
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  ------------ 10/2009               #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

!!!   License for LGA program has expired  !!!
#   For updated version of the LGA program   #
# please contact Adam Zemla:  adamz@llnl.gov #

# Molecule1: number of CA atoms   61 (  460),  selected   60 , name one
# Molecule2: number of CA atoms   60 (  451),  selected   60 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.35     0.35
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.35     0.35
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.35     0.35
  LCS_AVERAGE:    100.00

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   60
LCS_GDT     RESIDUE       RESIDUE       SEGMENT_SIZE    GLOBAL DISTANCE TEST COLUMNS: number of residues under the threshold assigned to each residue pair
LCS_GDT   NAME NUMBER   NAME NUMBER    1.0  2.0  5.0    0.5  1.0  1.5  2.0  2.5  3.0  3.5  4.0  4.5  5.0  5.5  6.0  6.5  7.0  7.5  8.0  8.5  9.0  9.5 10.0
LCS_GDT     D     1_A     D     1_A     60   60   60     50   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D     2_A     D     2_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K     3_A     K     3_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     4_A     A     4_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     5_A     A     5_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     C     6_A     C     6_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     7_A     A     7_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D     8_A     D     8_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G     9_A     G     9_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     I    10_A     I    10_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    11_A     A    11_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    12_A     A    12_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    13_A     V    13_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    14_A     K    14_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    15_A     A    15_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    16_A     R    16_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    17_A     V    17_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    18_A     E    18_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    19_A     K    19_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    20_A     L    20_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    21_A     A    21_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    22_A     P    22_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    23_A     E    23_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    24_A     A    24_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    25_A     V    25_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    26_A     P    26_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     Q    27_A     Q    27_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    28_A     K    28_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    29_A     L    29_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    30_A     K    30_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    31_A     R    31_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    32_A     A    32_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    33_A     L    33_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    34_A     K    34_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     I    35_A     I    35_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    36_A     A    36_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    37_A     E    37_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    38_A     R    38_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    39_A     E    39_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     Q    40_A     Q    40_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G    41_A     G    41_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    42_A     E    42_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G    43_A     G    43_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    44_A     E    44_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     F    45_A     F    45_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    46_A     D    46_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    47_A     E    47_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     C    48_A     C    48_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    49_A     L    49_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    50_A     E    50_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    51_A     A    51_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    52_A     L    52_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    53_A     D    53_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    54_A     D    54_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    55_A     A    55_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    56_A     K    56_A     60   60   60     50   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    57_A     R    57_A     60   60   60     55   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    58_A     A    58_A     60   60   60     45   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    59_A     L    59_A     60   60   60     52   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    60_A     P    60_A     60   60   60     47   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_AVERAGE  LCS_A: 100.00  ( 100.00  100.00  100.00 )

GLOBAL_DISTANCE_TEST (summary information about detected largest sets of residues (represented by selected AToms) that can fit under specified thresholds)
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_AT     55     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60 
GDT PERCENT_AT  91.67 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35
GDT RMS_ALL_AT   0.36   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35   0.35

