
#######################################################
#                                                     #
#                        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   13 (   13),  selected   13 , name T0318TS464_4-D2
# Molecule2: number of CA atoms  335 ( 2465),  selected   13 , name T0318_D2.pdb
# PARAMETERS: T0318TS464_4-D2.T0318_D2.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:    13       159 - 489         3.21     3.21
  LCS_AVERAGE:      3.88

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       163 - 488         1.35     3.97
  LCS_AVERAGE:      1.95

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       163 - 485         0.96     3.80
  LONGEST_CONTINUOUS_SEGMENT:     5       482 - 486         0.81     3.86
  LCS_AVERAGE:      1.22

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:  335
LCS_GDT     D     159     D     159      3    3   13     0    3    3    3    3    4    4    4    5    5   10   13   13   13   13   13   13   13   13   13 
LCS_GDT     A     160     A     160      3    3   13     4    5    6    7    8    9   10   12   12   12   12   13   13   13   13   13   13   13   13   13 
LCS_GDT     V     161     V     161      3    6   13     1    3    6    7    9    9   10   12   12   12   12   13   13   13   13   13   13   13   13   13 
LCS_GDT     F     162     F     162      3    6   13     0    3    3    4    5    7    9   12   12   12   12   13   13   13   13   13   13   13   13   13 
LCS_GDT     L     163     L     163      5    8   13     3    4    6    7    9    9   10   12   12   12   12   13   13   13   13   13   13   13   13   13 
LCS_GDT     K     482     K     482      5    8   13     3    4    6    7    9    9   10   12   12   12   12   13   13   13   13   13   13   13   13   13 
LCS_GDT     Y     483     Y     483      5    8   13     4    5    6    7    9    9   10   12   12   12   12   13   13   13   13   13   13   13   13   13 
LCS_GDT     T     484     T     484      5    8   13     4    5    6    7    9    9   10   12   12   12   12   13   13   13   13   13   13   13   13   13 
LCS_GDT     S     485     S     485      5    8   13     3    5    6    7    9    9   10   12   12   12   12   13   13   13   13   13   13   13   13   13 
LCS_GDT     V     486     V     486      5    8   13     4    5    6    7    9    9   10   12   12   12   12   13   13   13   13   13   13   13   13   13 
LCS_GDT     P     487     P     487      4    8   13     3    3    6    7    9    9   10   12   12   12   12   13   13   13   13   13   13   13   13   13 
LCS_GDT     M     488     M     488      4    8   13     1    3    5    7    9    9   10   12   12   12   12   13   13   13   13   13   13   13   13   13 
LCS_GDT     L     489     L     489      3    3   13     0    3    3    3    5    6    6   12   12   12   12   13   13   13   13   13   13   13   13   13 
LCS_AVERAGE  LCS_A:   2.35  (   1.22    1.95    3.88 )

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      4      5      6      7      9      9     10     12     12     12     12     13     13     13     13     13     13     13     13     13 
GDT PERCENT_CA   1.19   1.49   1.79   2.09   2.69   2.69   2.99   3.58   3.58   3.58   3.58   3.88   3.88   3.88   3.88   3.88   3.88   3.88   3.88   3.88
GDT RMS_LOCAL    0.18   0.52   0.79   1.03   1.66   1.66   1.94   2.63   2.63   2.63   2.63   3.21   3.21   3.21   3.21   3.21   3.21   3.21   3.21   3.21
GDT RMS_ALL_CA   4.79   4.09   3.97   4.03   3.68   3.68   3.48   3.27   3.27   3.27   3.27   3.21   3.21   3.21   3.21   3.21   3.21   3.21   3.21   3.21

#      Molecule1      Molecule2       DISTANCE
LGA    D     159      D     159          6.583
LGA    A     160      A     160          2.264
LGA    V     161      V     161          1.899
LGA    F     162      F     162          3.553
LGA    L     163      L     163          3.691
LGA    K     482      K     482          3.610
LGA    Y     483      Y     483          2.430
LGA    T     484      T     484          1.561
LGA    S     485      S     485          2.030
LGA    V     486      V     486          2.273
LGA    P     487      P     487          1.872
LGA    M     488      M     488          3.608
LGA    L     489      L     489          3.794

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   13  335    4.0     12    2.63     2.761     2.670     0.440

LGA_LOCAL      RMSD =  2.630  Number of atoms =   12  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.280  Number of atoms =   13 
Std_ALL_ATOMS  RMSD =  3.207  (standard rmsd on all 13 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.359959 * X  +  -0.647492 * Y  +  -0.671702 * Z  + 200.612808
  Y_new =  -0.620885 * X  +  -0.371131 * Y  +   0.690481 * Z  +  -9.773436
  Z_new =  -0.696371 * X  +   0.665594 * Y  +  -0.268426 * Z  +  90.073219 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.954134   -1.187459  [ DEG:   111.9636    -68.0364 ]
  Theta =   0.770328    2.371265  [ DEG:    44.1365    135.8635 ]
  Phi   =  -2.096194    1.045399  [ DEG:  -120.1031     59.8969 ]
 
# 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: T0318TS464_4-D2                               
REMARK     2: T0318_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0318TS464_4-D2.T0318_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   13  335   4.0   12   2.63   2.670     3.21
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS464_4-D2
PFRMAT TS
TARGET T0318
MODEL 4
PARENT N/A
ATOM     70  CA  ASP   159      29.972  30.490  11.518  1.00  0.00
ATOM     71  CA  ALA   160      26.465  31.625  12.494  1.00  0.00
ATOM     72  CA  VAL   161      25.028  34.955  11.289  1.00  0.00
ATOM     73  CA  PHE   162      23.052  36.836  13.932  1.00  0.00
ATOM     74  CA  LEU   163      20.111  39.171  13.245  1.00  0.00
ATOM     75  CA  LYS   482       9.072  25.667  14.043  1.00  0.00
ATOM     76  CA  TYR   483       9.336  26.967  10.486  1.00  0.00
ATOM     77  CA  THR   484      12.678  28.693   9.821  1.00  0.00
ATOM     78  CA  SER   485      15.179  26.474   7.932  1.00  0.00
ATOM     79  CA  VAL   486      17.990  27.864  10.108  1.00  0.00
ATOM     80  CA  PRO   487      17.796  27.688  13.907  1.00  0.00
ATOM     81  CA  MET   488      16.487  30.712  15.827  1.00  0.00
ATOM     82  CA  LEU   489      18.546  32.140  18.691  1.00  0.00
TER
END
