
#######################################################
#                                                     #
#                        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   22 (   88),  selected   22 , name T0316AL242_1-D2
# Molecule2: number of CA atoms   60 (  457),  selected   22 , name T0316_D2.pdb
# PARAMETERS: T0316AL242_1-D2.T0316_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:    15       269 - 283         4.96     8.04
  LCS_AVERAGE:     23.11

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       265 - 269         1.88    24.41
  LONGEST_CONTINUOUS_SEGMENT:     5       266 - 270         0.58    22.37
  LONGEST_CONTINUOUS_SEGMENT:     5       279 - 283         1.90    17.71
  LCS_AVERAGE:      7.35

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       266 - 270         0.58    22.37
  LCS_AVERAGE:      5.76

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:   60
LCS_GDT     V     262     V     262      3    4   11     3    3    3    4    4    4    6    8    9    9    9   10   10   10   10   11   11   11   12   13 
LCS_GDT     V     263     V     263      3    4   11     3    3    3    4    4    4    6    8    9    9    9   10   10   10   10   11   11   11   12   12 
LCS_GDT     G     264     G     264      3    4   11     3    3    3    4    4    5    6    8    9    9    9   10   10   11   11   12   12   19   20   20 
LCS_GDT     K     265     K     265      3    5   11     3    3    3    4    4    5    6    8    9    9    9   10   12   13   15   18   19   19   20   20 
LCS_GDT     D     266     D     266      5    5   12     4    5    5    5    5    5    6    8   11   12   13   14   16   17   18   18   19   19   20   20 
LCS_GDT     L     267     L     267      5    5   12     4    5    5    5    6    6    7    9   11   12   13   14   16   17   18   18   19   19   20   20 
LCS_GDT     S     268     S     268      5    5   12     4    5    5    5    5    5    6    7    9    9    9   12   15   17   18   18   19   19   20   20 
LCS_GDT     K     269     K     269      5    5   15     4    5    5    5    5    5    7    8    9   11   13   14   16   17   18   18   19   19   20   20 
LCS_GDT     N     270     N     270      5    5   15     3    5    5    5    5    5    6    8    9    9   12   14   15   16   18   18   19   19   20   20 
LCS_GDT     I     271     I     271      3    4   15     3    3    4    4    4    5    5    7    9   11   13   14   16   17   18   18   19   19   20   20 
LCS_GDT     L     272     L     272      3    4   15     3    4    5    5    6    6    7    9   11   12   13   14   16   17   18   18   19   19   20   20 
LCS_GDT     Y     273     Y     273      3    3   15     3    3    5    5    6    6    7    9   11   12   13   14   16   17   18   18   19   19   20   20 
LCS_GDT     V     274     V     274      3    3   15     0    3    3    3    4    5    6    9   11   12   13   14   16   17   18   18   19   19   20   20 
LCS_GDT     G     275     G     275      3    4   15     0    3    3    4    4    5    6    9   11   12   13   14   16   17   18   18   19   19   20   20 
LCS_GDT     Q     276     Q     276      3    4   15     2    3    3    4    4    5    6    7   11   12   13   14   16   17   18   18   19   19   20   20 
LCS_GDT     G     277     G     277      3    4   15     2    3    3    4    4    5    6    7    8   10   11   14   16   17   18   18   19   19   20   20 
LCS_GDT     F     278     F     278      3    4   15     3    3    3    4    4    5    6    7    8   10   11   14   16   17   18   18   19   19   20   20 
LCS_GDT     Y     279     Y     279      3    5   15     3    3    3    3    5    5    6    9   11   12   13   14   16   17   18   18   19   19   20   20 
LCS_GDT     H     280     H     280      3    5   15     3    4    5    5    6    6    7    9   11   12   13   14   16   17   18   18   19   19   20   20 
LCS_GDT     D     281     D     281      3    5   15     3    4    5    5    6    6    7    9   11   12   13   14   16   17   18   18   19   19   20   20 
LCS_GDT     S     282     S     282      3    5   15     0    3    3    4    6    6    7    9   11   12   13   14   16   17   18   18   19   19   20   20 
LCS_GDT     L     283     L     283      3    5   15     1    3    3    4    5    5    6    7   11   12   13   14   16   17   18   18   19   19   20   20 
LCS_AVERAGE  LCS_A:  12.07  (   5.76    7.35   23.11 )

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      4      5      5      5      6      6      7      9     11     12     13     14     16     17     18     18     19     19     20     20 
GDT PERCENT_CA   6.67   8.33   8.33   8.33  10.00  10.00  11.67  15.00  18.33  20.00  21.67  23.33  26.67  28.33  30.00  30.00  31.67  31.67  33.33  33.33
GDT RMS_LOCAL    0.26   0.58   0.58   0.58   1.37   1.37   2.00   3.07   3.55   3.72   3.90   4.11   4.68   4.89   5.06   5.06   5.41   5.41   5.87   5.87
GDT RMS_ALL_CA  23.18  22.37  22.37  22.37   8.76   8.76   9.00   8.19   8.00   7.81   8.13   7.98   7.80   7.91   8.00   8.00   7.85   7.85   7.72   7.72

