
#######################################################
#                                                     #
#                        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_3-D1
# Molecule2: number of CA atoms  214 ( 1760),  selected   22 , name T0320_D1.pdb
# PARAMETERS: T0320TS599_3-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:    22       206 - 227         4.60     4.60
  LCS_AVERAGE:     10.28

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       211 - 223         1.89     8.37
  LONGEST_CONTINUOUS_SEGMENT:    13       212 - 224         1.90     8.34
  LCS_AVERAGE:      5.48

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       215 - 223         0.77    10.77
  LCS_AVERAGE:      3.10

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      0   11   22     1    1    3    8   10   11   13   14   15   17   18   18   19   20   20   21   22   22   22   22 
LCS_GDT     L     207     L     207      0   11   22     0    1    3    8   10   11   13   14   15   17   18   18   19   20   20   21   22   22   22   22 
LCS_GDT     Y     208     Y     208      7   11   22     4    7    7    7    9   11   11   12   15   15   16   16   17   18   19   21   22   22   22   22 
LCS_GDT     S     209     S     209      7   11   22     4    7    7    7   10   11   13   14   16   17   18   18   19   20   20   21   22   22   22   22 
LCS_GDT     N     210     N     210      7   11   22     4    7    7    8   10   12   14   15   16   17   18   18   19   20   20   21   22   22   22   22 
LCS_GDT     E     211     E     211      7   13   22     4    7    9   12   12   13   14   15   16   17   18   18   19   20   20   21   22   22   22   22 
LCS_GDT     P     212     P     212      7   13   22     4    7    9   12   12   13   14   15   16   17   18   18   19   20   20   21   22   22   22   22 
LCS_GDT     I     213     I     213      7   13   22     4    7    9   12   12   13   14   15   16   17   18   18   19   20   20   21   22   22   22   22 
LCS_GDT     C     214     C     214      7   13   22     4    7    9   12   12   13   14   15   16   17   18   18   19   20   20   21   22   22   22   22 
LCS_GDT     G     215     G     215      9   13   22     4    6    9   12   12   13   14   15   16   17   18   18   19   20   20   21   22   22   22   22 
LCS_GDT     L     216     L     216      9   13   22     4    8    9   12   12   13   14   15   16   17   18   18   19   20   20   21   22   22   22   22 
LCS_GDT     Y     217     Y     217      9   13   22     5    8    9   12   12   13   14   15   16   17   18   18   19   20   20   21   22   22   22   22 
LCS_GDT     G     218     G     218      9   13   22     5    8    9   12   12   13   14   15   16   17   18   18   19   20   20   21   22   22   22   22 
LCS_GDT     K     219     K     219      9   13   22     5    8    9   12   12   13   14   15   16   17   18   18   19   20   20   21   22   22   22   22 
LCS_GDT     G     220     G     220      9   13   22     5    8    9   12   12   13   14   15   16   17   18   18   19   20   20   21   22   22   22   22 
LCS_GDT     F     221     F     221      9   13   22     4    8    9   11   12   13   14   15   16   17   18   18   19   20   20   21   22   22   22   22 
LCS_GDT     T     222     T     222      9   13   22     4    8    9   11   12   12   14   15   15   16   17   18   19   20   20   21   22   22   22   22 
LCS_GDT     S     223     S     223      9   13   22     5    8    9   11   12   12   14   15   15   16   16   16   19   20   20   20   22   22   22   22 
LCS_GDT     I     224     I     224      4   13   22     3    3    9   12   12   13   14   15   16   17   18   18   19   20   20   21   22   22   22   22 
LCS_GDT     G     225     G     225      4    9   22     3    6    9   12   12   13   14   15   16   17   18   18   19   20   20   21   22   22   22   22 
LCS_GDT     G     226     G     226      4    6   22     3    4    7    7    7   11   12   15   16   17   18   18   19   20   20   21   22   22   22   22 
LCS_GDT     I     227     I     227      4    6   22     0    3    7    7    7    8    8   10   10   11   12   12   12   14   20   21   22   22   22   22 
LCS_AVERAGE  LCS_A:   6.29  (   3.10    5.48   10.28 )

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      8      9     12     12     13     14     15     16     17     18     18     19     20     20     21     22     22     22     22 
GDT PERCENT_CA   2.34   3.74   4.21   5.61   5.61   6.07   6.54   7.01   7.48   7.94   8.41   8.41   8.88   9.35   9.35   9.81  10.28  10.28  10.28  10.28
GDT RMS_LOCAL    0.11   0.60   0.77   1.45   1.45   1.65   2.12   2.24   2.84   3.07   3.34   3.34   3.61   3.90   3.90   4.32   4.60   4.60   4.60   4.60
GDT RMS_ALL_CA  10.61  11.10  10.77   6.23   6.23   6.31   7.59   6.99   5.03   4.85   4.75   4.75   4.73   4.81   4.81   4.64   4.60   4.60   4.60   4.60

