
#######################################################
#                                                     #
#                        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 T0372TS464_5_2-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected   13 , name T0372_D1.pdb
# PARAMETERS: T0372TS464_5_2-D1.T0372_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:    13        98 - 110         1.37     1.37
  LCS_AVERAGE:     10.32

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13        98 - 110         1.37     1.37
  LCS_AVERAGE:     10.32

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10        99 - 108         0.95     1.91
  LCS_AVERAGE:      7.33

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:  126
LCS_GDT     S      98     S      98      9   13   13     7    7   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     N      99     N      99     10   13   13     7    7   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     M     100     M     100     10   13   13     7    7   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     R     101     R     101     10   13   13     7    7   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     A     102     A     102     10   13   13     7    7   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     D     103     D     103     10   13   13     7    7   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     L     104     L     104     10   13   13     7    7   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     E     105     E     105     10   13   13     5    7   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     A     106     A     106     10   13   13     5    6   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     I     107     I     107     10   13   13     5    6   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     L     108     L     108     10   13   13     5    6   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     P     109     P     109      7   13   13     1    3   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     E     110     E     110      4   13   13     0    6   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_AVERAGE  LCS_A:   9.32  (   7.33   10.32   10.32 )

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      7      7     10     12     13     13     13     13     13     13     13     13     13     13     13     13     13     13     13     13 
GDT PERCENT_CA   5.56   5.56   7.94   9.52  10.32  10.32  10.32  10.32  10.32  10.32  10.32  10.32  10.32  10.32  10.32  10.32  10.32  10.32  10.32  10.32
GDT RMS_LOCAL    0.30   0.30   0.95   1.24   1.37   1.37   1.37   1.37   1.37   1.37   1.37   1.37   1.37   1.37   1.37   1.37   1.37   1.37   1.37   1.37
GDT RMS_ALL_CA   2.80   2.80   1.91   1.39   1.37   1.37   1.37   1.37   1.37   1.37   1.37   1.37   1.37   1.37   1.37   1.37   1.37   1.37   1.37   1.37

#      Molecule1      Molecule2       DISTANCE
LGA    S      98      S      98          1.474
LGA    N      99      N      99          0.977
LGA    M     100      M     100          0.817
LGA    R     101      R     101          0.927
LGA    A     102      A     102          1.154
LGA    D     103      D     103          0.855
LGA    L     104      L     104          1.492
LGA    E     105      E     105          2.283
LGA    A     106      A     106          1.600
LGA    I     107      I     107          1.480
LGA    L     108      L     108          0.658
LGA    P     109      P     109          1.449
LGA    E     110      E     110          1.698

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   13  126    4.0     13    1.37     8.929     9.708     0.886

LGA_LOCAL      RMSD =  1.368  Number of atoms =   13  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.368  Number of atoms =   13 
Std_ALL_ATOMS  RMSD =  1.368  (standard rmsd on all 13 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.916665 * X  +   0.360677 * Y  +   0.172156 * Z  +  95.276085
  Y_new =  -0.098040 * X  +   0.214662 * Y  +  -0.971755 * Z  +  89.018257
  Z_new =  -0.387446 * X  +  -0.907652 * Y  +  -0.161412 * Z  + 108.466339 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.746791    1.394802  [ DEG:  -100.0837     79.9163 ]
  Theta =   0.397859    2.743734  [ DEG:    22.7956    157.2044 ]
  Phi   =  -3.035044    0.106548  [ DEG:  -173.8952      6.1048 ]
 
# 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: T0372TS464_5_2-D1                             
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS464_5_2-D1.T0372_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   13  126   4.0   13   1.37   9.708     1.37
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS464_5_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0372
PARENT N/A
ATOM      1  CA  SER    98      22.953  51.915   7.370  1.00  0.00
ATOM      2  CA  ASN    99      23.197  55.671   7.372  1.00  0.00
ATOM      3  CA  MET   100      25.010  55.584   4.030  1.00  0.00
ATOM      4  CA  ARG   101      21.901  53.952   2.530  1.00  0.00
ATOM      5  CA  ALA   102      19.938  57.016   3.707  1.00  0.00
ATOM      6  CA  ASP   103      22.457  59.440   2.194  1.00  0.00
ATOM      7  CA  LEU   104      22.649  57.496  -1.065  1.00  0.00
ATOM      8  CA  GLU   105      19.228  58.758  -2.135  1.00  0.00
ATOM      9  CA  ALA   106      21.070  62.033  -2.713  1.00  0.00
ATOM     10  CA  ILE   107      24.094  60.402  -4.308  1.00  0.00
ATOM     11  CA  LEU   108      22.646  58.091  -6.904  1.00  0.00
ATOM     12  CA  PRO   109      19.284  56.908  -8.317  1.00  0.00
ATOM     13  CA  GLU   110      20.560  53.338  -8.482  1.00  0.00
TER
END
