.704
LGA    R   129_A      R   129_A     0.540     0    0.029   1.150     6.280   95.238   69.177
LGA    C   130_A      C   130_A     0.993     0    0.054   0.068     2.393   90.476   83.254
LGA    G   131_A      G   131_A     1.820     0    0.664   0.664     2.934   75.476   75.476
LGA    L   132_A      L   132_A     2.286     0    0.108   0.265     9.369   75.357   44.702
LGA    D   133_A      D   133_A     2.368     0    0.251   1.316     5.614   68.929   47.619
LGA    N   134_A      N   134_A     4.079     0    0.270   1.337     7.629   31.548   28.274
LGA    T   135_A      T   135_A     9.670     0    0.369   1.101    10.988    2.619    1.701

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       25     100    100  100.00     198    198  100.00               141
SUMMARY(RMSD_GDC):     5.406          5.262                  5.341           11.646    9.570

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   25  141    4.0     20    1.64    13.298    13.334     1.151

LGA_LOCAL      RMSD:   1.637  Number of atoms:   20  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   6.748  Number of assigned atoms:   25 
Std_ASGN_ATOMS RMSD:   5.406  Standard rmsd on all 25 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.943363 * X  +  -0.009674 * Y  +  -0.331621 * Z  +  15.989639
  Y_new =   0.136789 * X  +  -0.921998 * Y  +  -0.362228 * Z  + 108.373482
  Z_new =  -0.302249 * X  +  -0.387075 * Y  +   0.871102 * Z  +  -7.618478 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.997595  0.307051 -0.418146   [DEG:  171.7495   17.5928  -23.9580 ]
ZXZ: -0.741315  0.513355 -2.478635   [DEG:  -42.4742   29.4130 -142.0153 ]
 
# END of job
