
#######################################################
#                                                     #
#                        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 (    5),  selected    5 , name T0301TS464_3_2-D2
# Molecule2: number of CA atoms  191 ( 1389),  selected    5 , name T0301_D2.pdb
# PARAMETERS: T0301TS464_3_2-D2.T0301_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:     5       319 - 323         2.74     2.74
  LCS_AVERAGE:      2.62

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       319 - 322         1.26     3.77
  LCS_AVERAGE:      1.99

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       319 - 321         0.32     5.41
  LONGEST_CONTINUOUS_SEGMENT:     3       320 - 322         0.95     4.22
  LONGEST_CONTINUOUS_SEGMENT:     3       321 - 323         0.44     5.60
  LCS_AVERAGE:      1.57

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:  191
LCS_GDT     T     319     T     319      3    4    5     3    3    3    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     A     320     A     320      3    4    5     3    3    3    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     A     321     A     321      3    4    5     3    3    3    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     V     322     V     322      3    4    5     3    3    3    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     A     323     A     323      3    3    5     3    3    3    3    3    3    4    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_AVERAGE  LCS_A:   2.06  (   1.57    1.99    2.62 )

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      4      4      4      4      5      5      5      5      5      5      5      5      5      5      5      5      5 
GDT PERCENT_CA   1.57   1.57   1.57   2.09   2.09   2.09   2.09   2.62   2.62   2.62   2.62   2.62   2.62   2.62   2.62   2.62   2.62   2.62   2.62   2.62
GDT RMS_LOCAL    0.32   0.32   0.32   1.26   1.26   1.26   1.26   2.74   2.74   2.74   2.74   2.74   2.74   2.74   2.74   2.74   2.74   2.74   2.74   2.74
GDT RMS_ALL_CA   5.41   5.41   5.41   3.77   3.77   3.77   3.77   2.74   2.74   2.74   2.74   2.74   2.74   2.74   2.74   2.74   2.74   2.74   2.74   2.74

#      Molecule1      Molecule2       DISTANCE
LGA    T     319      T     319          1.767
LGA    A     320      A     320          2.786
LGA    A     321      A     321          2.389
LGA    V     322      V     322          2.509
LGA    A     323      A     323          3.842

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    5  191    4.0      5    2.74     2.225     2.167     0.176

LGA_LOCAL      RMSD =  2.744  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.744  Number of atoms =    5 
Std_ALL_ATOMS  RMSD =  2.744  (standard rmsd on all 5 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.609697 * X  +   0.411837 * Y  +   0.677244 * Z  +  -9.908601
  Y_new =  -0.755035 * X  +   0.041724 * Y  +   0.654356 * Z  + -25.884172
  Z_new =   0.241231 * X  +  -0.910302 * Y  +   0.336390 * Z  +  37.175953 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.216824    1.924769  [ DEG:   -69.7189    110.2811 ]
  Theta =  -0.243634   -2.897959  [ DEG:   -13.9592   -166.0408 ]
  Phi   =  -0.891494    2.250099  [ DEG:   -51.0788    128.9212 ]
 
# 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: T0301TS464_3_2-D2                             
REMARK     2: T0301_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0301TS464_3_2-D2.T0301_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    5  191   4.0    5   2.74   2.167     2.74
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS464_3_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0301
PARENT N/A
ATOM     29  CA  THR   319      90.919  15.629  10.875  1.00  0.00
ATOM     30  CA  ALA   320      92.441  13.902  13.878  1.00  0.00
ATOM     31  CA  ALA   321      92.009  10.203  13.155  1.00  0.00
ATOM     32  CA  VAL   322      90.484   8.264  10.254  1.00  0.00
ATOM     33  CA  ALA   323      88.796   5.049  11.368  1.00  0.00
TER
END