# Checking swapping
#   possible swapping detected:  E    37_A      E    37_A
#   possible swapping detected:  E    39_A      E    39_A
#   possible swapping detected:  E    42_A      E    42_A
#   possible swapping detected:  E    44_A      E    44_A
#   possible swapping detected:  E    50_A      E    50_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_A      D     1_A     0.613     0    0.053   0.334     1.959   97.619   90.714
LGA    D     2_A      D     2_A     0.306     0    0.020   0.287     1.858  100.000   94.226
LGA    K     3_A      K     3_A     0.234     0    0.020   0.545     1.590  100.000   92.804
LGA    A     4_A      A     4_A     0.318     0    0.021   0.022     0.416  100.000  100.000
LGA    A     5_A      A     5_A     0.175     0    0.051   0.069     0.424  100.000  100.000
LGA    C     6_A      C     6_A     0.105     0    0.018   0.048     0.165  100.000  100.000
LGA    A     7_A      A     7_A     0.073     0    0.030   0.039     0.182  100.000  100.000
LGA    D     8_A      D     8_A     0.133     0    0.016   0.093     0.519  100.000   98.810
LGA    G     9_A      G     9_A     0.125     0    0.050   0.050     0.156  100.000  100.000
LGA    I    10_A      I    10_A     0.151     0    0.017   0.045     0.310  100.000  100.000
LGA    A    11_A      A    11_A     0.186     0    0.031   0.042     0.253  100.000  100.000
LGA    A    12_A      A    12_A     0.126     0    0.019   0.020     0.281  100.000  100.000
LGA    V    13_A      V    13_A     0.211     0    0.028   0.055     0.327  100.000  100.000
LGA    K    14_A      K    14_A     0.223     0    0.073   0.187     0.574  100.000   98.942
LGA    A    15_A      A    15_A     0.145     0    0.069   0.065     0.426  100.000  100.000
LGA    R    16_A      R    16_A     0.293     0    0.020   0.237     1.533  100.000   94.113
LGA    V    17_A      V    17_A     0.309     0    0.039   0.050     0.337  100.000  100.000
LGA    E    18_A      E    18_A     0.166     0    0.022   0.937     3.311  100.000   81.852
LGA    K    19_A      K    19_A     0.318     0    0.054   1.070     4.933   97.619   81.005
LGA    L    20_A      L    20_A     0.356     0    0.031   0.180     0.575  100.000   96.429
LGA    A    21_A      A    21_A     0.287     0    0.017   0.026     0.453  100.000  100.000
LGA    P    22_A      P    22_A     0.554     0    0.019   0.044     0.797   92.857   94.558
LGA    E    23_A      E    23_A     0.605     0    0.046   0.943     2.081   90.476   80.847
LGA    A    24_A      A    24_A     0.613     0    0.064   0.075     0.731   90.476   90.476
LGA    V    25_A      V    25_A     0.409     0    0.036   0.068     0.472  100.000  100.000
LGA    P    26_A      P    26_A     0.350     0    0.048   0.080     0.542  100.000   98.639
LGA    Q    27_A      Q    27_A     0.337     0    0.013   1.142     4.512  100.000   83.704
LGA    K    28_A      K    28_A     0.216     0    0.040   0.695     2.826  100.000   92.116
LGA    L    29_A      L    29_A     0.323     0    0.017   1.139     2.743   97.619   88.095
LGA    K    30_A      K    30_A     0.353     0    0.013   0.076     0.569  100.000   98.942
LGA    R    31_A      R    31_A     0.340     0    0.034   1.271     6.951  100.000   69.351
LGA    A    32_A      A    32_A     0.408     0    0.037   0.047     0.421  100.000  100.000
LGA    L    33_A      L    33_A     0.374     0    0.029   0.055     0.406  100.000  100.000
LGA    K    34_A      K    34_A     0.233     0    0.066   0.646     2.916  100.000   90.159
LGA    I    35_A      I    35_A     0.359     0    0.088   0.098     0.440  100.000  100.000
LGA    A    36_A      A    36_A     0.371     0    0.018   0.018     0.458  100.000  100.000
LGA    E    37_A      E    37_A     0.303     0    0.029   0.246     0.700  100.000   97.884
LGA    R    38_A      R    38_A     0.297     0    0.063   0.608     2.056  100.000   93.333
LGA    E    39_A      E    39_A     0.353     0    0.031   1.144     4.000  100.000   85.714
LGA    Q    40_A      Q    40_A     0.313     0    0.057   0.179     0.863   97.619   96.825
LGA    G    41_A      G    41_A     0.126     0    0.047   0.047     0.179  100.000  100.000
LGA    E    42_A      E    42_A     0.410     0    0.131   0.192     0.749  100.000   95.767
LGA    G    43_A      G    43_A     0.256     0    0.039   0.039     0.389  100.000  100.000
LGA    E    44_A      E    44_A     0.268     0    0.080   0.268     1.517  100.000   92.857
LGA    F    45_A      F    45_A     0.446     0    0.024   0.078     0.539  100.000   98.268
LGA    D    46_A      D    46_A     0.519     0    0.071   0.386     1.121   97.619   94.107
LGA    E    47_A      E    47_A     0.356     0    0.029   1.046     3.211  100.000   85.608
LGA    C    48_A      C    48_A     0.161     0    0.014   0.090     0.309  100.000  100.000
LGA    L    49_A      L    49_A     0.328     0    0.041   0.106     0.551  100.000   97.619
LGA    E    50_A      E    50_A     0.208     0    0.026   0.237     0.945  100.000   98.942
LGA    A    51_A      A    51_A     0.211     0    0.019   0.025     0.347  100.000  100.000
LGA    L    52_A      L    52_A     0.384     0    0.017   0.060     0.568  100.000   98.810
LGA    D    53_A      D    53_A     0.278     0    0.030   0.780     3.459  100.000   84.940
LGA    D    54_A      D    54_A     0.262     0    0.028   0.211     0.757  100.000   98.810
LGA    A    55_A      A    55_A     0.411     0    0.010   0.012     0.519   97.619   98.095
LGA    K    56_A      K    56_A     0.672     0    0.034   0.574     1.548   92.857   85.608
LGA    R    57_A      R    57_A     0.346     0    0.015   1.014     4.556   97.619   80.736
LGA    A    58_A      A    58_A     0.613     0    0.033   0.037     0.955   92.857   92.381
LGA    L    59_A      L    59_A     0.517     0    0.037   0.154     1.340   95.238   90.595
LGA    P    60_A      P    60_A     0.604     0    0.033   0.342     0.976   92.857   91.837

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       60     240    240  100.00     451    451  100.00                60
SUMMARY(RMSD_GDC):     0.353          0.351                  1.032           98.849   94.575

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   61   60    4.0     60    0.35   100.000   100.000    13.253

LGA_LOCAL      RMSD:   0.353  Number of atoms:   60  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.353  Number of assigned atoms:   60 
Std_ASGN_ATOMS RMSD:   0.353  Standard rmsd on all 60 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.037408 * X  +  -0.069590 * Y  +   0.996874 * Z  +  13.190659
  Y_new =  -0.976216 * X  +   0.215726 * Y  +  -0.021573 * Z  +   7.631656
  Z_new =  -0.213550 * X  +  -0.973971 * Y  +  -0.076004 * Z  +   9.298099 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.609097  0.215208 -1.648674   [DEG:  -92.1944   12.3305  -94.4621 ]
ZXZ:  1.549159  1.646874 -2.925751   [DEG:   88.7603   94.3589 -167.6332 ]
 
# END of job
