
#######################################################
#                                                     #
#                        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   30 (   30),  selected   30 , name T0356TS464_2-D2
# Molecule2: number of CA atoms  192 ( 1487),  selected   30 , name T0356_D2.pdb
# PARAMETERS: T0356TS464_2-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:    10       122 - 131         3.85    33.04
  LCS_AVERAGE:      4.13

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       306 - 313         1.50    28.45
  LCS_AVERAGE:      2.99

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       306 - 312         0.92    29.75
  LCS_AVERAGE:      2.26

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    3   10     0    3    3    3    3    3    4    8    9    9   12   12   14   14   14   15   15   15   15   15 
LCS_GDT     K     123     K     123      3    3   10     3    4    4    5    6    7    9    9   10   11   12   13   14   14   14   15   15   15   15   15 
LCS_GDT     R     124     R     124      3    3   10     3    4    4    5    6    7    9    9   10   11   12   13   14   14   14   15   15   15   15   15 
LCS_GDT     L     125     L     125      4    4   10     3    4    5    5    6    7    9    9   10   11   12   13   14   14   14   15   15   15   15   15 
LCS_GDT     R     126     R     126      4    4   10     3    3    5    5    5    5    5    7    8    9   12   13   14   14   14   15   15   15   15   15 
LCS_GDT     G     127     G     127      4    5   10     3    3    5    5    5    5    6    8    9    9   11   13   14   14   14   15   15   15   15   15 
LCS_GDT     A     128     A     128      4    5   10     4    4    5    5    5    7    9    9   10   11   12   13   14   14   14   15   15   15   15   15 
LCS_GDT     P     129     P     129      4    5   10     4    4    4    4    4    5    9    9   10   11   12   13   14   14   14   15   15   15   15   15 
LCS_GDT     C     130     C     130      4    5   10     4    4    4    4    4    6    9    9   10   11   12   13   14   14   14   15   15   15   15   15 
LCS_GDT     Q     131     Q     131      4    5   10     4    4    5    5    6    7    9    9   10   11   12   13   14   14   14   15   15   15   15   15 
LCS_GDT     A     220     A     220      3    5    7     1    3    4    5    5    5    7    7    7    7    7    7    7    7    7    9    9   10   10   12 
LCS_GDT     L     221     L     221      4    6    7     4    4    5    6    6    6    7    7    7    7    7    7    7    7    7    9    9   10   10   12 
LCS_GDT     G     222     G     222      4    6    7     4    4    5    6    6    6    7    7    7    7    7    7    7    7    7    7    8   10   10   12 
LCS_GDT     A     223     A     223      4    6    7     4    4    5    6    6    6    7    7    7    7    7    7    7    7    7    9    9   10   10   12 
LCS_GDT     D     224     D     224      4    6    7     4    4    5    6    6    6    7    7    7    7    7    7    7    7    7    9    9   10   10   12 
LCS_GDT     P     225     P     225      3    6    7     3    3    5    6    6    6    7    7    7    8    8    8    8   11   11   11   11   12   12   12 
LCS_GDT     A     226     A     226      0    6    7     0    0    4    6    6    6    7    7    7    8    8    8    9   11   11   11   11   12   12   12 
LCS_GDT     I     277     I     277      4    5    5     3    4    4    5    5    5    5    6    6    7    7   10   13   13   14   15   15   15   15   15 
LCS_GDT     E     278     E     278      4    5    5     3    4    4    5    6    7    9    9   10   11   12   13   14   14   14   15   15   15   15   15 
LCS_GDT     Q     279     Q     279      4    5    5     3    4    4    5    5    5    5    6   10   11   12   13   14   14   14   15   15   15   15   15 
LCS_GDT     G     280     G     280      4    5    5     3    4    4    5    5    5    5    5    5   11   12   13   14   14   14   15   15   15   15   15 
LCS_GDT     E     281     E     281      3    5    5     1    3    4    5    6    7    9    9   10   11   12   13   14   14   14   15   15   15   15   15 
LCS_GDT     V     306     V     306      7    8    8     6    6    6    7    7    8    8    8    8    8    8    8    8    9    9   10   10   10   12   12 
LCS_GDT     T     307     T     307      7    8    8     6    6    6    7    7    8    8    8    8    8    8    8    8    9    9   10   10   10   12   12 
LCS_GDT     H     308     H     308      7    8    8     6    6    6    7    7    8    8    8    8    8    8    8    8    9    9   10   10   10   12   12 
LCS_GDT     I     309     I     309      7    8    8     6    6    6    7    7    8    8    8    8    8    8    8    8    9    9   10   10   10   12   12 
LCS_GDT     T     310     T     310      7    8    8     6    6    6    7    7    8    8    8    8    8    8    8    8    9    9   10   10   10   12   12 
LCS_GDT     Q     311     Q     311      7    8    8     6    6    6    7    7    8    8    8    8    8    8    8    8    9    9   10   10   10   12   12 
LCS_GDT     R     312     R     312      7    8    8     3    3    6    7    7    8    8    8    8    8    8    8    8    9    9   10   10   10   12   12 
LCS_GDT     E     313     E     313      3    8    8     3    3    5    5    7    8    8    8    8    8    8    8    8    8    8   10   10   10   12   12 
LCS_AVERAGE  LCS_A:   3.12  (   2.26    2.99    4.13 )