#      Molecule1      Molecule2       DISTANCE
LGA    V     262      V     262         17.196
LGA    V     263      V     263         17.766
LGA    G     264      G     264         12.674
LGA    K     265      K     265         10.440
LGA    D     266      D     266          5.847
LGA    L     267      L     267          3.207
LGA    S     268      S     268          9.906
LGA    K     269      K     269          7.387
LGA    N     270      N     270          6.492
LGA    I     271      I     271          5.982
LGA    L     272      L     272          3.362
LGA    Y     273      Y     273          1.959
LGA    V     274      V     274          3.820
LGA    G     275      G     275          3.913
LGA    Q     276      Q     276          4.692
LGA    G     277      G     277          8.130
LGA    F     278      F     278          7.667
LGA    Y     279      Y     279          3.997
LGA    H     280      H     280          2.851
LGA    D     281      D     281          2.106
LGA    S     282      S     282          3.375
LGA    L     283      L     283          4.598

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   22   60    4.0      9    3.07    15.417    13.453     0.284

LGA_LOCAL      RMSD =  3.071  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  8.003  Number of atoms =   22 
Std_ALL_ATOMS  RMSD =  7.522  (standard rmsd on all 22 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.266030 * X  +  -0.270414 * Y  +   0.925259 * Z  +  31.012922
  Y_new =   0.181298 * X  +  -0.956754 * Y  +  -0.227492 * Z  +  43.559429
  Z_new =   0.946762 * X  +   0.107228 * Y  +   0.303551 * Z  +  21.954571 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.339565   -2.802028  [ DEG:    19.4556   -160.5444 ]
  Theta =  -1.243026   -1.898567  [ DEG:   -71.2201   -108.7799 ]
  Phi   =   2.543393   -0.598199  [ DEG:   145.7257    -34.2743 ]
 
