
#######################################################
#                                                     #
#                        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 (   37),  selected    5 , name T0320TS268_4_2-D2
# Molecule2: number of CA atoms   73 (  604),  selected    5 , name T0320_D2.pdb
# PARAMETERS: T0320TS268_4_2-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:     5       228 - 232         1.50     1.50
  LCS_AVERAGE:      6.85

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       228 - 232         1.50     1.50
  LCS_AVERAGE:      6.85

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         0.58     5.46
  LONGEST_CONTINUOUS_SEGMENT:     3       229 - 231         0.41     3.50
  LONGEST_CONTINUOUS_SEGMENT:     3       230 - 232         0.47     3.30
  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    5    5     2    3    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     N     229     N     229      3    5    5     3    3    3    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     S     230     S     230      3    5    5     3    3    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     L     231     L     231      3    5    5     3    3    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     P     232     P     232      3    5    5     3    3    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_AVERAGE  LCS_A:   5.94  (   4.11    6.85    6.85 )

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      4      4      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5 
GDT PERCENT_CA   4.11   4.11   5.48   5.48   6.85   6.85   6.85   6.85   6.85   6.85   6.85   6.85   6.85   6.85   6.85   6.85   6.85   6.85   6.85   6.85
GDT RMS_LOCAL    0.41   0.41   0.82   0.82   1.50   1.50   1.50   1.50   1.50   1.50   1.50   1.50   1.50   1.50   1.50   1.50   1.50   1.50   1.50   1.50
GDT RMS_ALL_CA   3.50   3.50   1.81   1.81   1.50   1.50   1.50   1.50   1.50   1.50   1.50   1.50   1.50   1.50   1.50   1.50   1.50   1.50   1.50   1.50

#      Molecule1      Molecule2       DISTANCE
LGA    N     228      N     228          0.960
LGA    N     229      N     229          2.292
LGA    S     230      S     230          1.392
LGA    L     231      L     231          1.108
LGA    P     232      P     232          1.386

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    5   73    4.0      5    1.50     5.822     6.435     0.312

LGA_LOCAL      RMSD =  1.501  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.501  Number of atoms =    5 
Std_ALL_ATOMS  RMSD =  1.501  (standard rmsd on all 5 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.618215 * X  +  -0.471758 * Y  +   0.628693 * Z  +  95.423737
  Y_new =   0.541657 * X  +  -0.835308 * Y  +  -0.094168 * Z  +  71.633926
  Z_new =   0.569576 * X  +   0.282320 * Y  +   0.771931 * Z  + -36.730335 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.350621   -2.790972  [ DEG:    20.0891   -159.9109 ]
  Theta =  -0.605990   -2.535602  [ DEG:   -34.7207   -145.2793 ]
  Phi   =   2.422105   -0.719488  [ DEG:   138.7764    -41.2236 ]
 
# 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: T0320TS268_4_2-D2                             
REMARK     2: T0320_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320TS268_4_2-D2.T0320_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    5   73   4.0    5   1.50   6.435     1.50
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS268_4_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0320
PARENT 1ni5_A
ATOM   1861  N   ASN   228      31.041  22.484   6.651  1.00  0.00
ATOM   1862  CA  ASN   228      30.961  21.147   7.157  1.00  0.00
ATOM   1863  C   ASN   228      29.667  21.055   7.891  1.00  0.00
ATOM   1864  O   ASN   228      29.559  21.492   9.036  1.00  0.00
ATOM   1865  CB  ASN   228      32.134  20.859   8.097  1.00  0.00
ATOM   1866  CG  ASN   228      32.157  19.420   8.573  1.00  0.00
ATOM   1867  OD1 ASN   228      31.145  18.723   8.522  1.00  0.00
ATOM   1868  ND2 ASN   228      33.317  18.972   9.041  1.00  0.00
ATOM   1869  N   ASN   229      28.642  20.483   7.235  1.00  0.00
ATOM   1870  CA  ASN   229      27.365  20.354   7.870  1.00  0.00
ATOM   1871  C   ASN   229      26.743  19.106   7.342  1.00  0.00
ATOM   1872  O   ASN   229      27.187  18.555   6.336  1.00  0.00
ATOM   1873  CB  ASN   229      26.483  21.563   7.549  1.00  0.00
ATOM   1874  CG  ASN   229      26.156  21.670   6.072  1.00  0.00
ATOM   1875  OD1 ASN   229      25.399  20.863   5.533  1.00  0.00
ATOM   1876  ND2 ASN   229      26.729  22.670   5.412  1.00  0.00
ATOM   1877  N   SER   230      25.702  18.610   8.035  1.00  0.00
ATOM   1878  CA  SER   230      25.030  17.446   7.548  1.00  0.00
ATOM   1879  C   SER   230      24.170  17.907   6.423  1.00  0.00
ATOM   1880  O   SER   230      23.841  19.089   6.327  1.00  0.00
ATOM   1881  CB  SER   230      24.182  16.815   8.655  1.00  0.00
ATOM   1882  OG  SER   230      23.105  17.661   9.017  1.00  0.00
ATOM   1883  N   LEU   231      23.795  16.986   5.521  1.00  0.00
ATOM   1884  CA  LEU   231      22.971  17.390   4.425  1.00  0.00
ATOM   1885  C   LEU   231      21.593  17.584   4.951  1.00  0.00
ATOM   1886  O   LEU   231      21.164  16.926   5.897  1.00  0.00
ATOM   1887  CB  LEU   231      22.968  16.317   3.333  1.00  0.00
ATOM   1888  CG  LEU   231      24.316  16.018   2.674  1.00  0.00
ATOM   1889  CD1 LEU   231      24.186  14.870   1.685  1.00  0.00
ATOM   1890  CD2 LEU   231      24.829  17.236   1.923  1.00  0.00
ATOM   1891  N   PRO   232      20.900  18.511   4.361  1.00  0.00
ATOM   1892  CA  PRO   232      19.550  18.742   4.788  1.00  0.00
ATOM   1893  C   PRO   232      18.671  17.668   4.246  1.00  0.00
ATOM   1894  O   PRO   232      19.150  16.892   3.376  1.00  0.00
ATOM   1895  CB  PRO   232      19.207  20.116   4.209  1.00  0.00
ATOM   1896  CG  PRO   232      19.949  20.171   2.916  1.00  0.00
ATOM   1897  CD  PRO   232      21.267  19.490   3.160  1.00  0.00
TER
END
