
#######################################################
#                                                     #
#                        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   22 (   22),  selected   22 , name T0320TS599_1-D1
# Molecule2: number of CA atoms  214 ( 1760),  selected   22 , name T0320_D1.pdb
# PARAMETERS: T0320TS599_1-D1.T0320_D1.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:    22       206 - 227         4.50     4.50
  LCS_AVERAGE:     10.28

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12       215 - 226         1.92    13.00
  LONGEST_CONTINUOUS_SEGMENT:    12       216 - 227         1.94    14.43
  LCS_AVERAGE:      5.42

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       215 - 223         0.91    12.85
  LCS_AVERAGE:      3.14

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:  214
LCS_GDT     L     206     L     206      0   11   22     0    0    7    9   11   11   12   14   16   17   18   20   20   21   21   22   22   22   22   22 
LCS_GDT     L     207     L     207      4   11   22     0    0    5    7   11   11   12   13   15   16   17   20   20   20   21   22   22   22   22   22 
LCS_GDT     Y     208     Y     208      7   11   22     4    7    7    9   11   11   12   14   16   17   18   20   20   21   21   22   22   22   22   22 
LCS_GDT     S     209     S     209      7   11   22     4    7    7    9   11   11   12   14   16   17   18   20   20   21   21   22   22   22   22   22 
LCS_GDT     N     210     N     210      7   11   22     4    7    7    9   11   11   12   14   16   17   18   20   20   21   21   22   22   22   22   22 
LCS_GDT     E     211     E     211      7   11   22     4    7    7    9   11   11   12   14   16   17   18   20   20   21   21   22   22   22   22   22 
LCS_GDT     P     212     P     212      7   11   22     4    7    7    9   11   11   12   14   16   17   18   20   20   21   21   22   22   22   22   22 
LCS_GDT     I     213     I     213      7   11   22     4    7    7    9   11   11   12   14   16   17   18   20   20   21   21   22   22   22   22   22 
LCS_GDT     C     214     C     214      7   11   22     4    7    7    9   11   11   12   14   16   17   18   20   20   21   21   22   22   22   22   22 
LCS_GDT     G     215     G     215      9   12   22     4    6    9    9   11   13   13   14   15   16   17   20   20   21   21   22   22   22   22   22 
LCS_GDT     L     216     L     216      9   12   22     4    6    9    9   11   13   13   14   16   17   18   20   20   21   21   22   22   22   22   22 
LCS_GDT     Y     217     Y     217      9   12   22     4    6    9    9   11   13   13   13   16   17   18   20   20   21   21   22   22   22   22   22 
LCS_GDT     G     218     G     218      9   12   22     4    6    9    9   11   13   13   14   16   17   18   20   20   21   21   22   22   22   22   22 
LCS_GDT     K     219     K     219      9   12   22     4    6    9    9   11   13   13   14   16   17   18   20   20   21   21   22   22   22   22   22 
LCS_GDT     G     220     G     220      9   12   22     4    6    9    9   11   13   13   13   16   17   18   20   20   21   21   22   22   22   22   22 
LCS_GDT     F     221     F     221      9   12   22     4    6    9    9   11   13   13   13   16   17   18   20   20   21   21   22   22   22   22   22 
LCS_GDT     T     222     T     222      9   12   22     4    6    9    9   11   13   13   13   13   15   16   17   19   21   21   22   22   22   22   22 
LCS_GDT     S     223     S     223      9   12   22     4    6    9    9   10   13   13   13   16   17   18   20   20   21   21   22   22   22   22   22 
LCS_GDT     I     224     I     224      4   12   22     4    4    4    5   10   13   13   13   14   17   18   20   20   21   21   22   22   22   22   22 
LCS_GDT     G     225     G     225      4   12   22     4    4    5    9   11   13   13   14   16   17   18   20   20   21   21   22   22   22   22   22 
LCS_GDT     G     226     G     226      3   12   22     3    3    5    8   11   13   13   14   15   17   18   20   20   21   21   22   22   22   22   22 
LCS_GDT     I     227     I     227      3   12   22     3    3    5    8   11   13   13   13   13   15   16   18   18   21   21   22   22   22   22   22 
LCS_AVERAGE  LCS_A:   6.28  (   3.14    5.42   10.28 )

