
#######################################################
#                                                     #
#                        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   13 (   52),  selected   13 , name T0295AL044_3-D2
# Molecule2: number of CA atoms   95 (  803),  selected   13 , name T0295_D2.pdb
# PARAMETERS: T0295AL044_3-D2.T0295_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       190 - 209         4.91     6.50
  LCS_AVERAGE:     10.28

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       200 - 205         1.57    15.45
  LCS_AVERAGE:      4.45

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       200 - 204         0.94    16.12
  LCS_AVERAGE:      2.27

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:   95
LCS_GDT     D     184     D     184      0    4    9     0    3    3    4    5    5    6    7    9   10   10   12   12   12   12   12   13   13   13   13 
LCS_GDT     N     188     N     188      0    4    9     0    1    2    4    4    5    5    5    9   10   10   12   12   12   12   12   13   13   13   13 
LCS_GDT     L     189     L     189      0    4    9     0    1    2    4    4    5    5    5    9   10   10   12   12   12   12   12   13   13   13   13 
LCS_GDT     L     190     L     190      0    4   10     0    1    4    4    5    5    6    7    9   10   10   12   12   12   12   12   13   13   13   13 
LCS_GDT     R     191     R     191      0    3   10     0    0    2    3    5    5    6    7    9   10   10   12   12   12   12   12   13   13   13   13 
LCS_GDT     T     200     T     200      4    5   10     0    3    4    4    5    5    5    6    6    7    8    8    8    9   10   12   13   13   13   13 
LCS_GDT     H     202     H     202      4    5   10     3    3    4    4    5    5    5    6    6    7    8   12   12   12   12   12   13   13   13   13 
LCS_GDT     A     203     A     203      4    5   10     3    3    4    4    5    5    5    6    6    8   10   12   12   12   12   12   13   13   13   13 
LCS_GDT     I     204     I     204      4    5   10     3    3    4    4    5    5    5    7    9   10   10   12   12   12   12   12   13   13   13   13 
LCS_GDT     F     205     F     205      3    5   10     3    3    3    4    5    5    5    5    8   10   10   12   12   12   12   12   13   13   13   13 
LCS_GDT     R     207     R     207      3    4   10     3    3    4    4    5    5    6    7    9   10   10   12   12   12   12   12   13   13   13   13 
LCS_GDT     N     208     N     208      3    4   10     3    3    4    4    5    5    6    7    9   10   10   12   12   12   12   12   13   13   13   13 
LCS_GDT     A     209     A     209      3    3   10     3    3    4    4    5    5    6    7    9   10   10   12   12   12   12   12   13   13   13   13 
LCS_AVERAGE  LCS_A:   5.67  (   2.27    4.45   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      3      3      4      4      5      5      6      7      9     10     10     12     12     12     12     12     13     13     13     13 
GDT PERCENT_CA   3.16   3.16   4.21   4.21   5.26   5.26   6.32   7.37   9.47  10.53  10.53  12.63  12.63  12.63  12.63  12.63  13.68  13.68  13.68  13.68
GDT RMS_LOCAL    0.07   0.07   0.94   0.94   1.56   1.56   2.08   2.65   3.37   3.64   3.64   4.38   4.38   4.38   4.38   4.38   5.24   5.24   5.24   5.24
GDT RMS_ALL_CA  12.01  12.01  16.12  16.12   6.30   6.30   6.25   5.93   5.64   5.70   5.70   5.34   5.34   5.34   5.34   5.34   5.24   5.24   5.24   5.24

#      Molecule1      Molecule2       DISTANCE
LGA    D     184      D     184          3.470
LGA    N     188      N     188          4.602
LGA    L     189      L     189          4.964
LGA    L     190      L     190          2.500
LGA    R     191      R     191          3.868
LGA    T     200      T     200         13.017
LGA    H     202      H     202          8.352
LGA    A     203      A     203          7.125
LGA    I     204      I     204          3.782
LGA    F     205      F     205          4.851
LGA    R     207      R     207          2.266
LGA    N     208      N     208          2.342
LGA    A     209      A     209          2.163

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   13   95    4.0      7    2.65     6.842     6.746     0.254

LGA_LOCAL      RMSD =  2.653  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.699  Number of atoms =   13 
Std_ALL_ATOMS  RMSD =  5.242  (standard rmsd on all 13 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.598836 * X  +   0.682685 * Y  +  -0.418732 * Z  +  30.956345
  Y_new =  -0.763932 * X  +  -0.643879 * Y  +   0.042755 * Z  +  73.992729
  Z_new =  -0.240425 * X  +   0.345486 * Y  +   0.907103 * Z  + -98.487381 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.363905   -2.777688  [ DEG:    20.8502   -159.1498 ]
  Theta =   0.242803    2.898789  [ DEG:    13.9116    166.0884 ]
  Phi   =  -2.235635    0.905958  [ DEG:  -128.0924     51.9076 ]
 
