
#######################################################
#                                                     #
#                        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    6 (   56),  selected    6 , name T0320TS277_3-D2
# Molecule2: number of CA atoms   73 (  604),  selected    6 , name T0320_D2.pdb
# PARAMETERS: T0320TS277_3-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:     6       228 - 233         1.33     1.33
  LCS_AVERAGE:      8.22

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       228 - 233         1.33     1.33
  LCS_AVERAGE:      8.22

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       228 - 232         0.95     1.80
  LCS_AVERAGE:      6.39

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      5    6    6     0    4    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     N     229     N     229      5    6    6     3    4    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     S     230     S     230      5    6    6     3    4    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     L     231     L     231      5    6    6     3    4    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     P     232     P     232      5    6    6     3    4    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     N     233     N     233      3    6    6     3    3    4    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_AVERAGE  LCS_A:   7.61  (   6.39    8.22    8.22 )

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      4      5      6      6      6      6      6      6      6      6      6      6      6      6      6      6      6      6      6 
GDT PERCENT_CA   4.11   5.48   6.85   8.22   8.22   8.22   8.22   8.22   8.22   8.22   8.22   8.22   8.22   8.22   8.22   8.22   8.22   8.22   8.22   8.22
GDT RMS_LOCAL    0.12   0.60   0.95   1.33   1.33   1.33   1.33   1.33   1.33   1.33   1.33   1.33   1.33   1.33   1.33   1.33   1.33   1.33   1.33   1.33
GDT RMS_ALL_CA   3.16   2.36   1.80   1.33   1.33   1.33   1.33   1.33   1.33   1.33   1.33   1.33   1.33   1.33   1.33   1.33   1.33   1.33   1.33   1.33

#      Molecule1      Molecule2       DISTANCE
LGA    N     228      N     228          1.374
LGA    N     229      N     229          0.875
LGA    S     230      S     230          1.447
LGA    L     231      L     231          1.585
LGA    P     232      P     232          0.741
LGA    N     233      N     233          1.696

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    6   73    4.0      6    1.33     7.534     7.901     0.418

LGA_LOCAL      RMSD =  1.334  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.334  Number of atoms =    6 
Std_ALL_ATOMS  RMSD =  1.334  (standard rmsd on all 6 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.548616 * X  +   0.833664 * Y  +   0.063435 * Z  +   5.277918
  Y_new =  -0.593084 * X  +  -0.441527 * Y  +   0.673280 * Z  + -17.251684
  Z_new =   0.589298 * X  +   0.331750 * Y  +   0.736662 * Z  + -25.408133 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.423138   -2.718454  [ DEG:    24.2440   -155.7560 ]
  Theta =  -0.630190   -2.511403  [ DEG:   -36.1072   -143.8928 ]
  Phi   =  -2.317266    0.824327  [ DEG:  -132.7695     47.2305 ]
 
