
#######################################################
#                                                     #
#                        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   10 (   40),  selected   10 , name T0318AL333_3-D2
# Molecule2: number of CA atoms  335 ( 2465),  selected   10 , name T0318_D2.pdb
# PARAMETERS: T0318AL333_3-D2.T0318_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:     7       156 - 162         0.54    15.21
  LCS_AVERAGE:      1.73

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       156 - 162         0.54    15.21
  LCS_AVERAGE:      1.73

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       156 - 162         0.54    15.21
  LCS_AVERAGE:      1.73

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:  335
LCS_GDT     T     156     T     156      7    7    7     3    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     N     157     N     157      7    7    7     6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     E     158     E     158      7    7    7     6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     D     159     D     159      7    7    7     6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     A     160     A     160      7    7    7     6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     V     161     V     161      7    7    7     6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     F     162     F     162      7    7    7     6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     A     377     A     377      3    3    3     0    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_GDT     A     378     A     378      3    3    3     0    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_GDT     M     379     M     379      3    3    3     0    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_AVERAGE  LCS_A:   1.73  (   1.73    1.73    1.73 )

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      6      7      7      7      7      7      7      7      7      7      7      7      7      7      7      7      7      7      7      7 
GDT PERCENT_CA   1.79   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09
GDT RMS_LOCAL    0.31   0.54   0.54   0.54   0.54   0.54   0.54   0.54   0.54   0.54   0.54   0.54   0.54   0.54   0.54   0.54   0.54   0.54   0.54   0.54
GDT RMS_ALL_CA  15.09  15.21  15.21  15.21  15.21  15.21  15.21  15.21  15.21  15.21  15.21  15.21  15.21  15.21  15.21  15.21  15.21  15.21  15.21  15.21

#      Molecule1      Molecule2       DISTANCE
LGA    T     156      T     156          0.866
LGA    N     157      N     157          0.499
LGA    E     158      E     158          0.454
LGA    D     159      D     159          0.436
LGA    A     160      A     160          0.460
LGA    V     161      V     161          0.521
LGA    F     162      F     162          0.384
LGA    A     377      A     377         25.442
LGA    A     378      A     378         28.003
LGA    M     379      M     379         29.660

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   10  335    4.0      7    0.54     2.090     2.000     1.097

LGA_LOCAL      RMSD =  0.538  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 15.209  Number of atoms =   10 
Std_ALL_ATOMS  RMSD = 11.143  (standard rmsd on all 10 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.947386 * X  +  -0.309034 * Y  +  -0.083417 * Z  +  87.448761
  Y_new =   0.306831 * X  +  -0.950990 * Y  +   0.038371 * Z  +  96.737404
  Z_new =  -0.091187 * X  +   0.010757 * Y  +   0.995776 * Z  +   1.821377 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.010802   -3.130790  [ DEG:     0.6189   -179.3811 ]
  Theta =   0.091313    3.050279  [ DEG:     5.2319    174.7681 ]
  Phi   =   2.828382   -0.313211  [ DEG:   162.0543    -17.9457 ]
 
# 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: T0318AL333_3-D2                               
REMARK     2: T0318_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0318AL333_3-D2.T0318_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   10  335   4.0    7   0.54   2.000    11.14
REMARK  ---------------------------------------------------------- 
MOLECULE T0318AL333_3-D2
REMARK Aligment from pdb entry: 1lam
ATOM    557  N   THR   156      28.850  26.976  14.591  1.00  0.00              
ATOM    558  CA  THR   156      27.626  27.780  14.618  1.00  0.00              
ATOM    559  C   THR   156      27.513  28.788  13.482  1.00  0.00              
ATOM    560  O   THR   156      27.001  29.890  13.670  1.00  0.00              
ATOM    561  N   ASN   157      27.891  28.365  12.284  1.00  0.00              
ATOM    562  CA  ASN   157      27.901  29.236  11.114  1.00  0.00              
ATOM    563  C   ASN   157      26.604  29.903  10.649  1.00  0.00              
ATOM    564  O   ASN   157      26.596  31.120  10.412  1.00  0.00              
ATOM    565  N   GLU   158      25.524  29.137  10.490  1.00  0.00              
ATOM    566  CA  GLU   158      24.261  29.727  10.033  1.00  0.00              
ATOM    567  C   GLU   158      23.740  30.779  11.009  1.00  0.00              
ATOM    568  O   GLU   158      23.348  31.867  10.590  1.00  0.00              
ATOM    569  N   ASP   159      23.773  30.462  12.300  1.00  0.00              
ATOM    570  CA  ASP   159      23.306  31.391  13.329  1.00  0.00              
ATOM    571  C   ASP   159      24.175  32.660  13.371  1.00  0.00              
ATOM    572  O   ASP   159      23.651  33.774  13.500  1.00  0.00              
ATOM    573  N   ALA   160      25.497  32.499  13.268  1.00  0.00              
ATOM    574  CA  ALA   160      26.398  33.656  13.272  1.00  0.00              
ATOM    575  C   ALA   160      26.064  34.534  12.075  1.00  0.00              
ATOM    576  O   ALA   160      25.928  35.748  12.198  1.00  0.00              
ATOM    577  N   VAL   161      25.929  33.919  10.910  1.00  0.00              
ATOM    578  CA  VAL   161      25.623  34.683   9.716  1.00  0.00              
ATOM    579  C   VAL   161      24.239  35.350   9.786  1.00  0.00              
ATOM    580  O   VAL   161      24.042  36.451   9.269  1.00  0.00              
ATOM    581  N   PHE   162      23.297  34.711  10.469  1.00  0.00              
ATOM    582  CA  PHE   162      21.964  35.283  10.618  1.00  0.00              
ATOM    583  C   PHE   162      22.086  36.572  11.425  1.00  0.00              
ATOM    584  O   PHE   162      21.436  37.576  11.111  1.00  0.00              
ATOM    585  N   ALA   377      22.954  36.543  12.438  1.00  0.00              
ATOM    586  CA  ALA   377      23.182  37.698  13.283  1.00  0.00              
ATOM    587  C   ALA   377      23.832  38.813  12.497  1.00  0.00              
ATOM    588  O   ALA   377      23.465  39.989  12.649  1.00  0.00              
ATOM    589  N   ALA   378      24.812  38.458  11.666  1.00  0.00              
ATOM    590  CA  ALA   378      25.491  39.448  10.829  1.00  0.00              
ATOM    591  C   ALA   378      24.470  40.123   9.896  1.00  0.00              
ATOM    592  O   ALA   378      24.478  41.340   9.731  1.00  0.00              
ATOM    593  N   MET   379      23.556  39.333   9.339  1.00  0.00              
ATOM    594  CA  MET   379      22.543  39.841   8.424  1.00  0.00              
ATOM    595  C   MET   379      21.567  40.809   9.123  1.00  0.00              
ATOM    596  O   MET   379      21.272  41.890   8.598  1.00  0.00              
END
