
#######################################################
#                                                     #
#                        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   15 (  100),  selected   15 , name one
# Molecule2: number of CA atoms   35 (  269),  selected   15 , 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      15_A - 29_A        3.17     3.17
  LCS_AVERAGE:     42.86

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7      23_A - 29_A        1.46     4.31
  LCS_AVERAGE:     16.95

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4      19_A - 22_A        0.41    10.65
  LONGEST_CONTINUOUS_SEGMENT:     4      20_A - 23_A        0.86    14.32
  LONGEST_CONTINUOUS_SEGMENT:     4      23_A - 26_A        0.65     5.71
  LCS_AVERAGE:     10.10

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   15
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     C    15_A     C    15_A      3    4   15      3    5    7    8   10   12   13   13   13   14   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     P    16_A     P    16_A      3    4   15      3    3    3    8   10   12   13   13   13   14   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     K    17_A     K    17_A      3    4   15      3    3    3    5    7   10   13   13   13   14   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     S    18_A     S    18_A      3    4   15      3    6    7    8   10   12   13   13   13   14   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     C    19_A     C    19_A      4    6   15      3    4    4    8   10   12   13   13   13   14   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     S    20_A     S    20_A      4    6   15      3    4    6    8   10   12   13   13   13   14   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     I    21_A     I    21_A      4    6   15      3    4    4    6    7    8    9   11   13   14   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     E    22_A     E    22_A      4    6   15      3    4    4    5    6    6    7    8   11   14   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     G    23_A     G    23_A      4    7   15      3    4    5    7   10   12   13   13   13   14   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     G    24_A     G    24_A      4    7   15      3    6    7    8   10   12   13   13   13   14   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     C    25_A     C    25_A      4    7   15      3    6    7    8   10   12   13   13   13   14   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     P    26_A     P    26_A      4    7   15      3    6    7    8   10   12   13   13   13   14   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     E    27_A     E    27_A      3    7   15      3    3    5    7    9   12   13   13   13   14   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     V    28_A     V    28_A      3    7   15      3    6    7    8   10   12   13   13   13   14   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     C    29_A     C    29_A      3    7   15      3    6    7    8   10   12   13   13   13   14   15   15   15   15   15   15   15   15   15   15 
LCS_AVERAGE  LCS_A:  23.30  (  10.10   16.95   42.86 )

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      3      6      7      8     10     12     13     13     13     14     15     15     15     15     15     15     15     15     15     15 
GDT PERCENT_AT   8.57  17.14  20.00  22.86  28.57  34.29  37.14  37.14  37.14  40.00  42.86  42.86  42.86  42.86  42.86  42.86  42.86  42.86  42.86  42.86
GDT RMS_LOCAL    0.05   0.81   1.08   1.17   1.70   2.01   2.19   2.19   2.19   2.78   3.17   3.17   3.17   3.17   3.17   3.17   3.17   3.17   3.17   3.17
GDT RMS_ALL_AT  11.72   3.98   4.10   4.21   3.73   3.46   3.48   3.48   3.48   3.23   3.17   3.17   3.17   3.17   3.17   3.17   3.17   3.17   3.17   3.17

# Checking swapping
#   possible swapping detected:  E    22_A      E    22_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    C    15_A      C    15_A     1.687     0    0.163   0.787     3.798   75.119   68.095
LGA    P    16_A      P    16_A     2.471     0    0.311   0.288     5.276   56.548   47.687
LGA    K    17_A      K    17_A     3.318     0    0.661   1.043    15.209   61.190   30.106
LGA    S    18_A      S    18_A     1.406     0    0.662   0.911     3.250   85.952   75.159
LGA    C    19_A      C    19_A     2.473     0    0.613   0.832     3.201   61.071   61.032
LGA    S    20_A      S    20_A     2.815     0    0.141   0.144     5.114   48.690   41.190
LGA    I    21_A      I    21_A     7.504     0    0.533   1.305    13.002   11.310    5.714
LGA    E    22_A      E    22_A     7.948     0    0.283   0.536    15.766   13.929    6.190
LGA    G    23_A      G    23_A     1.953     0    0.496   0.496     3.667   61.905   61.905
LGA    G    24_A      G    24_A     2.131     0    0.297   0.297     2.131   72.976   72.976
LGA    C    25_A      C    25_A     1.579     0    0.047   0.801     2.537   81.667   76.111
LGA    P    26_A      P    26_A     0.548     0    0.062   0.081     1.770   81.548   80.340
LGA    E    27_A      E    27_A     3.059     0    0.347   0.908    10.704   61.429   31.852
LGA    V    28_A      V    28_A     2.402     0    0.414   0.962     6.126   75.119   53.741
LGA    C    29_A      C    29_A     0.493     0    0.611   1.001     4.216   82.262   76.111

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       15      60     60  100.00     100    100  100.00                35
SUMMARY(RMSD_GDC):     3.172          2.961                  5.096           26.592   22.520

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   15   35    4.0     13    2.19    30.000    28.749     0.567

LGA_LOCAL      RMSD:   2.192  Number of atoms:   13  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   3.483  Number of assigned atoms:   15 
Std_ASGN_ATOMS RMSD:   3.172  Standard rmsd on all 15 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.216461 * X  +   0.557449 * Y  +  -0.801496 * Z  +  -3.915073
  Y_new =   0.617399 * X  +   0.714117 * Y  +   0.329934 * Z  +   0.427946
  Z_new =   0.756283 * X  +  -0.423425 * Y  +  -0.498746 * Z  +  -0.247044 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.908007 -0.857613 -2.437692   [DEG:  109.3207  -49.1376 -139.6695 ]
ZXZ: -1.961304  2.092948  2.081190   [DEG: -112.3744  119.9171  119.2434 ]
 
# END of job