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      4      7      9      9     11     13     13     14     16     17     18     20     20     21     21     22     22     22     22     22 
GDT PERCENT_CA   1.87   3.27   4.21   4.21   5.14   6.07   6.07   6.54   7.48   7.94   8.41   9.35   9.35   9.81   9.81  10.28  10.28  10.28  10.28  10.28
GDT RMS_LOCAL    0.11   0.56   0.91   0.91   1.65   2.01   2.01   2.55   3.35   3.49   3.64   3.92   3.92   4.36   4.22   4.50   4.50   4.50   4.50   4.50
GDT RMS_ALL_CA  13.21   6.66  12.85  12.85   6.40  13.39  13.39   5.19   4.67   4.71   4.55   4.59   4.59   4.53   4.54   4.50   4.50   4.50   4.50   4.50

#      Molecule1      Molecule2       DISTANCE
LGA    L     206      L     206          2.857
LGA    L     207      L     207          4.985
LGA    Y     208      Y     208          1.694
LGA    S     209      S     209          1.832
LGA    N     210      N     210          2.024
LGA    E     211      E     211          0.770
LGA    P     212      P     212          1.557
LGA    I     213      I     213          1.165
LGA    C     214      C     214          2.850
LGA    G     215      G     215          3.831
LGA    L     216      L     216          0.751
LGA    Y     217      Y     217          4.543
LGA    G     218      G     218          2.134
LGA    K     219      K     219          3.854
LGA    G     220      G     220          7.655
LGA    F     221      F     221          7.892
LGA    T     222      T     222         11.301
LGA    S     223      S     223          8.288
LGA    I     224      I     224          7.452
LGA    G     225      G     225          3.860
LGA    G     226      G     226          3.462
LGA    I     227      I     227          7.699

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   22  214    4.0     14    2.55     6.075     6.203     0.529

LGA_LOCAL      RMSD =  2.548  Number of atoms =   14  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.091  Number of atoms =   22 
Std_ALL_ATOMS  RMSD =  4.504  (standard rmsd on all 22 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.347196 * X  +   0.866754 * Y  +  -0.358039 * Z  +  14.688589
  Y_new =  -0.192740 * X  +   0.307687 * Y  +   0.931762 * Z  +  26.597799
  Z_new =   0.917772 * X  +   0.392513 * Y  +   0.060231 * Z  +  12.362457 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.418535   -1.723058  [ DEG:    81.2761    -98.7239 ]
  Theta =  -1.162434   -1.979159  [ DEG:   -66.6026   -113.3974 ]
  Phi   =  -2.634817    0.506776  [ DEG:  -150.9639     29.0361 ]
 
# 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: T0320TS599_1-D1                               
REMARK     2: T0320_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320TS599_1-D1.T0320_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   22  214   4.0   14   2.55   6.203     4.50
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS599_1-D1
PFRMAT TS                                                                       
TARGET T0320                                                                    
MODEL  1                                                                        
PARENT N/A                                                                      
ATOM    206  CA  LEU   206       6.824  25.456  18.133  1.00  0.00              
ATOM    207  CA  LEU   207       2.983  24.951  18.061  1.00  0.00              
ATOM    208  CA  TYR   208      -0.806  24.025  16.506  1.00  0.00              
ATOM    209  CA  SER   209       0.752  27.195  18.227  1.00  0.00              
ATOM    210  CA  ASN   210       1.086  29.448  15.256  1.00  0.00              
ATOM    211  CA  GLU   211       4.782  30.114  15.299  1.00  0.00              
ATOM    212  CA  PRO   212       6.783  30.333  12.176  1.00  0.00              
ATOM    213  CA  ILE   213       9.505  27.732  12.159  1.00  0.00              
ATOM    214  CA  CYS   214      11.797  27.518   9.160  1.00  0.00              
ATOM    215  CA  GLY   215      13.424  24.324   8.470  1.00  0.00              
ATOM    216  CA  LEU   216      16.867  24.467   6.803  1.00  0.00              
ATOM    217  CA  TYR   217      16.391  21.550   4.279  1.00  0.00              
ATOM    218  CA  GLY   218      12.952  22.762   3.274  1.00  0.00              
ATOM    219  CA  LYS   219      14.237  26.294   2.756  1.00  0.00              
ATOM    220  CA  GLY   220      17.171  25.307   0.592  1.00  0.00              
ATOM    221  CA  PHE   221      20.078  25.511   3.101  1.00  0.00              
ATOM    222  CA  THR   222      22.419  22.796   2.571  1.00  0.00              
ATOM    223  CA  SER   223      23.487  21.581   6.124  1.00  0.00              
ATOM    224  CA  ILE   224      26.633  23.455   7.460  1.00  0.00              
ATOM    225  CA  GLY   225      27.826  21.060  10.099  1.00  0.00              
ATOM    226  CA  GLY   226      29.283  22.710  13.158  1.00  0.00              
ATOM    227  CA  ILE   227      26.990  25.613  14.380  1.00  0.00              
TER                                                                             
END
