
#######################################################
#                                                     #
#                        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    9 (   70),  selected    9 , name T0320TS389_4-D2
# Molecule2: number of CA atoms   73 (  604),  selected    9 , name T0320_D2.pdb
# PARAMETERS: T0320TS389_4-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:     9       228 - 236         4.36     4.36
  LCS_AVERAGE:     12.33

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       228 - 232         1.50     9.63
  LONGEST_CONTINUOUS_SEGMENT:     5       229 - 233         1.31     6.18
  LONGEST_CONTINUOUS_SEGMENT:     5       231 - 235         1.69     5.42
  LCS_AVERAGE:      6.54

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       228 - 231         0.69    10.48
  LONGEST_CONTINUOUS_SEGMENT:     4       230 - 233         0.69     6.93
  LONGEST_CONTINUOUS_SEGMENT:     4       232 - 235         0.51     8.66
  LCS_AVERAGE:      5.33

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:   73
LCS_GDT     N     228     N     228      4    5    9     3    4    4    4    5    5    5    6    6    6    8    8    8    9    9    9    9    9    9    9 
LCS_GDT     N     229     N     229      4    5    9     3    4    4    4    5    5    6    7    7    7    8    8    8    9    9    9    9    9    9    9 
LCS_GDT     S     230     S     230      4    5    9     3    4    4    4    5    5    6    7    7    7    8    8    8    9    9    9    9    9    9    9 
LCS_GDT     L     231     L     231      4    5    9     3    4    4    5    5    5    6    7    7    7    8    8    8    9    9    9    9    9    9    9 
LCS_GDT     P     232     P     232      4    5    9     3    4    4    5    5    5    6    7    7    7    7    8    8    9    9    9    9    9    9    9 
LCS_GDT     N     233     N     233      4    5    9     3    4    4    5    5    5    6    7    7    7    8    8    8    9    9    9    9    9    9    9 
LCS_GDT     P     234     P     234      4    5    9     3    4    4    5    5    5    6    7    7    7    8    8    8    9    9    9    9    9    9    9 
LCS_GDT     H     235     H     235      4    5    9     0    4    4    5    5    5    6    7    7    7    8    8    8    9    9    9    9    9    9    9 
LCS_GDT     L     236     L     236      3    3    9     0    3    3    3    3    5    6    6    6    6    8    8    8    9    9    9    9    9    9    9 
LCS_AVERAGE  LCS_A:   8.07  (   5.33    6.54   12.33 )

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      4      5      5      5      6      7      7      7      8      8      8      9      9      9      9      9      9      9 
GDT PERCENT_CA   4.11   5.48   5.48   6.85   6.85   6.85   8.22   9.59   9.59   9.59  10.96  10.96  10.96  12.33  12.33  12.33  12.33  12.33  12.33  12.33
GDT RMS_LOCAL    0.06   0.51   0.51   1.69   1.31   1.31   2.14   2.68   2.68   2.68   4.21   3.55   3.55   4.36   4.36   4.36   4.36   4.36   4.36   4.36
GDT RMS_ALL_CA   7.85   8.66   8.66   5.42   6.18   6.18   5.75   4.98   4.98   4.98   4.91   4.76   4.76   4.36   4.36   4.36   4.36   4.36   4.36   4.36

#      Molecule1      Molecule2       DISTANCE
LGA    N     228      N     228          8.551
LGA    N     229      N     229          2.579
LGA    S     230      S     230          3.550
LGA    L     231      L     231          0.906
LGA    P     232      P     232          1.384
LGA    N     233      N     233          1.872
LGA    P     234      P     234          3.461
LGA    H     235      H     235          3.582
LGA    L     236      L     236          9.990

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    9   73    4.0      7    2.68     8.562     7.975     0.252

LGA_LOCAL      RMSD =  2.681  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.980  Number of atoms =    9 
Std_ALL_ATOMS  RMSD =  4.365  (standard rmsd on all 9 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.565729 * X  +  -0.417696 * Y  +  -0.710972 * Z  +  26.438192
  Y_new =  -0.757233 * X  +  -0.604470 * Y  +  -0.247414 * Z  +  17.252768
  Z_new =  -0.326417 * X  +   0.678341 * Y  +  -0.658259 * Z  +  15.884926 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.341171   -0.800421  [ DEG:   134.1392    -45.8608 ]
  Theta =   0.332511    2.809082  [ DEG:    19.0515    160.9485 ]
  Phi   =  -0.929154    2.212439  [ DEG:   -53.2366    126.7634 ]
 
