
#######################################################
#                                                     #
#                        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 (   22),  selected   22 , name T0320TS599_5-D1
# Molecule2: number of CA atoms  214 ( 1760),  selected   22 , name T0320_D1.pdb
# PARAMETERS: T0320TS599_5-D1.T0320_D1.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:    20       208 - 227         4.52     6.72
  LCS_AVERAGE:      9.18

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       212 - 224         1.94     9.91
  LONGEST_CONTINUOUS_SEGMENT:    13       213 - 225         2.00     9.76
  LCS_AVERAGE:      5.20

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       215 - 223         0.76    12.10
  LCS_AVERAGE:      3.31

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:  214
LCS_GDT     L     206     L     206      3    4   16     0    0    3    3    4    4    4    5    5    6    6    8   10   11   11   14   14   15   16   16 
LCS_GDT     L     207     L     207      3    4   16     0    1    3    3    4    4    6    7    9   10   10   10   13   15   15   15   16   17   20   21 
LCS_GDT     Y     208     Y     208      7    9   20     3    7    7    7    8    9    9   10   13   13   14   14   14   15   19   20   20   20   20   21 
LCS_GDT     S     209     S     209      7    9   20     4    7    7    7    8    9   11   12   13   15   16   18   18   19   19   20   20   20   20   21 
LCS_GDT     N     210     N     210      7   11   20     4    7    7    7    8   10   13   16   16   17   18   18   18   19   19   20   20   20   20   21 
LCS_GDT     E     211     E     211      7   12   20     4    7    7    8   10   12   15   16   16   17   18   18   18   19   19   20   20   20   20   21 
LCS_GDT     P     212     P     212      7   13   20     4    7    7   11   12   13   15   16   16   17   18   18   18   19   19   20   20   20   20   21 
LCS_GDT     I     213     I     213      7   13   20     4    7    7    8   11   13   15   16   16   17   18   18   18   19   19   20   20   20   20   21 
LCS_GDT     C     214     C     214      7   13   20     4    7    7   11   12   13   15   16   16   17   18   18   18   19   19   20   20   20   20   21 
LCS_GDT     G     215     G     215      9   13   20     5    7    9   11   12   13   15   16   16   17   18   18   18   19   19   20   20   20   20   21 
LCS_GDT     L     216     L     216      9   13   20     5    7    9   11   12   13   15   16   16   17   18   18   18   19   19   20   20   20   20   21 
LCS_GDT     Y     217     Y     217      9   13   20     5    7    9   11   12   13   15   16   16   17   18   18   18   19   19   20   20   20   20   21 
LCS_GDT     G     218     G     218      9   13   20     5    7    9   11   12   13   15   16   16   17   18   18   18   19   19   20   20   20   20   21 
LCS_GDT     K     219     K     219      9   13   20     5    7    9   11   12   13   15   16   16   17   18   18   18   19   19   20   20   20   20   21 
LCS_GDT     G     220     G     220      9   13   20     5    7    9   11   12   13   15   16   16   17   18   18   18   19   19   20   20   20   20   21 
LCS_GDT     F     221     F     221      9   13   20     5    7    9   11   12   13   15   16   16   17   18   18   18   19   19   20   20   20   20   21 
LCS_GDT     T     222     T     222      9   13   20     5    7    9   11   12   13   15   16   16   17   18   18   18   19   19   20   20   20   20   21 
LCS_GDT     S     223     S     223      9   13   20     5    7    9   10   11   12   14   14   15   17   18   18   18   19   19   20   20   20   20   21 
LCS_GDT     I     224     I     224      5   13   20     3    7    9   11   12   13   15   16   16   17   18   18   18   19   19   20   20   20   20   21 
LCS_GDT     G     225     G     225      5   13   20     3    4    8   10   12   13   15   16   16   17   18   18   18   19   19   20   20   20   20   21 
LCS_GDT     G     226     G     226      5    7   20     3    4    6    6    9   12   15   16   16   17   18   18   18   19   19   20   20   20   20   21 
LCS_GDT     I     227     I     227      5    7   20     0    4    6    6    9   11   13   14   15   17   18   18   18   19   19   20   20   20   20   21 
LCS_AVERAGE  LCS_A:   5.90  (   3.31    5.20    9.18 )

