
#######################################################
#                                                     #
#                        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   15 (   60),  selected   15 , name T0295AL044_5-D2
# Molecule2: number of CA atoms   95 (  803),  selected   15 , name T0295_D2.pdb
# PARAMETERS: T0295AL044_5-D2.T0295_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:    10       181 - 193         4.67    13.99
  LCS_AVERAGE:      9.89

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       189 - 193         1.61    14.12
  LCS_AVERAGE:      4.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       189 - 192         0.88    15.59
  LONGEST_CONTINUOUS_SEGMENT:     4       195 - 198         0.75    15.45
  LCS_AVERAGE:      3.30

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:   95
LCS_GDT     T     181     T     181      0    0   10     0    2    3    3    4    5    5    6    6    8    8    8    9   10   10   10   10   11   11   11 
LCS_GDT     D     184     D     184      3    3   10     0    3    3    3    3    4    5    5    6    8    8    8    9   10   10   10   10   11   11   11 
LCS_GDT     E     185     E     185      3    3   10     0    3    3    3    4    5    5    6    6    8    8    8    9   10   10   10   10   11   12   12 
LCS_GDT     W     186     W     186      3    3   10     0    3    3    3    3    4    5    6    6    8    8    8   10   10   11   11   11   12   12   12 
LCS_GDT     N     188     N     188      0    4   10     1    3    3    3    4    5    5    6    6    8    8    8   10   10   11   11   11   12   12   12 
LCS_GDT     L     189     L     189      4    5   10     3    3    4    4    5    5    5    5    6    7    8    8   10   10   11   11   11   12   12   12 
LCS_GDT     L     190     L     190      4    5   10     3    3    4    4    5    5    5    5    6    7    8    8    9   10   10   10   11   12   12   12 
LCS_GDT     R     191     R     191      4    5   10     3    3    4    4    5    5    5    6    6    8    8    8    9   10   11   11   11   12   12   12 
LCS_GDT     I     192     I     192      4    5   10     1    3    4    4    5    5    5    6    6    8    8    8   10   10   11   11   11   12   12   12 
LCS_GDT     C     193     C     193      3    5   10     0    3    3    3    5    5    5    5    6    8    8    8   10   10   11   11   11   12   12   12 
LCS_GDT     F     194     F     194      3    3    9     1    3    3    3    3    4    5    5    6    7    7    8   10   10   11   11   11   12   12   12 
LCS_GDT     S     195     S     195      4    4    9     2    4    4    4    4    4    5    5    6    7    7    8   10   10   11   11   11   12   12   12 
LCS_GDT     R     196     R     196      4    4    9     3    4    4    4    4    4    5    5    6    7    7    8   10   10   11   11   11   12   12   12 
LCS_GDT     K     197     K     197      4    4    7     3    4    4    4    4    4    4    4    5    6    7    8   10   10   11   11   11   12   12   12 
LCS_GDT     R     198     R     198      4    4    7     3    4    4    4    4    4    4    4    5    6    7    8   10   10   11   11   11   12   12   12 
LCS_AVERAGE  LCS_A:   5.73  (   3.30    4.00    9.89 )

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      4      4      5      5      5      6      6      8      8      8     10     10     11     11     11     12     12     12 
GDT PERCENT_CA   3.16   4.21   4.21   4.21   5.26   5.26   5.26   6.32   6.32   8.42   8.42   8.42  10.53  10.53  11.58  11.58  11.58  12.63  12.63  12.63
GDT RMS_LOCAL    0.14   0.75   0.75   0.75   1.61   1.61   1.61   2.43   2.43   3.44   3.44   3.44   5.25   4.67   5.65   5.65   5.65   6.17   6.17   6.17
GDT RMS_ALL_CA  17.15  15.45  15.45  15.45  14.12  14.12  14.12  13.07  13.07  12.86  12.86  12.86   9.68  13.99   9.63   9.63   9.63   9.97   9.97   9.97

#      Molecule1      Molecule2       DISTANCE
LGA    T     181      T     181          2.230
LGA    D     184      D     184          5.277
LGA    E     185      E     185          2.975
LGA    W     186      W     186          3.671
LGA    N     188      N     188          1.337
LGA    L     189      L     189          7.038
LGA    L     190      L     190          8.775
LGA    R     191      R     191          3.033
LGA    I     192      I     192          2.641
LGA    C     193      C     193          5.547
LGA    F     194      F     194         10.424
LGA    S     195      S     195         19.107
LGA    R     196      R     196         23.115
LGA    K     197      K     197         24.489
LGA    R     198      R     198         28.056

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   15   95    4.0      6    2.43     6.579     5.922     0.237

LGA_LOCAL      RMSD =  2.430  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 13.229  Number of atoms =   15 
Std_ALL_ATOMS  RMSD =  8.812  (standard rmsd on all 15 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.627127 * X  +   0.744314 * Y  +  -0.229583 * Z  +  19.477533
  Y_new =  -0.760503 * X  +   0.648811 * Y  +   0.026079 * Z  +  18.541597
  Z_new =   0.168367 * X  +   0.158244 * Y  +   0.972940 * Z  + -102.597107 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.161233   -2.980359  [ DEG:     9.2380   -170.7620 ]
  Theta =  -0.169173   -2.972420  [ DEG:    -9.6929   -170.3071 ]
  Phi   =  -0.881222    2.260371  [ DEG:   -50.4903    129.5097 ]
 
