
#######################################################
#                                                     #
#                        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   20 (   80),  selected    5 , name T0291AL170_2_2-D2
# Molecule2: number of CA atoms  181 ( 1450),  selected    5 , name T0291_D2.pdb
# PARAMETERS: T0291AL170_2_2-D2.T0291_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:     5       172 - 176         0.71     0.71
  LCS_AVERAGE:      2.76

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       172 - 176         0.71     0.71
  LCS_AVERAGE:      2.76

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       172 - 176         0.71     0.71
  LCS_AVERAGE:      2.76

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:  181
LCS_GDT     G     172     G     172      5    5    5     3    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     L     173     L     173      5    5    5     3    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     G     174     G     174      5    5    5     3    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     R     175     R     175      5    5    5     3    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     V     176     V     176      5    5    5     3    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_AVERAGE  LCS_A:   2.76  (   2.76    2.76    2.76 )

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      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5 
GDT PERCENT_CA   1.66   2.76   2.76   2.76   2.76   2.76   2.76   2.76   2.76   2.76   2.76   2.76   2.76   2.76   2.76   2.76   2.76   2.76   2.76   2.76
GDT RMS_LOCAL    0.18   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71
GDT RMS_ALL_CA   1.80   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71

#      Molecule1      Molecule2       DISTANCE
LGA    G     172      G     172          0.326
LGA    L     173      L     173          0.761
LGA    G     174      G     174          0.730
LGA    R     175      R     175          0.958
LGA    V     176      V     176          0.599

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   20  181    4.0      5    0.71     2.762     2.762     0.620

LGA_LOCAL      RMSD =  0.706  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.706  Number of atoms =    5 
Std_ALL_ATOMS  RMSD =  0.706  (standard rmsd on all 5 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.353542 * X  +   0.565310 * Y  +   0.745274 * Z  + -39.048218
  Y_new =   0.927821 * X  +   0.110582 * Y  +   0.356259 * Z  + -33.266384
  Z_new =   0.118982 * X  +   0.817433 * Y  +  -0.563602 * Z  +  78.669640 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.174426   -0.967167  [ DEG:   124.5854    -55.4146 ]
  Theta =  -0.119265   -3.022328  [ DEG:    -6.8334   -173.1666 ]
  Phi   =   1.934857   -1.206736  [ DEG:   110.8591    -69.1409 ]
 
