
#######################################################
#                                                     #
#                        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    4 (   39),  selected    4 , name T0320TS083_5-D2
# Molecule2: number of CA atoms   73 (  604),  selected    4 , name T0320_D2.pdb
# PARAMETERS: T0320TS083_5-D2.T0320_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:     4       228 - 231         1.35     1.35
  LCS_AVERAGE:      5.48

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       228 - 231         1.35     1.35
  LCS_AVERAGE:      5.48

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       228 - 230         0.31     3.32
  LONGEST_CONTINUOUS_SEGMENT:     3       229 - 231         0.60     3.27
  LCS_AVERAGE:      4.11

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:   73
LCS_GDT     N     228     N     228      3    4    4     3    3    3    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4 
LCS_GDT     N     229     N     229      3    4    4     3    3    3    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4 
LCS_GDT     S     230     S     230      3    4    4     3    3    3    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4 
LCS_GDT     L     231     L     231      3    4    4     3    3    3    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4 
LCS_AVERAGE  LCS_A:   5.02  (   4.11    5.48    5.48 )

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      4      4      4      4      4      4      4      4      4      4      4      4      4 
GDT PERCENT_CA   4.11   4.11   4.11   5.48   5.48   5.48   5.48   5.48   5.48   5.48   5.48   5.48   5.48   5.48   5.48   5.48   5.48   5.48   5.48   5.48
GDT RMS_LOCAL    0.21   0.21   0.21   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35
GDT RMS_ALL_CA   1.89   1.89   1.89   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35

#      Molecule1      Molecule2       DISTANCE
LGA    N     228      N     228          0.825
LGA    N     229      N     229          1.812
LGA    S     230      S     230          1.652
LGA    L     231      L     231          0.785

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    4   73    4.0      4    1.35     5.137     5.269     0.276

LGA_LOCAL      RMSD =  1.352  Number of atoms =    4  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.352  Number of atoms =    4 
Std_ALL_ATOMS  RMSD =  1.352  (standard rmsd on all 4 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.947342 * X  +  -0.223274 * Y  +  -0.229547 * Z  +  57.423359
  Y_new =   0.297279 * X  +  -0.879656 * Y  +  -0.371255 * Z  +  49.444523
  Z_new =  -0.119030 * X  +  -0.419945 * Y  +   0.899710 * Z  + -50.741539 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.436700    2.704893  [ DEG:   -25.0211    154.9789 ]
  Theta =   0.119313    3.022279  [ DEG:     6.8362    173.1638 ]
  Phi   =   2.837521   -0.304072  [ DEG:   162.5780    -17.4220 ]
 
# 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: T0320TS083_5-D2                               
REMARK     2: T0320_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320TS083_5-D2.T0320_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    4   73   4.0    4   1.35   5.269     1.35
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS083_5-D2
PFRMAT TS
TARGET T0320
MODEL 5
PARENT 1SA3_A
ATOM   2088  H   ASN   228      30.033  22.752   6.191  1.00  1.00              
ATOM   2089  N   ASN   228      30.257  21.908   5.839  1.00  5.81              
ATOM   2090  CA  ASN   228      30.933  20.933   6.687  1.00  1.00              
ATOM   2091  CB  ASN   228      32.140  21.573   7.378  1.00  1.00              
ATOM   2092  C   ASN   228      29.979  20.369   7.725  1.00  1.03              
ATOM   2093  O   ASN   228      30.383  19.622   8.620  1.00  1.00              
ATOM   2094  CG  ASN   228      33.266  21.887   6.411  1.00  1.00              
ATOM   2095  ND2 ASN   228      34.101  22.856   6.764  1.00  1.00              
ATOM   2096 HD21 ASN   228      33.962  23.295   7.585  1.00  1.00              
ATOM   2097 HD22 ASN   228      34.815  23.085   6.192  1.00  1.00              
ATOM   2098  OD1 ASN   228      33.383  21.262   5.354  1.00  1.00              
ATOM   2099  H   ASN   229      28.466  21.334   6.923  1.00  1.00              
ATOM   2100  N   ASN   229      28.709  20.713   7.586  1.00  3.35              
ATOM   2101  CA  ASN   229      27.679  20.153   8.440  1.00  1.20              
ATOM   2102  CB  ASN   229      26.828  21.269   9.055  1.00  1.00              
ATOM   2103  C   ASN   229      26.813  19.245   7.589  1.00  1.18              
ATOM   2104  O   ASN   229      26.590  19.523   6.412  1.00  2.55              
ATOM   2105  CG  ASN   229      27.602  22.107  10.054  1.00  1.00              
ATOM   2106  ND2 ASN   229      27.178  23.351  10.241  1.00  1.29              
ATOM   2107 HD21 ASN   229      26.431  23.652   9.752  1.00  1.00              
ATOM   2108 HD22 ASN   229      27.622  23.904  10.863  1.00  1.00              
ATOM   2109  OD1 ASN   229      28.562  21.634  10.667  1.00  1.29              
ATOM   2110  H   SER   230      26.579  17.911   9.026  1.00  1.00              
ATOM   2111  N   SER   230      26.348  18.144   8.151  1.00  1.64              
ATOM   2112  CA  SER   230      25.444  17.299   7.396  1.00  1.00              
ATOM   2113  CB  SER   230      25.019  16.132   8.287  1.00  1.00              
ATOM   2114  C   SER   230      24.240  18.155   7.055  1.00  1.18              
ATOM   2115  O   SER   230      23.776  18.915   7.906  1.00  2.16              
ATOM   2116  OG  SER   230      24.056  15.341   7.623  1.00  1.00              
ATOM   2117  H   LEU   231      24.170  17.480   5.202  1.00  1.00              
ATOM   2118  N   LEU   231      23.775  18.081   5.816  1.00  5.01              
ATOM   2119  CA  LEU   231      22.669  18.923   5.383  1.00  3.27              
ATOM   2120  CB  LEU   231      21.786  18.152   4.401  1.00  2.48              
ATOM   2121  C   LEU   231      21.800  19.344   6.569  1.00  1.84              
ATOM   2122  O   LEU   231      21.633  20.567   6.763  1.00  1.25              
ATOM   2123  OXT LEU   231      21.027  18.485   7.047  1.00  2.23              
ATOM   2124  CG  LEU   231      20.292  18.164   4.727  1.00  3.10              
ATOM   2125  CD1 LEU   231      19.681  19.507   4.346  1.00  2.19              
ATOM   2126  CD2 LEU   231      19.587  17.013   4.024  1.00  1.00              
TER
END
