
#######################################################
#                                                     #
#                        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   12 (   12),  selected   12 , name T0321TS464_5_2-D1
# Molecule2: number of CA atoms   96 (  710),  selected   12 , name T0321_D1.pdb
# PARAMETERS: T0321TS464_5_2-D1.T0321_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:    10         5 - 24          4.86     6.72
  LCS_AVERAGE:      9.90

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7        18 - 24          0.68    20.10
  LCS_AVERAGE:      6.42

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7        18 - 24          0.68    20.10
  LCS_AVERAGE:      6.42

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:   96
LCS_GDT     E       3     E       3      5    5    7     5    5    5    5    5    5    5    5    6    6    6    6    6    7    8    9   10   12   12   12 
LCS_GDT     I       4     I       4      5    5    7     5    5    5    5    5    5    5    5    6    6    6    6    6    7    7    9   10   12   12   12 
LCS_GDT     Y       5     Y       5      5    5   10     5    5    5    5    5    5    5    5    6    6    7    9   10   10   10   10   10   12   12   12 
LCS_GDT     D       6     D       6      5    5   10     5    5    5    5    5    5    5    5    6    6    8    9   10   10   10   10   10   12   12   12 
LCS_GDT     A       7     A       7      5    5   10     5    5    5    5    5    5    5    5    6    6    7    7   10   10   10   10   10   12   12   12 
LCS_GDT     V      18     V      18      7    7   10     5    6    7    7    7    7    7    7    7    7    8    9   10   10   10   10   10   12   12   12 
LCS_GDT     D      19     D      19      7    7   10     5    6    7    7    7    7    7    7    7    7    8    9   10   10   10   10   10   12   12   12 
LCS_GDT     E      20     E      20      7    7   10     5    6    7    7    7    7    7    7    7    7    8    9   10   10   10   10   10   12   12   12 
LCS_GDT     L      21     L      21      7    7   10     5    6    7    7    7    7    7    7    7    7    8    9   10   10   10   10   10   12   12   12 
LCS_GDT     V      22     V      22      7    7   10     3    5    7    7    7    7    7    7    7    7    8    9   10   10   10   10   10   12   12   12 
LCS_GDT     C      23     C      23      7    7   10     3    6    7    7    7    7    7    7    7    7    8    9   10   10   10   10   10   12   12   12 
LCS_GDT     G      24     G      24      7    7   10     5    6    7    7    7    7    7    7    7    7    8    9   10   10   10   10   10   12   12   12 
LCS_AVERAGE  LCS_A:   7.58  (   6.42    6.42    9.90 )

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      6      7      7      7      7      7      7      7      7      8      9     10     10     10     10     10     12     12     12 
GDT PERCENT_CA   5.21   6.25   7.29   7.29   7.29   7.29   7.29   7.29   7.29   7.29   8.33   9.38  10.42  10.42  10.42  10.42  10.42  12.50  12.50  12.50
GDT RMS_LOCAL    0.28   0.43   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   3.67   4.36   4.86   4.86   4.86   4.86   4.86   6.36   6.36   6.36
GDT RMS_ALL_CA  19.37  19.59  20.10  20.10  20.10  20.10  20.10  20.10  20.10  20.10   7.38   7.07   6.72   6.72   6.72   6.72   6.72   6.36   6.36   6.36

#      Molecule1      Molecule2       DISTANCE
LGA    E       3      E       3         35.855
LGA    I       4      I       4         29.460
LGA    Y       5      Y       5         26.684
LGA    D       6      D       6         31.950
LGA    A       7      A       7         30.926
LGA    V      18      V      18          0.566
LGA    D      19      D      19          0.269
LGA    E      20      E      20          0.625
LGA    L      21      L      21          0.393
LGA    V      22      V      22          1.272
LGA    C      23      C      23          0.689
LGA    G      24      G      24          0.423

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   12   96    4.0      7    0.68     7.812     7.518     0.901

LGA_LOCAL      RMSD =  0.677  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 20.096  Number of atoms =   12 
Std_ALL_ATOMS  RMSD =  6.355  (standard rmsd on all 12 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.036095 * X  +  -0.757909 * Y  +  -0.651361 * Z  +  52.538177
  Y_new =  -0.442387 * X  +   0.572327 * Y  +  -0.690461 * Z  + 107.547050
  Z_new =   0.896098 * X  +   0.313075 * Y  +  -0.314631 * Z  +   2.111279 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.358672   -0.782920  [ DEG:   135.1420    -44.8580 ]
  Theta =  -1.110898   -2.030694  [ DEG:   -63.6498   -116.3502 ]
  Phi   =  -1.489386    1.652207  [ DEG:   -85.3355     94.6645 ]
 
# 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: T0321TS464_5_2-D1                             
REMARK     2: T0321_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0321TS464_5_2-D1.T0321_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   12   96   4.0    7   0.68   7.518     6.36
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS464_5_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0321
PARENT N/A
ATOM      1  CA  GLU     3      -5.564  68.130  73.491  1.00  0.00
ATOM      2  CA  ILE     4      -6.596  64.691  72.208  1.00  0.00
ATOM      3  CA  TYR     5      -5.152  62.666  75.104  1.00  0.00
ATOM      4  CA  ASP     6      -6.067  65.365  77.648  1.00  0.00
ATOM      5  CA  ALA     7      -9.551  65.771  76.271  1.00  0.00
ATOM      6  CA  VAL    18     -15.595  55.646  66.091  1.00  0.00
ATOM      7  CA  ASP    19     -15.932  59.055  67.768  1.00  0.00
ATOM      8  CA  GLU    20     -12.973  61.027  66.451  1.00  0.00
ATOM      9  CA  LEU    21     -10.069  60.732  64.097  1.00  0.00
ATOM     10  CA  VAL    22      -6.535  61.838  64.505  1.00  0.00
ATOM     11  CA  CYS    23      -4.919  62.339  61.107  1.00  0.00
ATOM     12  CA  GLY    24      -1.286  63.378  61.393  1.00  0.00
TER
END