# 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: T0295AL044_3-D2                               
REMARK     2: T0295_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0295AL044_3-D2.T0295_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   13   95   4.0    7   2.65   6.746     5.24
REMARK  ---------------------------------------------------------- 
MOLECULE T0295AL044_3-D2
REMARK Aligment from pdb entry: 1xxl_A
ATOM    641  N   ASP   184      12.767  16.087   7.607  1.00  0.00              
ATOM    642  CA  ASP   184      12.514  17.430   7.056  1.00  0.00              
ATOM    643  C   ASP   184      13.710  17.950   6.263  1.00  0.00              
ATOM    644  O   ASP   184      13.547  18.455   5.148  1.00  0.00              
ATOM    645  N   ASN   188      14.908  17.810   6.827  1.00  0.00              
ATOM    646  CA  ASN   188      16.108  18.233   6.129  1.00  0.00              
ATOM    647  C   ASN   188      16.327  17.455   4.849  1.00  0.00              
ATOM    648  O   ASN   188      16.722  18.046   3.851  1.00  0.00              
ATOM    649  N   LEU   189      16.082  16.146   4.851  1.00  0.00              
ATOM    650  CA  LEU   189      16.259  15.371   3.628  1.00  0.00              
ATOM    651  C   LEU   189      15.363  15.938   2.519  1.00  0.00              
ATOM    652  O   LEU   189      15.773  15.972   1.361  1.00  0.00              
ATOM    653  N   LEU   190      16.672  17.417  -1.124  1.00  0.00              
ATOM    654  CA  LEU   190      16.064  17.003  -2.407  1.00  0.00              
ATOM    655  C   LEU   190      15.545  18.213  -3.210  1.00  0.00              
ATOM    656  O   LEU   190      15.747  18.297  -4.412  1.00  0.00              
ATOM    657  N   ARG   191      14.873  19.134  -2.525  1.00  0.00              
ATOM    658  CA  ARG   191      14.326  20.349  -3.143  1.00  0.00              
ATOM    659  C   ARG   191      15.425  21.169  -3.811  1.00  0.00              
ATOM    660  O   ARG   191      15.292  21.582  -4.958  1.00  0.00              
ATOM    661  N   THR   200      16.519  21.385  -3.084  1.00  0.00              
ATOM    662  CA  THR   200      17.672  22.149  -3.596  1.00  0.00              
ATOM    663  C   THR   200      18.402  21.417  -4.718  1.00  0.00              
ATOM    664  O   THR   200      18.796  22.023  -5.703  1.00  0.00              
ATOM    665  N   HIS   202      18.578  20.107  -4.566  1.00  0.00              
ATOM    666  CA  HIS   202      19.269  19.297  -5.567  1.00  0.00              
ATOM    667  C   HIS   202      18.503  19.129  -6.857  1.00  0.00              
ATOM    668  O   HIS   202      19.108  18.932  -7.898  1.00  0.00              
ATOM    669  N   ALA   203      17.172  19.184  -6.790  1.00  0.00              
ATOM    670  CA  ALA   203      16.338  19.059  -7.980  1.00  0.00              
ATOM    671  C   ALA   203      15.846  20.407  -8.530  1.00  0.00              
ATOM    672  O   ALA   203      14.994  20.448  -9.403  1.00  0.00              
ATOM    673  N   ILE   204      16.389  21.511  -8.029  1.00  0.00              
ATOM    674  CA  ILE   204      16.071  22.846  -8.561  1.00  0.00              
ATOM    675  C   ILE   204      16.285  22.977 -10.092  1.00  0.00              
ATOM    676  O   ILE   204      17.279  22.504 -10.626  1.00  0.00              
ATOM    677  N   PHE   205      15.355  23.628 -10.791  1.00  0.00              
ATOM    678  CA  PHE   205      15.554  23.961 -12.208  1.00  0.00              
ATOM    679  C   PHE   205      16.777  24.858 -12.383  1.00  0.00              
ATOM    680  O   PHE   205      17.285  25.434 -11.417  1.00  0.00              
ATOM    681  N   ARG   207      17.237  24.989 -13.616  1.00  0.00              
ATOM    682  CA  ARG   207      18.322  25.892 -13.925  1.00  0.00              
ATOM    683  C   ARG   207      17.989  27.317 -13.517  1.00  0.00              
ATOM    684  O   ARG   207      18.835  28.018 -12.990  1.00  0.00              
ATOM    685  N   ASN   208      16.746  27.729 -13.743  1.00  0.00              
ATOM    686  CA  ASN   208      16.314  29.080 -13.410  1.00  0.00              
ATOM    687  C   ASN   208      16.343  29.306 -11.878  1.00  0.00              
ATOM    688  O   ASN   208      16.750  30.371 -11.436  1.00  0.00              
ATOM    689  N   ALA   209      15.910  28.320 -11.091  1.00  0.00              
ATOM    690  CA  ALA   209      15.945  28.411  -9.628  1.00  0.00              
ATOM    691  C   ALA   209      17.388  28.441  -9.084  1.00  0.00              
ATOM    692  O   ALA   209      17.722  29.201  -8.154  1.00  0.00              
END