# 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: T0295AL044_5-D2                               
REMARK     2: T0295_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0295AL044_5-D2.T0295_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   15   95   4.0    6   2.43   5.922     8.81
REMARK  ---------------------------------------------------------- 
MOLECULE T0295AL044_5-D2
REMARK Aligment from pdb entry: 1ve3_A
ATOM    645  N   THR   181      19.450  11.743  10.810  1.00  0.00              
ATOM    646  CA  THR   181      20.253  12.768  11.465  1.00  0.00              
ATOM    647  C   THR   181      19.762  14.156  11.047  1.00  0.00              
ATOM    648  O   THR   181      19.515  15.010  11.890  1.00  0.00              
ATOM    649  N   ASP   184      19.613  14.369   9.740  1.00  0.00              
ATOM    650  CA  ASP   184      19.163  15.657   9.221  1.00  0.00              
ATOM    651  C   ASP   184      18.481  15.507   7.861  1.00  0.00              
ATOM    652  O   ASP   184      18.506  14.435   7.259  1.00  0.00              
ATOM    653  N   GLU   185      17.882  16.595   7.382  1.00  0.00              
ATOM    654  CA  GLU   185      17.204  16.584   6.094  1.00  0.00              
ATOM    655  C   GLU   185      17.132  17.990   5.513  1.00  0.00              
ATOM    656  O   GLU   185      16.710  18.927   6.188  1.00  0.00              
ATOM    657  N   TRP   186      17.556  18.131   4.261  1.00  0.00              
ATOM    658  CA  TRP   186      17.549  19.421   3.585  1.00  0.00              
ATOM    659  C   TRP   186      16.652  19.355   2.354  1.00  0.00              
ATOM    660  O   TRP   186      16.778  18.437   1.539  1.00  0.00              
ATOM    661  N   ASN   188      15.754  20.325   2.211  1.00  0.00              
ATOM    662  CA  ASN   188      14.882  20.358   1.046  1.00  0.00              
ATOM    663  C   ASN   188      15.619  21.100  -0.065  1.00  0.00              
ATOM    664  O   ASN   188      16.108  22.206   0.138  1.00  0.00              
ATOM    665  N   LEU   189      15.361  22.497  -4.028  1.00  0.00              
ATOM    666  CA  LEU   189      14.460  22.785  -5.124  1.00  0.00              
ATOM    667  C   LEU   189      13.018  22.647  -4.686  1.00  0.00              
ATOM    668  O   LEU   189      12.701  22.806  -3.506  1.00  0.00              
ATOM    669  N   LEU   190      12.142  22.334  -5.632  1.00  0.00              
ATOM    670  CA  LEU   190      10.724  22.193  -5.335  1.00  0.00              
ATOM    671  C   LEU   190      10.335  20.849  -4.743  1.00  0.00              
ATOM    672  O   LEU   190       9.401  20.774  -3.946  1.00  0.00              
ATOM    673  N   ARG   191      11.044  19.789  -5.116  1.00  0.00              
ATOM    674  CA  ARG   191      10.713  18.477  -4.579  1.00  0.00              
ATOM    675  C   ARG   191      11.860  17.490  -4.430  1.00  0.00              
ATOM    676  O   ARG   191      11.669  16.288  -4.580  1.00  0.00              
ATOM    677  N   ILE   192      13.048  17.992  -4.119  1.00  0.00              
ATOM    678  CA  ILE   192      14.203  17.123  -3.932  1.00  0.00              
ATOM    679  C   ILE   192      14.684  17.196  -2.493  1.00  0.00              
ATOM    680  O   ILE   192      14.490  18.210  -1.811  1.00  0.00              
ATOM    681  N   CYS   193      15.309  16.119  -2.028  1.00  0.00              
ATOM    682  CA  CYS   193      15.779  16.055  -0.646  1.00  0.00              
ATOM    683  C   CYS   193      17.148  15.452  -0.438  1.00  0.00              
ATOM    684  O   CYS   193      17.516  14.471  -1.085  1.00  0.00              
ATOM    685  N   PHE   194      17.906  16.051   0.476  1.00  0.00              
ATOM    686  CA  PHE   194      19.213  15.544   0.851  1.00  0.00              
ATOM    687  C   PHE   194      18.964  15.048   2.263  1.00  0.00              
ATOM    688  O   PHE   194      18.608  15.835   3.136  1.00  0.00              
ATOM    689  N   SER   195      20.338  12.781   5.717  1.00  0.00              
ATOM    690  CA  SER   195      21.484  12.221   6.421  1.00  0.00              
ATOM    691  C   SER   195      20.985  11.146   7.391  1.00  0.00              
ATOM    692  O   SER   195      20.190  11.423   8.285  1.00  0.00              
ATOM    693  N   ARG   196      21.462   9.920   7.207  1.00  0.00              
ATOM    694  CA  ARG   196      21.042   8.793   8.036  1.00  0.00              
ATOM    695  C   ARG   196      22.169   8.158   8.846  1.00  0.00              
ATOM    696  O   ARG   196      23.325   8.161   8.434  1.00  0.00              
ATOM    697  N   LYS   197      21.809   7.601   9.999  1.00  0.00              
ATOM    698  CA  LYS   197      22.763   6.912  10.861  1.00  0.00              
ATOM    699  C   LYS   197      22.259   5.473  10.949  1.00  0.00              
ATOM    700  O   LYS   197      21.069   5.242  11.157  1.00  0.00              
ATOM    701  N   ARG   198      23.158   4.492  10.786  1.00  0.00              
ATOM    702  CA  ARG   198      22.814   3.070  10.842  1.00  0.00              
ATOM    703  C   ARG   198      22.405   2.580  12.226  1.00  0.00              
ATOM    704  O   ARG   198      22.847   3.117  13.239  1.00  0.00              
END