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      5      7      9     11     12     13     15     16     16     17     18     18     18     19     19     20     20     20     20     21 
GDT PERCENT_CA   2.34   3.27   4.21   5.14   5.61   6.07   7.01   7.48   7.48   7.94   8.41   8.41   8.41   8.88   8.88   9.35   9.35   9.35   9.35   9.81
GDT RMS_LOCAL    0.22   0.46   0.76   1.48   1.57   1.81   2.35   2.62   2.62   2.88   3.13   3.13   3.13   3.70   3.70   4.52   4.52   4.52   4.52   5.37
GDT RMS_ALL_CA  12.53  12.14  12.10   9.93   9.74   9.32   8.39   7.89   7.89   8.46   7.91   7.91   7.91   7.25   7.25   6.72   6.72   6.72   6.72   6.45

#      Molecule1      Molecule2       DISTANCE
LGA    L     206      L     206         21.033
LGA    L     207      L     207         17.040
LGA    Y     208      Y     208         13.491
LGA    S     209      S     209          8.342
LGA    N     210      N     210          3.600
LGA    E     211      E     211          2.722
LGA    P     212      P     212          3.920
LGA    I     213      I     213          1.827
LGA    C     214      C     214          2.001
LGA    G     215      G     215          1.163
LGA    L     216      L     216          1.049
LGA    Y     217      Y     217          2.071
LGA    G     218      G     218          3.593
LGA    K     219      K     219          3.345
LGA    G     220      G     220          2.109
LGA    F     221      F     221          1.453
LGA    T     222      T     222          3.420
LGA    S     223      S     223          5.877
LGA    I     224      I     224          3.191
LGA    G     225      G     225          3.544
LGA    G     226      G     226          3.183
LGA    I     227      I     227          6.403

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   22  214    4.0     16    2.62     6.308     6.201     0.587

LGA_LOCAL      RMSD =  2.624  Number of atoms =   16  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.339  Number of atoms =   22 
Std_ALL_ATOMS  RMSD =  6.350  (standard rmsd on all 22 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.865777 * X  +  -0.383518 * Y  +  -0.321471 * Z  +  15.700615
  Y_new =   0.438516 * X  +   0.890929 * Y  +   0.118111 * Z  +  30.641777
  Z_new =   0.241110 * X  +  -0.243228 * Y  +   0.939524 * Z  +   6.814929 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.253322    2.888270  [ DEG:   -14.5143    165.4857 ]
  Theta =  -0.243510   -2.898083  [ DEG:   -13.9521   -166.0479 ]
  Phi   =   0.468834   -2.672759  [ DEG:    26.8622   -153.1378 ]
 
# 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: T0320TS599_5-D1                               
REMARK     2: T0320_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320TS599_5-D1.T0320_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   22  214   4.0   16   2.62   6.201     6.35
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS599_5-D1
PFRMAT TS                                                                       
TARGET T0320                                                                    
MODEL  5                                                                        
PARENT N/A                                                                      
ATOM    206  CA  LEU   206      -2.952  37.622   4.132  1.00  0.00              
ATOM    207  CA  LEU   207      -0.571  38.316   7.308  1.00  0.00              
ATOM    208  CA  TYR   208       0.893  35.766  10.151  1.00  0.00              
ATOM    209  CA  SER   209      -0.481  32.093  11.633  1.00  0.00              
ATOM    210  CA  ASN   210       1.455  31.827  14.883  1.00  0.00              
ATOM    211  CA  GLU   211       3.413  28.585  14.258  1.00  0.00              
ATOM    212  CA  PRO   212       6.982  28.308  15.301  1.00  0.00              
ATOM    213  CA  ILE   213       8.876  27.517  12.110  1.00  0.00              
ATOM    214  CA  CYS   214      12.633  27.197  11.840  1.00  0.00              
ATOM    215  CA  GLY   215      13.750  27.266   7.956  1.00  0.00              
ATOM    216  CA  LEU   216      16.342  24.436   7.495  1.00  0.00              
ATOM    217  CA  TYR   217      14.120  22.283   9.773  1.00  0.00              
ATOM    218  CA  GLY   218      10.751  22.917   8.115  1.00  0.00              
ATOM    219  CA  LYS   219      12.084  22.105   4.735  1.00  0.00              
ATOM    220  CA  GLY   220      13.573  18.799   5.766  1.00  0.00              
ATOM    221  CA  PHE   221      17.319  19.511   5.575  1.00  0.00              
ATOM    222  CA  THR   222      18.942  17.789   8.475  1.00  0.00              
ATOM    223  CA  SER   223      22.676  18.351   7.660  1.00  0.00              
ATOM    224  CA  ILE   224      23.591  20.971  10.092  1.00  0.00              
ATOM    225  CA  GLY   225      27.306  21.019   9.973  1.00  0.00              
ATOM    226  CA  GLY   226      29.210  22.533  12.776  1.00  0.00              
ATOM    227  CA  ILE   227      27.956  26.136  12.958  1.00  0.00              
TER                                                                             
END
