
#######################################################
#                                                     #
#                        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 (   51),  selected    6 , name T0356TS349_4-D2
# Molecule2: number of CA atoms  192 ( 1487),  selected    6 , name T0356_D2.pdb
# PARAMETERS: T0356TS349_4-D2.T0356_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       122 - 127         2.09     2.09
  LCS_AVERAGE:      3.12

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       122 - 126         1.57     2.62
  LONGEST_CONTINUOUS_SEGMENT:     5       123 - 127         1.15     2.79
  LCS_AVERAGE:      2.60

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       123 - 126         0.62     2.59
  LONGEST_CONTINUOUS_SEGMENT:     4       124 - 127         0.94     3.70
  LCS_AVERAGE:      2.00

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:  192
LCS_GDT     T     122     T     122      3    5    6     0    3    4    4    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     K     123     K     123      4    5    6     3    4    4    5    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     R     124     R     124      4    5    6     3    4    4    5    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     L     125     L     125      4    5    6     3    4    4    5    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     R     126     R     126      4    5    6     3    4    4    5    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     G     127     G     127      4    5    6     0    3    4    5    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_AVERAGE  LCS_A:   2.58  (   2.00    2.60    3.12 )

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      6      6      6      6      6      6      6      6      6      6      6      6      6      6      6 
GDT PERCENT_CA   1.56   2.08   2.08   2.60   2.60   3.12   3.12   3.12   3.12   3.12   3.12   3.12   3.12   3.12   3.12   3.12   3.12   3.12   3.12   3.12
GDT RMS_LOCAL    0.07   0.62   0.62   1.15   1.15   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09
GDT RMS_ALL_CA   3.23   2.59   2.59   2.79   2.79   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09

#      Molecule1      Molecule2       DISTANCE
LGA    T     122      T     122          2.702
LGA    K     123      K     123          0.779
LGA    R     124      R     124          2.745
LGA    L     125      L     125          1.329
LGA    R     126      R     126          1.536
LGA    G     127      G     127          2.584

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    6  192    4.0      6    2.09     2.734     2.764     0.274

LGA_LOCAL      RMSD =  2.092  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.091  Number of atoms =    6 
Std_ALL_ATOMS  RMSD =  2.092  (standard rmsd on all 6 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.849161 * X  +  -0.480845 * Y  +   0.218434 * Z  + 125.973259
  Y_new =   0.438267 * X  +  -0.872360 * Y  +  -0.216589 * Z  + 184.369843
  Z_new =   0.294698 * X  +  -0.088187 * Y  +   0.951512 * Z  +  76.127800 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.092417    3.049176  [ DEG:    -5.2951    174.7049 ]
  Theta =  -0.299140   -2.842453  [ DEG:   -17.1395   -162.8605 ]
  Phi   =   2.665134   -0.476458  [ DEG:   152.7010    -27.2990 ]
 
