
#######################################################
#                                                     #
#                        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   10 (   10),  selected   10 , name T0342TS464_4_2-D1
# Molecule2: number of CA atoms  122 (  967),  selected   10 , name T0342_D1.pdb
# PARAMETERS: T0342TS464_4_2-D1.T0342_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:     9        78 - 86          4.80    10.90
  LONGEST_CONTINUOUS_SEGMENT:     9        79 - 135         4.65     5.58
  LCS_AVERAGE:      7.38

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        84 - 135         1.80     8.53
  LCS_AVERAGE:      2.79

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3        78 - 80          0.55    15.26
  LONGEST_CONTINUOUS_SEGMENT:     3        81 - 83          0.57    10.01
  LONGEST_CONTINUOUS_SEGMENT:     3        82 - 84          0.40    14.16
  LONGEST_CONTINUOUS_SEGMENT:     3        83 - 85          0.70    11.52
  LONGEST_CONTINUOUS_SEGMENT:     3        84 - 86          0.52    16.20
  LONGEST_CONTINUOUS_SEGMENT:     3        85 - 135         0.63     7.61
  LCS_AVERAGE:      2.46

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:  122
LCS_GDT     E      78     E      78      3    3    9     0    3    3    3    3    3    4    4    5    6    7    8    8    9    9   10   10   10   10   10 
LCS_GDT     V      79     V      79      3    3    9     1    3    3    3    3    3    5    5    6    6    8    8    9    9    9   10   10   10   10   10 
LCS_GDT     W      80     W      80      3    3    9     0    3    3    3    3    4    5    5    6    8    8    8    9    9    9   10   10   10   10   10 
LCS_GDT     G      81     G      81      3    3    9     0    3    3    3    3    4    5    5    7    8    8    8    9    9    9   10   10   10   10   10 
LCS_GDT     V      82     V      82      3    3    9     3    3    3    3    3    4    5    6    7    8    8    8    9    9    9   10   10   10   10   10 
LCS_GDT     V      83     V      83      3    3    9     3    3    3    3    3    4    5    6    7    8    8    8    9    9    9   10   10   10   10   10 
LCS_GDT     W      84     W      84      3    4    9     3    3    3    3    3    4    5    6    7    8    8    8    9    9    9   10   10   10   10   10 
LCS_GDT     K      85     K      85      3    4    9     1    3    3    3    3    4    5    6    7    8    8    8    9    9    9   10   10   10   10   10 
LCS_GDT     M      86     M      86      3    4    9     1    3    3    3    3    4    5    6    7    8    8    8    9    9    9   10   10   10   10   10 
LCS_GDT     P     135     P     135      3    4    9     0    3    3    3    3    4    5    6    7    8    8    8    9    9    9   10   10   10   10   10 
LCS_AVERAGE  LCS_A:   4.21  (   2.46    2.79    7.38 )

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      3      3      3      3      4      5      6      7      8      8      8      9      9      9     10     10     10     10     10 
GDT PERCENT_CA   2.46   2.46   2.46   2.46   2.46   3.28   4.10   4.92   5.74   6.56   6.56   6.56   7.38   7.38   7.38   8.20   8.20   8.20   8.20   8.20
GDT RMS_LOCAL    0.40   0.40   0.40   0.40   0.40   1.80   2.41   3.22   3.62   3.99   3.99   3.99   4.65   4.80   4.80   5.28   5.28   5.28   5.28   5.28
GDT RMS_ALL_CA  14.16  14.16  14.16  14.16  14.16   8.53   8.73   6.76   6.04   6.02   6.02   6.02   5.58  10.90  10.90   5.28   5.28   5.28   5.28   5.28

#      Molecule1      Molecule2       DISTANCE
LGA    E      78      E      78         12.056
LGA    V      79      V      79          9.195
LGA    W      80      W      80          6.601
LGA    G      81      G      81          4.811
LGA    V      82      V      82          3.424
LGA    V      83      V      83          3.665
LGA    W      84      W      84          3.673
LGA    K      85      K      85          3.239
LGA    M      86      M      86          3.422
LGA    P     135      P     135          2.786

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   10  122    4.0      6    3.22     4.508     4.098     0.181

LGA_LOCAL      RMSD =  3.219  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.043  Number of atoms =   10 
Std_ALL_ATOMS  RMSD =  5.278  (standard rmsd on all 10 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.459582 * X  +  -0.771036 * Y  +  -0.440780 * Z  + 126.111343
  Y_new =  -0.864073 * X  +  -0.502920 * Y  +  -0.021197 * Z  + 163.882523
  Z_new =  -0.205333 * X  +   0.390608 * Y  +  -0.897365 * Z  +  -9.572690 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.731044   -0.410549  [ DEG:   156.4773    -23.5227 ]
  Theta =   0.206804    2.934788  [ DEG:    11.8490    168.1510 ]
  Phi   =  -1.081972    2.059621  [ DEG:   -61.9924    118.0076 ]
 
# 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: T0342TS464_4_2-D1                             
REMARK     2: T0342_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0342TS464_4_2-D1.T0342_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   10  122   4.0    6   3.22   4.098     5.28
REMARK  ---------------------------------------------------------- 
MOLECULE T0342TS464_4_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0342
PARENT N/A
ATOM      6  CA  GLU    78       9.639  85.133   6.677  1.00  0.00
ATOM      7  CA  VAL    79       6.286  86.385   5.422  1.00  0.00
ATOM      8  CA  TRP    80       7.671  87.562   2.078  1.00  0.00
ATOM      9  CA  GLY    81       9.276  84.145   1.535  1.00  0.00
ATOM     10  CA  VAL    82       5.902  82.442   2.012  1.00  0.00
ATOM     11  CA  VAL    83       4.060  84.876  -0.269  1.00  0.00
ATOM     12  CA  TRP    84       6.584  84.331  -3.087  1.00  0.00
ATOM     13  CA  LYS    85       6.428  80.572  -2.602  1.00  0.00
ATOM     14  CA  MET    86       2.645  80.610  -3.054  1.00  0.00
ATOM     15  CA  PRO   135      -0.164  95.392  20.644  1.00  0.00
TER
END
