
#######################################################
#                                                     #
#                        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    5 (   36),  selected    5 , name T0316TS464_2-D1
# Molecule2: number of CA atoms  188 ( 1493),  selected    5 , name T0316_D1.pdb
# PARAMETERS: T0316TS464_2-D1.T0316_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:     5       189 - 193         2.41     2.41
  LCS_AVERAGE:      2.66

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       189 - 192         1.19     3.53
  LCS_AVERAGE:      2.02

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       189 - 191         0.29     4.21
  LONGEST_CONTINUOUS_SEGMENT:     3       190 - 192         0.76     4.01
  LONGEST_CONTINUOUS_SEGMENT:     3       191 - 193         0.53     5.22
  LCS_AVERAGE:      1.60

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:  188
LCS_GDT     S     189     S     189      3    4    5     3    3    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     T     190     T     190      3    4    5     3    3    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     A     191     A     191      3    4    5     3    3    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     K     192     K     192      3    4    5     0    3    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     K     193     K     193      3    3    5     0    3    3    3    3    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_AVERAGE  LCS_A:   2.09  (   1.60    2.02    2.66 )

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      4      4      4      4      5      5      5      5      5      5      5      5      5      5      5      5      5      5 
GDT PERCENT_CA   1.60   1.60   2.13   2.13   2.13   2.13   2.66   2.66   2.66   2.66   2.66   2.66   2.66   2.66   2.66   2.66   2.66   2.66   2.66   2.66
GDT RMS_LOCAL    0.29   0.29   1.19   1.19   1.19   1.19   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41
GDT RMS_ALL_CA   4.21   4.21   3.53   3.53   3.53   3.53   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41

#      Molecule1      Molecule2       DISTANCE
LGA    S     189      S     189          1.639
LGA    T     190      T     190          2.657
LGA    A     191      A     191          2.102
LGA    K     192      K     192          2.159
LGA    K     193      K     193          3.198

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    5  188    4.0      5    2.41     2.261     2.271     0.199

LGA_LOCAL      RMSD =  2.410  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.410  Number of atoms =    5 
Std_ALL_ATOMS  RMSD =  2.410  (standard rmsd on all 5 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.431861 * X  +   0.370155 * Y  +   0.822485 * Z  + -26.611778
  Y_new =  -0.666750 * X  +  -0.483096 * Y  +   0.567505 * Z  +  50.477364
  Z_new =   0.607404 * X  +  -0.793475 * Y  +   0.038171 * Z  +  22.437595 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.522728    1.618865  [ DEG:   -87.2459     92.7541 ]
  Theta =  -0.652789   -2.488804  [ DEG:   -37.4020   -142.5980 ]
  Phi   =  -0.996033    2.145560  [ DEG:   -57.0685    122.9315 ]
 
# 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: T0316TS464_2-D1                               
REMARK     2: T0316_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS464_2-D1.T0316_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    5  188   4.0    5   2.41   2.271     2.41
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS464_2-D1
PFRMAT TS
TARGET T0316
MODEL 2
PARENT N/A
ATOM    753  N   SER   189      26.091  49.771  14.754  1.00  0.00
ATOM    754  CA  SER   189      24.722  49.376  14.879  1.00  0.00
ATOM    755  CB  SER   189      23.724  50.473  14.471  1.00  0.00
ATOM    756  OG  SER   189      22.393  49.997  14.599  1.00  0.00
ATOM    757  C   SER   189      24.502  48.203  13.993  1.00  0.00
ATOM    758  O   SER   189      25.282  47.941  13.079  1.00  0.00
ATOM    759  N   THR   190      23.432  47.437  14.272  1.00  0.00
ATOM    760  CA  THR   190      23.145  46.321  13.429  1.00  0.00
ATOM    761  CB  THR   190      22.168  45.351  14.025  1.00  0.00
ATOM    762  OG1 THR   190      22.668  44.840  15.251  1.00  0.00
ATOM    763  CG2 THR   190      21.939  44.205  13.025  1.00  0.00
ATOM    764  C   THR   190      22.526  46.882  12.198  1.00  0.00
ATOM    765  O   THR   190      21.562  47.643  12.265  1.00  0.00
ATOM    766  N   ALA   191      23.088  46.534  11.028  1.00  0.00
ATOM    767  CA  ALA   191      22.540  47.028   9.806  1.00  0.00
ATOM    768  CB  ALA   191      23.228  48.310   9.308  1.00  0.00
ATOM    769  C   ALA   191      22.752  45.961   8.788  1.00  0.00
ATOM    770  O   ALA   191      23.669  45.150   8.909  1.00  0.00
ATOM    771  N   LYS   192      21.888  45.918   7.757  1.00  0.00
ATOM    772  CA  LYS   192      22.040  44.900   6.764  1.00  0.00
ATOM    773  CB  LYS   192      20.790  44.023   6.622  1.00  0.00
ATOM    774  CG  LYS   192      20.502  43.235   7.904  1.00  0.00
ATOM    775  CD  LYS   192      19.100  42.632   7.976  1.00  0.00
ATOM    776  CE  LYS   192      18.829  41.849   9.263  1.00  0.00
ATOM    777  NZ  LYS   192      17.452  41.307   9.243  1.00  0.00
ATOM    778  C   LYS   192      22.351  45.576   5.478  1.00  0.00
ATOM    779  O   LYS   192      21.910  46.694   5.219  1.00  0.00
ATOM    780  N   LYS   193      23.186  44.938   4.645  1.00  0.00
ATOM    781  CA  LYS   193      23.546  45.625   3.448  1.00  0.00
ATOM    782  CB  LYS   193      24.316  46.917   3.739  1.00  0.00
ATOM    783  CG  LYS   193      25.702  46.595   4.316  1.00  0.00
ATOM    784  CD  LYS   193      26.647  47.787   4.470  1.00  0.00
ATOM    785  CE  LYS   193      28.013  47.397   5.038  1.00  0.00
ATOM    786  NZ  LYS   193      28.877  48.592   5.156  1.00  0.00
ATOM    787  C   LYS   193      24.544  44.770   2.764  1.00  0.00
ATOM    788  O   LYS   193      25.039  43.790   3.319  1.00  0.00
TER
END