# 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: T0316AL242_1-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316AL242_1-D2.T0316_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   22   60   4.0    9   3.07  13.453     7.52
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL242_1-D2
REMARK Aligment from pdb entry: 1xng_B
ATOM    709  N   VAL   262      45.356  14.538  -9.778  1.00  0.00              
ATOM    710  CA  VAL   262      45.818  15.093 -11.042  1.00  0.00              
ATOM    711  C   VAL   262      45.843  16.611 -11.022  1.00  0.00              
ATOM    712  O   VAL   262      45.114  17.239 -10.255  1.00  0.00              
ATOM    713  N   VAL   263      46.685  17.219 -11.871  1.00  0.00              
ATOM    714  CA  VAL   263      46.781  18.679 -11.946  1.00  0.00              
ATOM    715  C   VAL   263      45.648  19.151 -12.857  1.00  0.00              
ATOM    716  O   VAL   263      45.059  18.348 -13.582  1.00  0.00              
ATOM    717  N   GLY   264      45.347  20.443 -12.833  1.00  0.00              
ATOM    718  CA  GLY   264      44.271  20.964 -13.662  1.00  0.00              
ATOM    719  C   GLY   264      44.569  20.897 -15.153  1.00  0.00              
ATOM    720  O   GLY   264      43.658  20.971 -15.974  1.00  0.00              
ATOM    721  N   LYS   265      45.839  20.738 -15.502  1.00  0.00              
ATOM    722  CA  LYS   265      46.230  20.644 -16.904  1.00  0.00              
ATOM    723  C   LYS   265      45.691  19.346 -17.517  1.00  0.00              
ATOM    724  O   LYS   265      45.510  19.243 -18.735  1.00  0.00              
ATOM    725  N   ASP   266      45.447  18.361 -16.658  1.00  0.00              
ATOM    726  CA  ASP   266      44.917  17.066 -17.069  1.00  0.00              
ATOM    727  C   ASP   266      43.409  17.002 -16.824  1.00  0.00              
ATOM    728  O   ASP   266      42.661  16.412 -17.608  1.00  0.00              
ATOM    729  N   LEU   267      42.961  17.619 -15.734  1.00  0.00              
ATOM    730  CA  LEU   267      41.547  17.600 -15.385  1.00  0.00              
ATOM    731  C   LEU   267      40.655  18.460 -16.271  1.00  0.00              
ATOM    732  O   LEU   267      39.627  17.991 -16.764  1.00  0.00              
ATOM    733  N   SER   268      41.053  19.707 -16.483  1.00  0.00              
ATOM    734  CA  SER   268      40.238  20.630 -17.261  1.00  0.00              
ATOM    735  C   SER   268      39.860  20.154 -18.657  1.00  0.00              
ATOM    736  O   SER   268      38.711  20.292 -19.072  1.00  0.00              
ATOM    737  N   LYS   269      40.810  19.573 -19.402  1.00  0.00              
ATOM    738  CA  LYS   269      40.415  19.119 -20.737  1.00  0.00              
ATOM    739  C   LYS   269      39.255  18.117 -20.675  1.00  0.00              
ATOM    740  O   LYS   269      38.339  18.153 -21.504  1.00  0.00              
ATOM    741  N   ASN   270      39.282  17.235 -19.675  1.00  0.00              
ATOM    742  CA  ASN   270      38.227  16.246 -19.523  1.00  0.00              
ATOM    743  C   ASN   270      36.910  16.894 -19.111  1.00  0.00              
ATOM    744  O   ASN   270      35.851  16.512 -19.600  1.00  0.00              
ATOM    745  N   ILE   271      36.972  17.881 -18.219  1.00  0.00              
ATOM    746  CA  ILE   271      35.756  18.551 -17.779  1.00  0.00              
ATOM    747  C   ILE   271      35.095  19.276 -18.944  1.00  0.00              
ATOM    748  O   ILE   271      33.867  19.294 -19.057  1.00  0.00              
ATOM    749  N   LEU   272      35.904  19.872 -19.814  1.00  0.00              
ATOM    750  CA  LEU   272      35.354  20.584 -20.958  1.00  0.00              
ATOM    751  C   LEU   272      34.612  19.628 -21.890  1.00  0.00              
ATOM    752  O   LEU   272      33.582  19.993 -22.453  1.00  0.00              
ATOM    753  N   TYR   273      35.119  18.408 -22.059  1.00  0.00              
ATOM    754  CA  TYR   273      34.429  17.446 -22.922  1.00  0.00              
ATOM    755  C   TYR   273      33.141  16.975 -22.255  1.00  0.00              
ATOM    756  O   TYR   273      32.116  16.794 -22.914  1.00  0.00              
ATOM    757  N   VAL   274      33.190  16.774 -20.943  1.00  0.00              
ATOM    758  CA  VAL   274      32.010  16.344 -20.207  1.00  0.00              
ATOM    759  C   VAL   274      30.922  17.408 -20.339  1.00  0.00              
ATOM    760  O   VAL   274      29.742  17.085 -20.467  1.00  0.00              
ATOM    761  N   GLY   275      31.327  18.671 -20.321  1.00  0.00              
ATOM    762  CA  GLY   275      30.388  19.778 -20.463  1.00  0.00              
ATOM    763  C   GLY   275      29.751  19.791 -21.850  1.00  0.00              
ATOM    764  O   GLY   275      28.575  20.118 -22.003  1.00  0.00              
ATOM    765  N   GLN   276      30.534  19.430 -22.861  1.00  0.00              
ATOM    766  CA  GLN   276      30.036  19.425 -24.230  1.00  0.00              
ATOM    767  C   GLN   276      29.239  18.173 -24.583  1.00  0.00              
ATOM    768  O   GLN   276      28.257  18.244 -25.321  1.00  0.00              
ATOM    769  N   GLY   277      29.653  17.033 -24.045  1.00  0.00              
ATOM    770  CA  GLY   277      28.992  15.768 -24.340  1.00  0.00              
ATOM    771  C   GLY   277      27.793  15.437 -23.470  1.00  0.00              
ATOM    772  O   GLY   277      26.804  14.886 -23.951  1.00  0.00              
ATOM    773  N   PHE   278      27.881  15.767 -22.187  1.00  0.00              
ATOM    774  CA  PHE   278      26.805  15.450 -21.264  1.00  0.00              
ATOM    775  C   PHE   278      26.264  16.674 -20.550  1.00  0.00              
ATOM    776  O   PHE   278      26.998  17.382 -19.864  1.00  0.00              
ATOM    777  N   TYR   279      24.973  16.915 -20.720  1.00  0.00              
ATOM    778  CA  TYR   279      24.313  18.048 -20.092  1.00  0.00              
ATOM    779  C   TYR   279      22.817  17.777 -20.067  1.00  0.00              
ATOM    780  O   TYR   279      22.079  18.366 -19.279  1.00  0.00              
ATOM    781  N   HIS   280      22.384  16.870 -20.934  1.00  0.00              
ATOM    782  CA  HIS   280      20.982  16.485 -21.028  1.00  0.00              
ATOM    783  C   HIS   280      20.875  15.014 -20.649  1.00  0.00              
ATOM    784  O   HIS   280      19.781  14.487 -20.447  1.00  0.00              
ATOM    785  N   ASP   281      22.028  14.356 -20.560  1.00  0.00              
ATOM    786  CA  ASP   281      22.089  12.945 -20.207  1.00  0.00              
ATOM    787  C   ASP   281      23.284  12.689 -19.293  1.00  0.00              
ATOM    788  O   ASP   281      24.240  13.465 -19.271  1.00  0.00              
ATOM    789  N   SER   282      23.245  11.592 -18.524  1.00  0.00              
ATOM    790  CA  SER   282      24.346  11.265 -17.615  1.00  0.00              
ATOM    791  C   SER   282      25.660  10.946 -18.333  1.00  0.00              
ATOM    792  O   SER   282      25.670  10.579 -19.508  1.00  0.00              
ATOM    793  N   LEU   283      26.762  11.093 -17.610  1.00  0.00              
ATOM    794  CA  LEU   283      28.091  10.829 -18.151  1.00  0.00              
ATOM    795  C   LEU   283      28.219   9.378 -18.611  1.00  0.00              
ATOM    796  O   LEU   283      27.787   8.456 -17.922  1.00  0.00              
END
