
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   13 (   52),  selected   13 , name T0386AL381_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   13 , name T0386_D2.pdb
# PARAMETERS: T0386AL381_1-D2.T0386_D2.pdb  -3  -ie  -o1  -sda  -d:4  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       234 - 246         4.10     4.10
  LCS_AVERAGE:     16.05

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       238 - 243         1.67     6.96
  LCS_AVERAGE:      6.17

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       234 - 237         0.61    18.84
  LONGEST_CONTINUOUS_SEGMENT:     4       238 - 241         0.69    10.36
  LCS_AVERAGE:      4.46

LCS_GDT    MOLECULE-1    MOLECULE-2    LENGTH_OF_THE
LCS_GDT     RESIDUE       RESIDUE         CONTINUOUS
LCS_GDT   NAME NUMBER   NAME NUMBER          SEGMENT     GLOBAL DISTANCE TEST - GDT_DATA_COLUMNS                             NUMBER OF THE RESIDUES:   81
LCS_GDT     K     234     K     234      4    5   13     3    4    4    4    4    5    5    6    6    6   12   12   13   13   13   13   13   13   13   13 
LCS_GDT     N     235     N     235      4    5   13     3    4    4    4    4    5    7    9   10   11   12   12   13   13   13   13   13   13   13   13 
LCS_GDT     T     236     T     236      4    5   13     3    4    4    4    6    7    8    9   10   11   12   12   13   13   13   13   13   13   13   13 
LCS_GDT     G     237     G     237      4    5   13     0    4    4    4    6    7    8    9   10   11   12   12   13   13   13   13   13   13   13   13 
LCS_GDT     R     238     R     238      4    6   13     0    4    5    5    6    7    8    9   10   11   12   12   13   13   13   13   13   13   13   13 
LCS_GDT     N     239     N     239      4    6   13     3    4    5    5    6    7    8    9   10   11   12   12   13   13   13   13   13   13   13   13 
LCS_GDT     V     240     V     240      4    6   13     3    4    5    5    6    7    8    9   10   11   12   12   13   13   13   13   13   13   13   13 
LCS_GDT     N     241     N     241      4    6   13     3    4    5    5    6    7    8    9   10   11   12   12   13   13   13   13   13   13   13   13 
LCS_GDT     D     242     D     242      3    6   13     3    4    5    5    6    7    8    9   10   11   12   12   13   13   13   13   13   13   13   13 
LCS_GDT     R     243     R     243      3    6   13     3    3    4    4    6    7    8    9   10   11   12   12   13   13   13   13   13   13   13   13 
LCS_GDT     P     244     P     244      3    3   13     3    3    3    5    5    7    8    9   10   11   12   12   13   13   13   13   13   13   13   13 
LCS_GDT     V     245     V     245      3    3   13     3    3    3    3    4    7    8    9    9   11   12   12   13   13   13   13   13   13   13   13 
LCS_GDT     M     246     M     246      3    3   13     0    3    3    3    3    3    4    4    6    9    9   11   13   13   13   13   13   13   13   13 
LCS_AVERAGE  LCS_A:   8.90  (   4.46    6.17   16.05 )

GLOBAL_DISTANCE_TEST (the largest set of residues that can fit under specified DISTANCE_CUTOFF)
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_CA      3      4      5      5      6      7      8      9     10     11     12     12     13     13     13     13     13     13     13     13 
GDT PERCENT_CA   3.70   4.94   6.17   6.17   7.41   8.64   9.88  11.11  12.35  13.58  14.81  14.81  16.05  16.05  16.05  16.05  16.05  16.05  16.05  16.05
GDT RMS_LOCAL    0.04   0.61   1.05   1.05   1.58   2.11   2.26   2.65   3.13   3.39   3.67   3.67   4.10   4.10   4.10   4.10   4.10   4.10   4.10   4.10
GDT RMS_ALL_CA  10.41  18.84   8.55   8.55   5.57   5.74   5.70   4.91   4.41   4.29   4.24   4.24   4.10   4.10   4.10   4.10   4.10   4.10   4.10   4.10

#      Molecule1      Molecule2       DISTANCE
LGA    K     234      K     234         10.256
LGA    N     235      N     235          7.966
LGA    T     236      T     236          1.568
LGA    G     237      G     237          3.914
LGA    R     238      R     238          2.401
LGA    N     239      N     239          1.879
LGA    V     240      V     240          3.753
LGA    N     241      N     241          0.956
LGA    D     242      D     242          2.222
LGA    R     243      R     243          1.971
LGA    P     244      P     244          3.501
LGA    V     245      V     245          5.627
LGA    M     246      M     246          7.055

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   13   81    4.0      9    2.65     9.568     9.259     0.327