# 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: T0356TS349_4-D2                               
REMARK     2: T0356_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356TS349_4-D2.T0356_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    6  192   4.0    6   2.09   2.764     2.09
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS349_4-D2
PFRMAT TS
TARGET T0356
MODEL  4  REFINED
PARENT 1FX7_D
ATOM    726  N   THR   122      89.191  74.811  72.593  1.00  0.00
ATOM    727  CA  THR   122      87.710  74.734  72.747  1.00  0.00
ATOM    728  C   THR   122      87.160  75.980  73.517  1.00  0.00
ATOM    729  O   THR   122      85.928  76.098  73.587  1.00  0.00
ATOM    730  CB  THR   122      87.076  73.479  73.399  1.00  0.00
ATOM    731  OG1 THR   122      87.784  72.264  73.181  1.00  0.00
ATOM    732  CG2 THR   122      85.605  73.293  72.870  1.00  0.00
ATOM    733  N   LYS   123      87.951  76.987  73.861  1.00  0.00
ATOM    734  CA  LYS   123      87.564  78.170  74.658  1.00  0.00
ATOM    735  C   LYS   123      86.884  77.824  76.015  1.00  0.00
ATOM    736  O   LYS   123      86.321  78.736  76.644  1.00  0.00
ATOM    737  CB  LYS   123      86.592  79.019  73.849  1.00  0.00
ATOM    738  CG  LYS   123      87.229  79.827  72.753  1.00  0.00
ATOM    739  CD  LYS   123      87.903  81.081  73.272  1.00  0.00
ATOM    740  CE  LYS   123      87.929  82.177  72.204  1.00  0.00
ATOM    741  NZ  LYS   123      89.245  82.884  72.364  1.00  0.00
ATOM    742  N   ARG   124      87.304  76.717  76.626  1.00  0.00
ATOM    743  CA  ARG   124      86.810  76.256  77.860  1.00  0.00
ATOM    744  C   ARG   124      87.842  76.561  78.904  1.00  0.00
ATOM    745  O   ARG   124      89.054  76.299  78.619  1.00  0.00
ATOM    746  CB  ARG   124      86.633  74.724  77.749  1.00  0.00
ATOM    747  CG  ARG   124      87.809  73.766  77.932  1.00  0.00
ATOM    748  CD  ARG   124      88.617  73.500  76.649  1.00  0.00
ATOM    749  NE  ARG   124      88.675  72.080  76.252  1.00  0.00
ATOM    750  CZ  ARG   124      89.212  71.100  77.004  1.00  0.00
ATOM    751  NH1 ARG   124      89.756  71.327  78.205  1.00  0.00
ATOM    752  NH2 ARG   124      89.200  69.847  76.542  1.00  0.00
ATOM    753  N   LEU   125      87.512  77.040  80.069  1.00  0.00
ATOM    754  CA  LEU   125      88.558  77.250  80.992  1.00  0.00
ATOM    755  C   LEU   125      89.133  75.955  81.643  1.00  0.00
ATOM    756  O   LEU   125      88.788  74.847  81.224  1.00  0.00
ATOM    757  CB  LEU   125      88.353  78.423  81.921  1.00  0.00
ATOM    758  CG  LEU   125      87.708  79.664  81.355  1.00  0.00
ATOM    759  CD1 LEU   125      87.316  80.634  82.467  1.00  0.00
ATOM    760  CD2 LEU   125      88.666  80.349  80.386  1.00  0.00
ATOM    761  N   ARG   126      90.319  76.135  82.084  1.00  0.00
ATOM    762  CA  ARG   126      91.173  75.149  82.693  1.00  0.00
ATOM    763  C   ARG   126      91.703  75.833  83.987  1.00  0.00
ATOM    764  O   ARG   126      90.950  76.645  84.580  1.00  0.00
ATOM    765  CB  ARG   126      92.316  74.806  81.660  1.00  0.00
ATOM    766  CG  ARG   126      93.362  73.861  82.327  1.00  0.00
ATOM    767  CD  ARG   126      94.230  73.007  81.407  1.00  0.00
ATOM    768  NE  ARG   126      94.990  72.046  82.203  1.00  0.00
ATOM    769  CZ  ARG   126      94.566  70.832  82.580  1.00  0.00
ATOM    770  NH1 ARG   126      93.384  70.394  82.222  1.00  0.00
ATOM    771  NH2 ARG   126      95.316  70.005  83.322  1.00  0.00
ATOM    772  N   GLY   127      92.492  75.133  84.767  1.00  0.00
ATOM    773  CA  GLY   127      93.033  75.631  86.051  1.00  0.00
ATOM    774  C   GLY   127      93.665  74.547  86.925  1.00  0.00
ATOM    775  O   GLY   127      93.972  74.773  88.096  1.00  0.00
ATOM    776  OXT GLY   127      94.024  73.472  86.341  1.00  0.00
TER
END
