
#######################################################
#                                                     #
#                        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    4 (   31),  selected    4 , name T0298TS022_2_2-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected    4 , name T0298_D1.pdb
# PARAMETERS: T0298TS022_2_2-D1.T0298_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:     4       316 - 319         0.44     0.44
  LCS_AVERAGE:      2.70

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       316 - 319         0.44     0.44
  LCS_AVERAGE:      2.70

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       316 - 319         0.44     0.44
  LCS_AVERAGE:      2.70

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:  148
LCS_GDT     V     316     V     316      4    4    4     3    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4 
LCS_GDT     R     317     R     317      4    4    4     3    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4 
LCS_GDT     K     318     K     318      4    4    4     3    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4 
LCS_GDT     G     319     G     319      4    4    4     0    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4 
LCS_AVERAGE  LCS_A:   2.70  (   2.70    2.70    2.70 )

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      4      4      4      4      4      4      4      4      4      4      4      4      4      4      4      4 
GDT PERCENT_CA   2.03   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70
GDT RMS_LOCAL    0.10   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44
GDT RMS_ALL_CA   0.57   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44   0.44

#      Molecule1      Molecule2       DISTANCE
LGA    V     316      V     316          0.308
LGA    R     317      R     317          0.326
LGA    K     318      K     318          0.295
LGA    G     319      G     319          0.704

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    4  148    4.0      4    0.44     2.703     2.703     0.737

LGA_LOCAL      RMSD =  0.443  Number of atoms =    4  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.443  Number of atoms =    4 
Std_ALL_ATOMS  RMSD =  0.443  (standard rmsd on all 4 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.134445 * X  +  -0.574237 * Y  +   0.807574 * Z  +  56.705803
  Y_new =  -0.969037 * X  +   0.246519 * Y  +   0.013965 * Z  + 214.335236
  Z_new =  -0.207102 * X  +  -0.780692 * Y  +  -0.589600 * Z  +  -8.008121 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.217635    0.923958  [ DEG:  -127.0611     52.9389 ]
  Theta =   0.208612    2.932981  [ DEG:    11.9526    168.0474 ]
  Phi   =  -1.708657    1.432935  [ DEG:   -97.8988     82.1012 ]
 
# 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: T0298TS022_2_2-D1                             
REMARK     2: T0298_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0298TS022_2_2-D1.T0298_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    4  148   4.0    4   0.44   2.703     0.44
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS022_2_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0298
PARENT 1mb4_A
ATOM   2303  N   VAL   316     -13.534  66.010   4.227  1.00  0.00
ATOM   2304  CA  VAL   316     -14.166  65.522   3.041  1.00  0.00
ATOM   2305  C   VAL   316     -15.629  65.847   3.044  1.00  0.00
ATOM   2306  O   VAL   316     -16.112  66.519   2.133  1.00  0.00
ATOM   2307  CB  VAL   316     -14.026  63.994   2.915  1.00  0.00
ATOM   2308  CG1 VAL   316     -14.854  63.477   1.748  1.00  0.00
ATOM   2309  CG2 VAL   316     -12.573  63.609   2.679  1.00  0.00
ATOM   2310  N   ARG   317     -16.388  65.382   4.060  1.00  0.00
ATOM   2311  CA  ARG   317     -17.807  65.592   3.961  1.00  0.00
ATOM   2312  C   ARG   317     -18.201  67.031   4.097  1.00  0.00
ATOM   2313  O   ARG   317     -18.735  67.632   3.165  1.00  0.00
ATOM   2314  CB  ARG   317     -18.541  64.821   5.060  1.00  0.00
ATOM   2315  CG  ARG   317     -18.513  63.312   4.884  1.00  0.00
ATOM   2316  CD  ARG   317     -19.277  62.612   5.997  1.00  0.00
ATOM   2317  NE  ARG   317     -19.252  61.158   5.847  1.00  0.00
ATOM   2318  CZ  ARG   317     -19.886  60.313   6.653  1.00  0.00
ATOM   2319  NH1 ARG   317     -19.807  59.007   6.441  1.00  0.00
ATOM   2320  NH2 ARG   317     -20.600  60.777   7.670  1.00  0.00
ATOM   2321  N   LYS   318     -17.915  67.630   5.271  1.00  0.00
ATOM   2322  CA  LYS   318     -18.347  68.972   5.552  1.00  0.00
ATOM   2323  C   LYS   318     -17.553  69.915   4.725  1.00  0.00
ATOM   2324  O   LYS   318     -18.084  70.864   4.150  1.00  0.00
ATOM   2325  CB  LYS   318     -18.143  69.302   7.032  1.00  0.00
ATOM   2326  CG  LYS   318     -18.630  70.685   7.432  1.00  0.00
ATOM   2327  CD  LYS   318     -20.141  70.795   7.310  1.00  0.00
ATOM   2328  CE  LYS   318     -20.640  72.136   7.820  1.00  0.00
ATOM   2329  NZ  LYS   318     -22.119  72.262   7.699  1.00  0.00
ATOM   2330  N   GLY   319     -16.237  69.660   4.654  1.00  0.00
ATOM   2331  CA  GLY   319     -15.369  70.534   3.933  1.00  0.00
ATOM   2332  C   GLY   319     -15.501  70.170   2.465  1.00  0.00
ATOM   2333  O   GLY   319     -14.729  70.731   1.644  1.00  0.00
TER
END
