
#######################################################
#                                                     #
#                        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    7 (   28),  selected    7 , name T0356AL044_5-D2
# Molecule2: number of CA atoms  192 ( 1487),  selected    7 , name T0356_D2.pdb
# PARAMETERS: T0356AL044_5-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:     7       305 - 313         4.15     4.15
  LCS_AVERAGE:      3.65

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       305 - 309         0.97     5.47
  LCS_AVERAGE:      1.19

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       305 - 309         0.97     5.47
  LCS_AVERAGE:      1.19

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     305     T     305      4    4    7     0    3    4    4    4    5    5    5    5    5    6    6    7    7    7    7    7    7    7    7 
LCS_GDT     V     306     V     306      4    4    7     0    3    4    4    4    5    5    5    5    5    6    6    7    7    7    7    7    7    7    7 
LCS_GDT     H     308     H     308      4    4    7     0    3    4    4    4    5    5    5    5    5    6    6    7    7    7    7    7    7    7    7 
LCS_GDT     I     309     I     309      4    4    7     1    3    4    4    4    5    5    5    5    5    6    6    7    7    7    7    7    7    7    7 
LCS_GDT     T     310     T     310      0    0    7     0    0    0    1    1    2    2    3    3    4    4    6    7    7    7    7    7    7    7    7 
LCS_GDT     Q     311     Q     311      0    0    7     0    0    0    0    0    0    1    3    4    5    6    6    7    7    7    7    7    7    7    7 
LCS_GDT     E     313     E     313      0    0    7     0    0    0    0    0    5    5    5    5    5    6    6    7    7    7    7    7    7    7    7 
LCS_AVERAGE  LCS_A:   2.01  (   1.19    1.19    3.65 )

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      1      3      4      4      4      5      5      5      5      5      6      6      7      7      7      7      7      7      7      7 
GDT PERCENT_CA   0.52   1.56   2.08   2.08   2.08   2.60   2.60   2.60   2.60   2.60   3.12   3.12   3.65   3.65   3.65   3.65   3.65   3.65   3.65   3.65
GDT RMS_LOCAL   31.62   0.60   0.97   0.97   0.97   1.81   1.81   1.81   1.81   1.81   3.00   3.00   4.15   4.15   4.15   4.15   4.15   4.15   4.15   4.15
GDT RMS_ALL_CA   5.42   6.77   5.47   5.47   5.47   4.73   4.73   4.73   4.73   4.73   4.42   4.42   4.15   4.15   4.15   4.15   4.15   4.15   4.15   4.15

#      Molecule1      Molecule2       DISTANCE
LGA    T     305      T     305          2.069
LGA    V     306      V     306          1.572
LGA    H     308      H     308          0.929
LGA    I     309      I     309          1.545
LGA    T     310      T     310          9.750
LGA    Q     311      Q     311          6.737
LGA    E     313      E     313          2.533

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    7  192    4.0      5    1.81     2.474     2.226     0.261

LGA_LOCAL      RMSD =  1.812  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.734  Number of atoms =    7 
Std_ALL_ATOMS  RMSD =  4.153  (standard rmsd on all 7 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.488593 * X  +  -0.176525 * Y  +   0.854468 * Z  + -28.266644
  Y_new =  -0.166090 * X  +  -0.980230 * Y  +  -0.107535 * Z  +  91.719849
  Z_new =   0.856558 * X  +  -0.089378 * Y  +  -0.508252 * Z  + 109.147888 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.967518    0.174074  [ DEG:  -170.0263      9.9737 ]
  Theta =  -1.028562   -2.113030  [ DEG:   -58.9323   -121.0677 ]
  Phi   =  -0.327681    2.813911  [ DEG:   -18.7748    161.2252 ]
 
# 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: T0356AL044_5-D2                               
REMARK     2: T0356_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356AL044_5-D2.T0356_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    7  192   4.0    5   1.81   2.226     4.15
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL044_5-D2
REMARK Aligment from pdb entry: 1yw4_A
ATOM      1  N   THR   305      81.373  53.376  88.754  1.00  0.00              
ATOM      2  CA  THR   305      81.355  54.502  89.671  1.00  0.00              
ATOM      3  C   THR   305      82.208  55.662  89.183  1.00  0.00              
ATOM      4  O   THR   305      83.024  55.513  88.272  1.00  0.00              
ATOM      5  N   VAL   306      81.991  56.828  89.775  1.00  0.00              
ATOM      6  CA  VAL   306      82.730  58.012  89.383  1.00  0.00              
ATOM      7  C   VAL   306      83.502  58.598  90.551  1.00  0.00              
ATOM      8  O   VAL   306      83.160  58.385  91.713  1.00  0.00              
ATOM      9  N   HIS   308      84.552  59.338  90.214  1.00  0.00              
ATOM     10  CA  HIS   308      85.380  60.011  91.199  1.00  0.00              
ATOM     11  C   HIS   308      85.210  61.496  90.919  1.00  0.00              
ATOM     12  O   HIS   308      85.465  61.950  89.801  1.00  0.00              
ATOM     13  N   ILE   309      84.758  62.242  91.922  1.00  0.00              
ATOM     14  CA  ILE   309      84.547  63.682  91.789  1.00  0.00              
ATOM     15  C   ILE   309      85.759  64.387  92.388  1.00  0.00              
ATOM     16  O   ILE   309      86.007  64.309  93.592  1.00  0.00              
ATOM     17  N   THR   310      87.757  73.245  95.313  1.00  0.00              
ATOM     18  CA  THR   310      88.159  74.281  96.262  1.00  0.00              
ATOM     19  C   THR   310      87.072  75.345  96.398  1.00  0.00              
ATOM     20  O   THR   310      87.358  76.546  96.429  1.00  0.00              
ATOM     21  N   GLN   311      80.245  77.104  94.497  1.00  0.00              
ATOM     22  CA  GLN   311      79.559  76.183  93.598  1.00  0.00              
ATOM     23  C   GLN   311      79.312  74.817  94.220  1.00  0.00              
ATOM     24  O   GLN   311      78.227  74.251  94.073  1.00  0.00              
ATOM     25  N   GLU   313      80.319  74.290  94.910  1.00  0.00              
ATOM     26  CA  GLU   313      80.211  72.981  95.540  1.00  0.00              
ATOM     27  C   GLU   313      80.049  71.953  94.422  1.00  0.00              
ATOM     28  O   GLU   313      80.346  72.246  93.262  1.00  0.00              
END