LGA_LOCAL      RMSD =  2.649  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.909  Number of atoms =   13 
Std_ALL_ATOMS  RMSD =  4.097  (standard rmsd on all 13 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.629674 * X  +  -0.631306 * Y  +  -0.452730 * Z  +  57.609467
  Y_new =  -0.641605 * X  +  -0.751186 * Y  +   0.155118 * Z  + 105.290115
  Z_new =  -0.438011 * X  +   0.192800 * Y  +  -0.878051 * Z  +  55.874252 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.925446   -0.216147  [ DEG:   167.6157    -12.3843 ]
  Theta =   0.453385    2.688207  [ DEG:    25.9771    154.0229 ]
  Phi   =  -0.794783    2.346809  [ DEG:   -45.5377    134.4623 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0386AL381_1-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386AL381_1-D2.T0386_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   13   81   4.0    9   2.65   9.259     4.10
REMARK  ---------------------------------------------------------- 
MOLECULE T0386AL381_1-D2
REMARK Aligment from pdb entry: 2g03A
ATOM    617  N   LYS   234      19.808  78.861  80.801  1.00  0.00              
ATOM    618  CA  LYS   234      21.016  78.171  81.273  1.00  0.00              
ATOM    619  C   LYS   234      21.280  76.824  80.588  1.00  0.00              
ATOM    620  O   LYS   234      22.368  76.270  80.698  1.00  0.00              
ATOM    621  N   ASN   235      20.271  76.279  79.925  1.00  0.00              
ATOM    622  CA  ASN   235      20.360  74.912  79.490  1.00  0.00              
ATOM    623  C   ASN   235      20.005  74.734  78.016  1.00  0.00              
ATOM    624  O   ASN   235      19.582  73.667  77.619  1.00  0.00              
ATOM    625  N   THR   236      20.210  75.761  77.197  1.00  0.00              
ATOM    626  CA  THR   236      20.006  75.602  75.757  1.00  0.00              
ATOM    627  C   THR   236      21.254  74.975  75.173  1.00  0.00              
ATOM    628  O   THR   236      22.332  75.090  75.763  1.00  0.00              
ATOM    629  N   GLY   237      21.111  74.294  74.035  1.00  0.00              
ATOM    630  CA  GLY   237      22.250  73.778  73.286  1.00  0.00              
ATOM    631  C   GLY   237      21.955  74.011  71.819  1.00  0.00              
ATOM    632  O   GLY   237      20.809  73.933  71.409  1.00  0.00              
ATOM    633  N   ARG   238      22.965  74.302  71.007  1.00  0.00              
ATOM    634  CA  ARG   238      22.692  74.353  69.579  1.00  0.00              
ATOM    635  C   ARG   238      23.009  73.054  68.860  1.00  0.00              
ATOM    636  O   ARG   238      22.945  72.991  67.641  1.00  0.00              
ATOM    637  N   ASN   239      23.296  72.010  69.626  1.00  0.00              
ATOM    638  CA  ASN   239      23.558  70.695  69.048  1.00  0.00              
ATOM    639  C   ASN   239      22.207  69.963  68.931  1.00  0.00              
ATOM    640  O   ASN   239      21.962  68.988  69.634  1.00  0.00              
ATOM    641  N   VAL   240      21.346  70.442  68.034  1.00  0.00              
ATOM    642  CA  VAL   240      19.903  70.175  68.098  1.00  0.00              
ATOM    643  C   VAL   240      19.525  68.753  67.656  1.00  0.00              
ATOM    644  O   VAL   240      18.391  68.303  67.912  1.00  0.00              
ATOM    645  N   ASN   241      20.462  68.062  67.009  1.00  0.00              
ATOM    646  CA  ASN   241      20.202  66.747  66.433  1.00  0.00              
ATOM    647  C   ASN   241      21.088  65.665  67.035  1.00  0.00              
ATOM    648  O   ASN   241      21.169  64.563  66.516  1.00  0.00              
ATOM    649  N   ASP   242      21.747  65.992  68.130  1.00  0.00              
ATOM    650  CA  ASP   242      22.620  65.058  68.805  1.00  0.00              
ATOM    651  C   ASP   242      21.817  63.925  69.470  1.00  0.00              
ATOM    652  O   ASP   242      20.881  64.177  70.228  1.00  0.00              
ATOM    653  N   ARG   243      22.160  62.679  69.152  1.00  0.00              
ATOM    654  CA  ARG   243      21.439  61.522  69.683  1.00  0.00              
ATOM    655  C   ARG   243      21.362  61.500  71.225  1.00  0.00              
ATOM    656  O   ARG   243      20.315  61.184  71.783  1.00  0.00              
ATOM    657  N   PRO   244      22.446  61.858  71.903  1.00  0.00              
ATOM    658  CA  PRO   244      22.478  61.811  73.356  1.00  0.00              
ATOM    659  C   PRO   244      21.575  62.878  73.990  1.00  0.00              
ATOM    660  O   PRO   244      20.842  62.603  74.955  1.00  0.00              
ATOM    661  N   VAL   245      21.616  64.093  73.443  1.00  0.00              
ATOM    662  CA  VAL   245      20.746  65.175  73.886  1.00  0.00              
ATOM    663  C   VAL   245      19.290  64.816  73.627  1.00  0.00              
ATOM    664  O   VAL   245      18.444  65.007  74.503  1.00  0.00              
ATOM    665  N   MET   246      18.984  64.293  72.441  1.00  0.00              
ATOM    666  CA  MET   246      17.603  63.902  72.143  1.00  0.00              
ATOM    667  C   MET   246      17.123  62.789  73.115  1.00  0.00              
ATOM    668  O   MET   246      16.146  62.959  73.837  1.00  0.00              
END