# 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: T0320TS389_4-D2                               
REMARK     2: T0320_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320TS389_4-D2.T0320_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    9   73   4.0    7   2.68   7.975     4.36
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS389_4-D2
PFRMAT TS
TARGET T0320
MODEL  4
PARENT N/A
ATOM   1597  N   ASN   228      23.663  16.365  11.085  1.00  0.00
ATOM   1598  CA  ASN   228      23.861  17.806  10.865  1.00  0.00
ATOM   1599  CB  ASN   228      24.120  18.521  12.192  1.00  0.00
ATOM   1600  CG  ASN   228      22.911  18.510  13.105  1.00  0.00
ATOM   1601  ND2 ASN   228      23.156  18.515  14.410  1.00  0.00
ATOM   1602  OD1 ASN   228      21.770  18.498  12.641  1.00  0.00
ATOM   1603  O   ASN   228      25.477  19.187   9.687  1.00  0.00
ATOM   1604  C   ASN   228      25.072  18.047   9.934  1.00  0.00
ATOM   1605  N   ASN   229      25.635  16.948   9.430  1.00  0.00
ATOM   1606  CA  ASN   229      26.772  16.989   8.511  1.00  0.00
ATOM   1607  CB  ASN   229      27.778  15.889   8.853  1.00  0.00
ATOM   1608  CG  ASN   229      28.428  16.094  10.208  1.00  0.00
ATOM   1609  ND2 ASN   229      28.797  14.998  10.858  1.00  0.00
ATOM   1610  OD1 ASN   229      28.593  17.226  10.663  1.00  0.00
ATOM   1611  O   ASN   229      26.962  16.984   6.105  1.00  0.00
ATOM   1612  C   ASN   229      26.242  16.777   7.080  1.00  0.00
ATOM   1613  N   SER   230      25.002  16.303   6.978  1.00  0.00
ATOM   1614  CA  SER   230      24.331  16.081   5.697  1.00  0.00
ATOM   1615  CB  SER   230      23.670  14.700   5.671  1.00  0.00
ATOM   1616  OG  SER   230      22.965  14.496   4.460  1.00  0.00
ATOM   1617  O   SER   230      22.303  17.213   6.346  1.00  0.00
ATOM   1618  C   SER   230      23.283  17.193   5.588  1.00  0.00
ATOM   1619  N   LEU   231      23.501  18.122   4.661  1.00  0.00
ATOM   1620  CA  LEU   231      22.597  19.249   4.483  1.00  0.00
ATOM   1621  CB  LEU   231      23.150  20.220   3.437  1.00  0.00
ATOM   1622  CG  LEU   231      24.435  20.961   3.811  1.00  0.00
ATOM   1623  CD1 LEU   231      24.942  21.784   2.638  1.00  0.00
ATOM   1624  CD2 LEU   231      24.192  21.900   4.983  1.00  0.00
ATOM   1625  O   LEU   231      21.101  18.040   3.089  1.00  0.00
ATOM   1626  C   LEU   231      21.227  18.825   4.024  1.00  0.00
ATOM   1627  N   PRO   232      20.201  19.383   4.662  1.00  0.00
ATOM   1628  CA  PRO   232      18.834  19.044   4.323  1.00  0.00
ATOM   1629  CB  PRO   232      18.776  19.213   2.804  1.00  0.00
ATOM   1630  CG  PRO   232      20.173  18.957   2.346  1.00  0.00
ATOM   1631  CD  PRO   232      21.070  19.496   3.424  1.00  0.00
ATOM   1632  O   PRO   232      18.892  17.090   5.744  1.00  0.00
ATOM   1633  C   PRO   232      18.447  17.620   4.717  1.00  0.00
ATOM   1634  N   ASN   233      17.599  17.012   3.896  1.00  0.00
ATOM   1635  CA  ASN   233      17.116  15.658   4.111  1.00  0.00
ATOM   1636  CB  ASN   233      16.217  15.220   2.952  1.00  0.00
ATOM   1637  CG  ASN   233      15.535  13.890   3.215  1.00  0.00
ATOM   1638  ND2 ASN   233      14.440  13.641   2.508  1.00  0.00
ATOM   1639  OD1 ASN   233      15.991  13.102   4.043  1.00  0.00
ATOM   1640  O   ASN   233      19.129  14.593   3.374  1.00  0.00
ATOM   1641  C   ASN   233      18.244  14.640   4.217  1.00  0.00
ATOM   1642  N   PRO   234      18.218  13.837   5.278  1.00  0.00
ATOM   1643  CA  PRO   234      19.225  12.806   5.513  1.00  0.00
ATOM   1644  CB  PRO   234      19.312  12.715   7.038  1.00  0.00
ATOM   1645  CG  PRO   234      17.947  13.090   7.513  1.00  0.00
ATOM   1646  CD  PRO   234      17.406  14.062   6.503  1.00  0.00
ATOM   1647  O   PRO   234      17.655  11.026   5.171  1.00  0.00
ATOM   1648  C   PRO   234      18.748  11.509   4.878  1.00  0.00
ATOM   1649  N   HIS   235      19.571  10.945   4.009  1.00  0.00
ATOM   1650  CA  HIS   235      19.236   9.701   3.338  1.00  0.00
ATOM   1651  CB  HIS   235      18.994   9.944   1.848  1.00  0.00
ATOM   1652  CG  HIS   235      17.832  10.842   1.564  1.00  0.00
ATOM   1653  CD2 HIS   235      17.665  12.246   1.211  1.00  0.00
ATOM   1654  ND1 HIS   235      16.525  10.404   1.598  1.00  0.00
ATOM   1655  CE1 HIS   235      15.710  11.432   1.302  1.00  0.00
ATOM   1656  NE2 HIS   235      16.387  12.540   1.068  1.00  0.00
ATOM   1657  O   HIS   235      21.567   9.219   3.567  1.00  0.00
ATOM   1658  C   HIS   235      20.407   8.773   3.534  1.00  0.00
ATOM   1659  N   LEU   236      20.114   7.479   3.644  1.00  0.00
ATOM   1660  CA  LEU   236      21.158   6.486   3.823  1.00  0.00
ATOM   1661  CB  LEU   236      20.578   5.074   3.713  1.00  0.00
ATOM   1662  CG  LEU   236      21.564   3.919   3.901  1.00  0.00
ATOM   1663  CD1 LEU   236      22.152   3.936   5.304  1.00  0.00
ATOM   1664  CD2 LEU   236      20.872   2.581   3.690  1.00  0.00
ATOM   1665  O   LEU   236      23.442   6.544   3.103  1.00  0.00
ATOM   1666  C   LEU   236      22.257   6.621   2.770  1.00  0.00
TER
END
