
#######################################################
#                                                     #
#                        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    3 (   25),  selected    3 , name T0318TS338_4-D1
# Molecule2: number of CA atoms  154 ( 1200),  selected    3 , name T0318_D1.pdb
# PARAMETERS: T0318TS338_4-D1.T0318_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
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3       153 - 155         0.16     0.16
  LCS_AVERAGE:      1.95

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       153 - 155         0.16     0.16
  LCS_AVERAGE:      1.95

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       153 - 155         0.16     0.16
  LCS_AVERAGE:      1.95

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:  154
LCS_GDT     D     153     D     153      3    3    3     3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_GDT     K     154     K     154      3    3    3     3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_GDT     L     155     L     155      3    3    3     3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_AVERAGE  LCS_A:   1.95  (   1.95    1.95    1.95 )

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      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3 
GDT PERCENT_CA   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95
GDT RMS_LOCAL    0.16   0.16   0.16   0.16   0.16   0.16   0.16   0.16   0.16   0.16   0.16   0.16   0.16   0.16   0.16   0.16   0.16   0.16   0.16   0.16
GDT RMS_ALL_CA   0.16   0.16   0.16   0.16   0.16   0.16   0.16   0.16   0.16   0.16   0.16   0.16   0.16   0.16   0.16   0.16   0.16   0.16   0.16   0.16

#      Molecule1      Molecule2       DISTANCE
LGA    D     153      D     153          0.177
LGA    K     154      K     154          0.082
LGA    L     155      L     155          0.187

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    3  154    4.0      3    0.16     1.948     1.948     1.171

LGA_LOCAL      RMSD =  0.156  Number of atoms =    3  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.156  Number of atoms =    3 
Std_ALL_ATOMS  RMSD =  0.156  (standard rmsd on all 3 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.450755 * X  +   0.628384 * Y  +  -0.633998 * Z  + -14.108112
  Y_new =   0.605376 * X  +   0.306762 * Y  +   0.734450 * Z  +  24.517502
  Z_new =   0.656003 * X  +  -0.714865 * Y  +  -0.242134 * Z  +  11.405566 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.897381    1.244212  [ DEG:  -108.7119     71.2881 ]
  Theta =  -0.715510   -2.426082  [ DEG:   -40.9957   -139.0043 ]
  Phi   =   0.930769   -2.210824  [ DEG:    53.3291   -126.6709 ]
 
# 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: T0318TS338_4-D1                               
REMARK     2: T0318_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0318TS338_4-D1.T0318_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    3  154   4.0    3   0.16   1.948     0.16
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS338_4-D1
PFRMAT TS
TARGET T0318
MODEL  4
PARENT 1gyt_A
ATOM      1  N   ASP   153      30.731  26.969  21.234  1.00  0.00
ATOM      2  CA  ASP   153      29.763  26.114  21.958  1.00  0.00
ATOM      3  CB  ASP   153      29.097  26.914  23.091  1.00  0.00
ATOM      4  CG  ASP   153      30.145  27.253  24.144  1.00  0.00
ATOM      5  OD1 ASP   153      31.272  26.694  24.063  1.00  0.00
ATOM      6  OD2 ASP   153      29.833  28.075  25.047  1.00  0.00
ATOM      7  C   ASP   153      28.689  25.646  21.029  1.00  0.00
ATOM      8  O   ASP   153      28.958  25.076  19.973  1.00  0.00
ATOM      9  N   LYS   154      27.426  25.880  21.422  1.00  0.01
ATOM     10  CA  LYS   154      26.295  25.494  20.633  1.00  0.01
ATOM     11  CB  LYS   154      24.960  25.704  21.372  1.00  0.01
ATOM     12  CG  LYS   154      24.747  27.108  21.944  1.00  0.01
ATOM     13  CD  LYS   154      24.452  28.181  20.896  1.00  0.01
ATOM     14  CE  LYS   154      24.222  29.573  21.493  1.00  0.01
ATOM     15  NZ  LYS   154      23.936  30.541  20.411  1.00  0.01
ATOM     16  C   LYS   154      26.310  26.286  19.366  1.00  0.01
ATOM     17  O   LYS   154      25.918  25.793  18.309  1.00  0.01
ATOM     18  N   LEU   155      26.789  27.541  19.440  1.00  0.01
ATOM     19  CA  LEU   155      26.805  28.386  18.283  1.00  0.01
ATOM     20  CB  LEU   155      27.461  29.751  18.557  1.00  0.01
ATOM     21  CG  LEU   155      27.488  30.680  17.329  1.00  0.01
ATOM     22  CD1 LEU   155      26.062  31.082  16.909  1.00  0.01
ATOM     23  CD2 LEU   155      28.403  31.891  17.562  1.00  0.01
ATOM     24  C   LEU   155      27.642  27.692  17.266  1.00  0.01
ATOM     25  O   LEU   155      27.287  27.624  16.090  1.00  0.01
TER
END