# 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: T0291AL170_2_2-D2                             
REMARK     2: T0291_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0291AL170_2_2-D2.T0291_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   20  181   4.0    5   0.71   2.762     0.71
REMARK  ---------------------------------------------------------- 
MOLECULE T0291AL170_2_2-D2
REMARK PARENT number 2
PARENT 1M14A
REMARK Aligment from pdb entry: 1M14A
ATOM   1077  N   GLY   172      -7.503  17.194  58.176  1.00  0.00              
ATOM   1078  CA  GLY   172      -8.562  17.492  59.123  1.00  0.00              
ATOM   1079  C   GLY   172      -8.189  18.369  60.315  1.00  0.00              
ATOM   1080  O   GLY   172      -9.043  18.690  61.132  1.00  0.00              
ATOM   1081  N   LEU   173      -6.920  18.739  60.440  1.00  0.00              
ATOM   1082  CA  LEU   173      -6.487  19.580  61.545  1.00  0.00              
ATOM   1083  C   LEU   173      -5.584  20.678  61.026  1.00  0.00              
ATOM   1084  O   LEU   173      -5.157  21.551  61.781  1.00  0.00              
ATOM   1085  N   GLY   174      -5.320  20.650  59.724  1.00  0.00              
ATOM   1086  CA  GLY   174      -4.441  21.636  59.096  1.00  0.00              
ATOM   1087  C   GLY   174      -4.940  23.057  59.270  1.00  0.00              
ATOM   1088  O   GLY   174      -6.146  23.318  59.206  1.00  0.00              
ATOM   1089  N   ARG   175      -4.010  23.976  59.481  1.00  0.00              
ATOM   1090  CA  ARG   175      -4.352  25.379  59.634  1.00  0.00              
ATOM   1091  C   ARG   175      -3.460  26.269  58.784  1.00  0.00              
ATOM   1092  O   ARG   175      -2.255  26.075  58.758  1.00  0.00              
ATOM   1093  N   VAL   176      -4.063  27.186  58.026  1.00  0.00              
ATOM   1094  CA  VAL   176      -3.303  28.140  57.204  1.00  0.00              
ATOM   1095  C   VAL   176      -2.887  29.343  58.063  1.00  0.00              
ATOM   1096  O   VAL   176      -3.711  29.917  58.776  1.00  0.00              
ATOM   1097  N   LEU   177      -1.603  29.685  58.043  1.00  0.00              
ATOM   1098  CA  LEU   177      -1.104  30.808  58.832  1.00  0.00              
ATOM   1099  C   LEU   177      -1.132  32.119  58.054  1.00  0.00              
ATOM   1100  O   LEU   177      -0.861  32.141  56.844  1.00  0.00              
ATOM   1101  N   GLU   178      -1.407  33.213  58.765  1.00  0.00              
ATOM   1102  CA  GLU   178      -1.438  34.524  58.140  1.00  0.00              
ATOM   1103  C   GLU   178      -0.073  35.004  57.665  1.00  0.00              
ATOM   1104  O   GLU   178       0.854  34.209  57.467  1.00  0.00              
ATOM   1105  N   ASP   179       0.042  36.310  57.453  1.00  0.00              
ATOM   1106  CA  ASP   179       1.296  36.910  56.999  1.00  0.00              
ATOM   1107  C   ASP   179       2.105  37.417  58.189  1.00  0.00              
ATOM   1108  O   ASP   179       3.325  37.248  58.247  1.00  0.00              
ATOM   1109  N   ASP   180       1.398  38.040  59.131  1.00  0.00              
ATOM   1110  CA  ASP   180       1.990  38.599  60.346  1.00  0.00              
ATOM   1111  C   ASP   180       1.946  37.564  61.469  1.00  0.00              
ATOM   1112  O   ASP   180       2.175  37.884  62.640  1.00  0.00              
ATOM   1113  N   GLU   182       1.651  36.323  61.101  1.00  0.00              
ATOM   1114  CA  GLU   182       1.549  35.238  62.063  1.00  0.00              
ATOM   1115  C   GLU   182       2.718  34.274  61.907  1.00  0.00              
ATOM   1116  O   GLU   182       3.293  34.167  60.826  1.00  0.00              
ATOM   1117  N   ALA   183       3.081  33.598  62.993  1.00  0.00              
ATOM   1118  CA  ALA   183       4.187  32.640  62.971  1.00  0.00              
ATOM   1119  C   ALA   183       3.870  31.341  63.720  1.00  0.00              
ATOM   1120  O   ALA   183       4.657  30.397  63.681  1.00  0.00              
ATOM   1121  N   ALA   184       2.734  31.307  64.419  1.00  0.00              
ATOM   1122  CA  ALA   184       2.320  30.126  65.175  1.00  0.00              
ATOM   1123  C   ALA   184       0.816  30.072  65.431  1.00  0.00              
ATOM   1124  O   ALA   184       0.187  31.086  65.726  1.00  0.00              
ATOM   1125  N   TYR   185       0.248  28.879  65.308  1.00  0.00              
ATOM   1126  CA  TYR   185      -1.172  28.667  65.523  1.00  0.00              
ATOM   1127  C   TYR   185      -1.496  28.285  66.967  1.00  0.00              
ATOM   1128  O   TYR   185      -0.961  27.310  67.508  1.00  0.00              
ATOM   1129  N   THR   186      -2.424  29.032  67.564  1.00  0.00              
ATOM   1130  CA  THR   186      -2.850  28.794  68.937  1.00  0.00              
ATOM   1131  C   THR   186      -4.158  28.015  68.983  1.00  0.00              
ATOM   1132  O   THR   186      -5.235  28.577  68.787  1.00  0.00              
ATOM   1133  N   THR   187      -4.044  26.714  69.227  1.00  0.00              
ATOM   1134  CA  THR   187      -5.192  25.816  69.306  1.00  0.00              
ATOM   1135  C   THR   187      -6.040  26.103  70.540  1.00  0.00              
ATOM   1136  O   THR   187      -5.622  26.843  71.427  1.00  0.00              
ATOM   1137  N   ARG   188      -7.210  25.479  70.611  1.00  0.00              
ATOM   1138  CA  ARG   188      -8.104  25.700  71.733  1.00  0.00              
ATOM   1139  C   ARG   188      -8.849  24.428  72.137  1.00  0.00              
ATOM   1140  O   ARG   188      -9.216  24.266  73.303  1.00  0.00              
ATOM   1141  N   GLY   189      -9.048  23.523  71.181  1.00  0.00              
ATOM   1142  CA  GLY   189      -9.759  22.281  71.455  1.00  0.00              
ATOM   1143  C   GLY   189      -9.048  21.312  72.388  1.00  0.00              
ATOM   1144  O   GLY   189      -8.937  21.558  73.595  1.00  0.00              
ATOM   1145  N   GLY   190      -8.592  20.191  71.828  1.00  0.00              
ATOM   1146  CA  GLY   190      -7.891  19.187  72.618  1.00  0.00              
ATOM   1147  C   GLY   190      -8.223  17.768  72.193  1.00  0.00              
ATOM   1148  O   GLY   190      -8.934  17.043  72.894  1.00  0.00              
ATOM   1149  N   LYS   191      -7.678  17.363  71.051  1.00  0.00              
ATOM   1150  CA  LYS   191      -7.917  16.033  70.506  1.00  0.00              
ATOM   1151  C   LYS   191      -6.786  15.650  69.557  1.00  0.00              
ATOM   1152  O   LYS   191      -6.976  14.865  68.623  1.00  0.00              
ATOM   1153  N   ILE   192      -5.615  16.229  69.790  1.00  0.00              
ATOM   1154  CA  ILE   192      -4.450  15.951  68.963  1.00  0.00              
ATOM   1155  C   ILE   192      -3.704  14.752  69.553  1.00  0.00              
ATOM   1156  O   ILE   192      -3.676  14.582  70.771  1.00  0.00              
TER
END