# 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: T0320TS277_3-D2                               
REMARK     2: T0320_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320TS277_3-D2.T0320_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    6   73   4.0    6   1.33   7.901     1.33
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS277_3-D2
PFRMAT TS 
TARGET T0320
MODEL 3
PARENT 1WY5_A
ATOM   4063  H   ASN   228      30.267  21.739   9.868  1.00  0.00                              
ATOM   4065  N   ASN   228      30.620  22.137   9.094  1.00  0.00                              
ATOM   4067  CA  ASN   228      30.693  21.355   7.842  1.00  0.00                              
ATOM   4069  CB  ASN   228      32.126  21.282   7.346  1.00  0.00                              
ATOM   4071  C   ASN   228      30.129  19.944   7.993  1.00  0.00                              
ATOM   4073  O   ASN   228      30.894  18.976   8.114  1.00  0.00                              
ATOM   4075  CG  ASN   228      32.234  20.568   6.022  1.00  0.00                              
ATOM   4077  ND2 ASN   228      33.441  20.125   5.676  1.00  0.00                              
ATOM   4079 HD21 ASN   228      34.167  20.288   6.259  1.00  0.00                              
ATOM   4081 HD22 ASN   228      33.547  19.648   4.869  1.00  0.00                              
ATOM   4083  OD1 ASN   228      31.244  20.389   5.324  1.00  0.00                              
ATOM   4085  H   ASN   229      28.244  20.563   7.845  1.00  0.00                              
ATOM   4087  N   ASN   229      28.792  19.802   7.934  1.00  0.00                              
ATOM   4089  CA  ASN   229      28.155  18.447   8.038  1.00  0.00                              
ATOM   4091  CB  ASN   229      28.625  17.689   9.310  1.00  0.00                              
ATOM   4093  C   ASN   229      26.626  18.513   7.985  1.00  0.00                              
ATOM   4095  O   ASN   229      25.979  18.969   8.942  1.00  0.00                              
ATOM   4097  CG  ASN   229      28.203  16.208   9.307  1.00  0.00                              
ATOM   4099  ND2 ASN   229      27.781  15.696  10.475  1.00  0.00                              
ATOM   4101 HD21 ASN   229      27.763  16.256  11.233  1.00  0.00                              
ATOM   4103 HD22 ASN   229      27.526  14.789  10.518  1.00  0.00                              
ATOM   4105  OD1 ASN   229      28.294  15.529   8.282  1.00  0.00                              
ATOM   4107  H   SER   230      26.605  17.752   6.195  1.00  0.00                              
ATOM   4109  N   SER   230      26.070  18.099   6.877  1.00  0.00                              
ATOM   4111  CA  SER   230      24.598  18.109   6.681  1.00  0.00                              
ATOM   4113  CB  SER   230      23.871  18.653   7.937  1.00  0.00                              
ATOM   4115  C   SER   230      24.127  18.900   5.383  1.00  0.00                              
ATOM   4117  O   SER   230      24.940  19.359   4.574  1.00  0.00                              
ATOM   4119  OG  SER   230      24.030  20.068   8.052  1.00  0.00                              
ATOM   4121  H   LEU   231      22.285  18.810   6.011  1.00  0.00                              
ATOM   4123  N   LEU   231      22.822  19.074   5.283  1.00  0.00                              
ATOM   4125  CA  LEU   231      22.156  19.709   4.121  1.00  0.00                              
ATOM   4127  CB  LEU   231      22.912  19.483   2.809  1.00  0.00                              
ATOM   4129  C   LEU   231      20.793  19.124   3.996  1.00  0.00                              
ATOM   4131  O   LEU   231      19.812  19.830   4.048  1.00  0.00                              
ATOM   4133  CG  LEU   231      22.207  20.008   1.549  1.00  0.00                              
ATOM   4135  CD1 LEU   231      22.388  21.514   1.427  1.00  0.00                              
ATOM   4137  CD2 LEU   231      22.723  19.307   0.324  1.00  0.00                              
ATOM   4139  N   PRO   232      20.719  17.810   3.780  1.00  0.00                              
ATOM   4141  CA  PRO   232      19.464  17.140   3.651  1.00  0.00                              
ATOM   4143  CB  PRO   232      19.776  16.032   2.681  1.00  0.00                              
ATOM   4145  C   PRO   232      18.998  16.584   4.992  1.00  0.00                              
ATOM   4147  O   PRO   232      18.476  17.330   5.833  1.00  0.00                              
ATOM   4149  CG  PRO   232      21.159  15.600   3.082  1.00  0.00                              
ATOM   4151  CD  PRO   232      21.843  16.880   3.588  1.00  0.00                              
ATOM   4153  H   ASN   233      19.626  14.766   4.540  1.00  0.00                              
ATOM   4155  N   ASN   233      19.222  15.285   5.213  1.00  0.00                              
ATOM   4157  CA  ASN   233      18.869  14.644   6.481  1.00  0.00                              
ATOM   4159  CB  ASN   233      19.474  13.230   6.553  1.00  0.00                              
ATOM   4161  C   ASN   233      19.340  15.476   7.670  1.00  0.00                              
ATOM   4163  O   ASN   233      18.895  15.263   8.799  1.00  0.00                              
ATOM   4165  CG  ASN   233      18.937  12.417   7.722  1.00  0.00                              
ATOM   4167  ND2 ASN   233      19.804  12.094   8.669  1.00  0.00                              
ATOM   4169 HD21 ASN   233      20.694  12.389   8.585  1.00  0.00                              
ATOM   4171 HD22 ASN   233      19.516  11.584   9.407  1.00  0.00                              
ATOM   4173  OD1 ASN   233      17.744  12.105   7.781  1.00  0.00                              
TER 
END