#      Molecule1      Molecule2       DISTANCE
LGA    L     206      L     206         11.498
LGA    L     207      L     207         13.266
LGA    Y     208      Y     208         17.594
LGA    S     209      S     209         12.141
LGA    N     210      N     210          7.408
LGA    E     211      E     211          3.844
LGA    P     212      P     212          0.904
LGA    I     213      I     213          2.434
LGA    C     214      C     214          1.222
LGA    G     215      G     215          1.044
LGA    L     216      L     216          0.541
LGA    Y     217      Y     217          1.047
LGA    G     218      G     218          2.243
LGA    K     219      K     219          2.360
LGA    G     220      G     220          1.348
LGA    F     221      F     221          1.712
LGA    T     222      T     222          3.175
LGA    S     223      S     223          3.662
LGA    I     224      I     224          2.275
LGA    G     225      G     225          3.228
LGA    G     226      G     226          9.932
LGA    I     227      I     227         15.361

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   22  214    4.0     15    2.24     6.542     6.359     0.640

LGA_LOCAL      RMSD =  2.245  Number of atoms =   15  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.491  Number of atoms =   22 
Std_ALL_ATOMS  RMSD =  4.605  (standard rmsd on all 22 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.438545 * X  +  -0.800825 * Y  +  -0.407870 * Z  +  12.939664
  Y_new =  -0.450067 * X  +   0.588529 * Y  +  -0.671621 * Z  +  26.252592
  Z_new =   0.777893 * X  +  -0.110968 * Y  +  -0.618521 * Z  +  14.053626 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.964073    0.177519  [ DEG:  -169.8289     10.1711 ]
  Theta =  -0.891306   -2.250286  [ DEG:   -51.0681   -128.9319 ]
  Phi   =  -2.343230    0.798363  [ DEG:  -134.2572     45.7428 ]
 
# 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_3-D1                               
REMARK     2: T0320_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320TS599_3-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   15   2.24   6.359     4.60
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS599_3-D1
PFRMAT TS                                                                       
TARGET T0320                                                                    
MODEL  3                                                                        
PARENT N/A                                                                      
ATOM    206  CA  LEU   206       1.660  30.962   9.265  1.00  0.00              
ATOM    207  CA  LEU   207       2.089  34.397   6.869  1.00  0.00              
ATOM    208  CA  TYR   208       3.126  38.496   6.907  1.00  0.00              
ATOM    209  CA  SER   209       1.402  35.406   8.974  1.00  0.00              
ATOM    210  CA  ASN   210       3.438  35.509  12.047  1.00  0.00              
ATOM    211  CA  GLU   211       4.840  32.049  11.968  1.00  0.00              
ATOM    212  CA  PRO   212       8.363  31.480  13.174  1.00  0.00              
ATOM    213  CA  ILE   213      10.339  29.559  10.400  1.00  0.00              
ATOM    214  CA  CYS   214      13.202  28.385  10.110  1.00  0.00              
ATOM    215  CA  GLY   215      14.489  27.409   6.279  1.00  0.00              
ATOM    216  CA  LEU   216      16.507  24.610   6.371  1.00  0.00              
ATOM    217  CA  TYR   217      14.157  22.700   8.701  1.00  0.00              
ATOM    218  CA  GLY   218      10.897  23.439   6.816  1.00  0.00              
ATOM    219  CA  LYS   219      12.479  22.452   3.610  1.00  0.00              
ATOM    220  CA  GLY   220      13.612  19.063   4.764  1.00  0.00              
ATOM    221  CA  PHE   221      17.293  19.599   5.312  1.00  0.00              
ATOM    222  CA  THR   222      18.437  17.408   8.068  1.00  0.00              
ATOM    223  CA  SER   223      21.447  19.360   9.784  1.00  0.00              
ATOM    224  CA  ILE   224      20.508  19.927  13.506  1.00  0.00              
ATOM    225  CA  GLY   225      23.734  20.142  15.187  1.00  0.00              
ATOM    226  CA  GLY   226      23.980  18.964  18.730  1.00  0.00              
ATOM    227  CA  ILE   227      21.402  21.155  20.476  1.00  0.00              
TER                                                                             
END