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      6      6      6      7      7      8      9      9     10     11     12     13     14     14     14     15     15     15     15     15 
GDT PERCENT_CA   3.12   3.12   3.12   3.65   3.65   4.17   4.69   4.69   5.21   5.73   6.25   6.77   7.29   7.29   7.29   7.81   7.81   7.81   7.81   7.81
GDT RMS_LOCAL    0.36   0.36   0.36   0.92   0.92   1.50   2.60   2.60   3.06   3.31   3.61   3.92   4.24   4.24   4.24   4.70   4.70   4.70   4.70   4.70
GDT RMS_ALL_CA  30.43  30.43  30.43  29.75  29.75  28.45  23.60  23.60  23.62  23.65  23.93  24.06  24.50  24.50  24.50  24.14  24.14  24.14  24.14  24.14

#      Molecule1      Molecule2       DISTANCE
LGA    T     122      T     122          6.741
LGA    K     123      K     123          3.235
LGA    R     124      R     124          2.506
LGA    L     125      L     125          1.742
LGA    R     126      R     126          6.766
LGA    G     127      G     127          7.306
LGA    A     128      A     128          3.622
LGA    P     129      P     129          3.438
LGA    C     130      C     130          2.389
LGA    Q     131      Q     131          2.628
LGA    A     220      A     220         23.300
LGA    L     221      L     221         27.140
LGA    G     222      G     222         32.348
LGA    A     223      A     223         31.785
LGA    D     224      D     224         35.586
LGA    P     225      P     225         35.191
LGA    A     226      A     226         32.106
LGA    I     277      I     277          9.447
LGA    E     278      E     278          3.460
LGA    Q     279      Q     279          4.496
LGA    G     280      G     280          4.854
LGA    E     281      E     281          2.745
LGA    V     306      V     306         34.166
LGA    T     307      T     307         27.620
LGA    H     308      H     308         27.897
LGA    I     309      I     309         32.743
LGA    T     310      T     310         32.491
LGA    Q     311      Q     311         38.237
LGA    R     312      R     312         38.475
LGA    E     313      E     313         42.197

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   30  192    4.0      9    2.60     4.818     4.397     0.333

LGA_LOCAL      RMSD =  2.602  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 23.654  Number of atoms =   30 
Std_ALL_ATOMS  RMSD = 16.001  (standard rmsd on all 30 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.684819 * X  +  -0.087823 * Y  +   0.723401 * Z  + 110.541878
  Y_new =   0.448240 * X  +   0.731925 * Y  +   0.513192 * Z  +  27.460299
  Z_new =  -0.574546 * X  +   0.675702 * Y  +  -0.461871 * Z  +  65.684761 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.170391   -0.971201  [ DEG:   124.3543    -55.6457 ]
  Theta =   0.612049    2.529544  [ DEG:    35.0678    144.9322 ]
  Phi   =   2.562034   -0.579559  [ DEG:   146.7937    -33.2063 ]
 
# 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: T0356TS464_2-D2                               
REMARK     2: T0356_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356TS464_2-D2.T0356_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   30  192   4.0    9   2.60   4.397    16.00
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS464_2-D2
PFRMAT TS
TARGET T0356
MODEL 2
PARENT N/A
ATOM     69  CA  THR   122      88.939  78.656  77.427  1.00  0.00
ATOM     70  CA  LYS   123      85.888  76.392  77.713  1.00  0.00
ATOM     71  CA  ARG   124      88.122  73.617  79.075  1.00  0.00
ATOM     72  CA  LEU   125      89.377  75.755  81.968  1.00  0.00
ATOM     73  CA  ARG   126      85.878  76.867  82.998  1.00  0.00
ATOM     74  CA  GLY   127      84.682  73.258  82.728  1.00  0.00
ATOM     75  CA  ALA   128      87.366  72.164  85.211  1.00  0.00
ATOM     76  CA  PRO   129      86.883  75.297  87.326  1.00  0.00
ATOM     77  CA  CYS   130      83.169  74.528  87.690  1.00  0.00
ATOM     78  CA  GLN   131      84.109  70.993  88.782  1.00  0.00
ATOM     79  CA  ALA   220      87.369  47.009  92.941  1.00  0.00
ATOM     80  CA  LEU   221      88.867  44.482  90.501  1.00  0.00
ATOM     81  CA  GLY   222      92.296  45.174  91.960  1.00  0.00
ATOM     82  CA  ALA   223      93.960  47.536  89.513  1.00  0.00
ATOM     83  CA  ASP   224      96.665  49.758  91.006  1.00  0.00
ATOM     84  CA  PRO   225      96.147  52.538  88.482  1.00  0.00
ATOM     85  CA  ALA   226      93.969  53.495  85.553  1.00  0.00
ATOM     86  CA  ILE   277      90.010  44.714  82.699  1.00  0.00
ATOM     87  CA  GLU   278      87.035  46.490  81.247  1.00  0.00
ATOM     88  CA  GLN   279      85.071  48.320  83.968  1.00  0.00
ATOM     89  CA  GLY   280      81.648  47.347  82.703  1.00  0.00
ATOM     90  CA  GLU   281      79.742  44.197  81.691  1.00  0.00
ATOM     91  CA  VAL   306     111.654  68.628 103.071  1.00  0.00
ATOM     92  CA  THR   307     110.059  65.369 101.952  1.00  0.00
ATOM     93  CA  HIS   308     112.197  65.048  98.840  1.00  0.00
ATOM     94  CA  ILE   309     115.199  66.921  97.335  1.00  0.00
ATOM     95  CA  THR   310     116.239  66.722  93.648  1.00  0.00
ATOM     96  CA  GLN   311     119.640  68.063  92.605  1.00  0.00
ATOM     97  CA  ARG   312     119.006  69.025  88.976  1.00  0.00
ATOM     98  CA  GLU   313     121.642  70.821  86.830  1.00  0.00
TER
END
