
#######################################################
#                                                     #
#                        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        0.34     0.34
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.34     0.34
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.34     0.34
  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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     58   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     54   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     58   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     58   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     58   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     37   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     58     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60 
GDT PERCENT_AT  96.67 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.31   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34
GDT RMS_ALL_AT   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34

# Checking swapping
#   possible swapping detected:  E    18_A      E    18_A
#   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     0.454     0    0.085   0.702     1.951  100.000   91.905
LGA    D     2_A      D     2_A     0.244     0    0.005   0.127     0.821  100.000   98.810
LGA    K     3_A      K     3_A     0.229     0    0.016   0.592     1.459  100.000   93.757
LGA    A     4_A      A     4_A     0.314     0    0.005   0.007     0.381  100.000  100.000
LGA    A     5_A      A     5_A     0.225     0    0.042   0.046     0.360  100.000  100.000
LGA    C     6_A      C     6_A     0.136     0    0.009   0.081     0.623  100.000   98.413
LGA    A     7_A      A     7_A     0.161     0    0.018   0.018     0.208  100.000  100.000
LGA    D     8_A      D     8_A     0.215     0    0.013   0.103     0.550  100.000   97.619
LGA    G     9_A      G     9_A     0.103     0    0.029   0.029     0.187  100.000  100.000
LGA    I    10_A      I    10_A     0.243     0    0.009   0.018     0.323  100.000  100.000
LGA    A    11_A      A    11_A     0.263     0    0.004   0.005     0.293  100.000  100.000
LGA    A    12_A      A    12_A     0.113     0    0.019   0.019     0.157  100.000  100.000
LGA    V    13_A      V    13_A     0.206     0    0.008   0.019     0.308  100.000  100.000
LGA    K    14_A      K    14_A     0.296     0    0.006   0.135     0.668  100.000   97.884
LGA    A    15_A      A    15_A     0.265     0    0.025   0.028     0.366  100.000  100.000
LGA    R    16_A      R    16_A     0.298     0    0.011   0.248     1.673  100.000   92.511
LGA    V    17_A      V    17_A     0.238     0    0.016   0.041     0.264  100.000  100.000
LGA    E    18_A      E    18_A     0.260     0    0.019   0.676     3.309  100.000   83.598
LGA    K    19_A      K    19_A     0.277     0    0.023   1.080     4.829  100.000   83.704
LGA    L    20_A      L    20_A     0.391     0    0.016   0.147     0.552  100.000   97.619
LGA    A    21_A      A    21_A     0.386     0    0.027   0.027     0.445  100.000  100.000
LGA    P    22_A      P    22_A     0.431     0    0.022   0.071     0.611   97.619   98.639
LGA    E    23_A      E    23_A     0.414     0    0.024   0.787     2.170  100.000   85.079
LGA    A    24_A      A    24_A     0.499     0    0.053   0.057     0.634  100.000   98.095
LGA    V    25_A      V    25_A     0.271     0    0.021   0.057     0.366  100.000  100.000
LGA    P    26_A      P    26_A     0.397     0    0.024   0.054     0.572  100.000   95.918
LGA    Q    27_A      Q    27_A     0.337     0    0.016   1.153     3.039  100.000   83.598
LGA    K    28_A      K    28_A     0.239     0    0.017   0.679     1.982  100.000   95.926
LGA    L    29_A      L    29_A     0.297     0    0.011   1.180     2.963  100.000   89.286
LGA    K    30_A      K    30_A     0.417     0    0.012   0.049     0.506   97.619   98.942
LGA    R    31_A      R    31_A     0.496     0    0.026   1.264     6.794   95.238   66.753
LGA    A    32_A      A    32_A     0.387     0    0.009   0.009     0.394  100.000  100.000
LGA    L    33_A      L    33_A     0.385     0    0.011   0.043     0.483  100.000  100.000
LGA    K    34_A      K    34_A     0.416     0    0.012   0.665     2.946  100.000   90.053
LGA    I    35_A      I    35_A     0.380     0    0.018   0.050     0.471  100.000  100.000
LGA    A    36_A      A    36_A     0.400     0    0.005   0.006     0.407  100.000  100.000
LGA    E    37_A      E    37_A     0.317     0    0.024   0.121     0.436  100.000  100.000
LGA    R    38_A      R    38_A     0.345     0    0.015   1.021     4.135  100.000   83.290
LGA    E    39_A      E    39_A     0.398     0    0.017   1.024     3.822  100.000   85.714
LGA    Q    40_A      Q    40_A     0.339     0    0.008   1.065     4.261  100.000   85.185
LGA    G    41_A      G    41_A     0.167     0    0.037   0.037     0.224  100.000  100.000
LGA    E    42_A      E    42_A     0.361     0    0.029   0.271     1.396  100.000   94.762
LGA    G    43_A      G    43_A     0.231     0    0.030   0.030     0.311  100.000  100.000
LGA    E    44_A      E    44_A     0.084     0    0.060   0.856     3.922  100.000   85.026
LGA    F    45_A      F    45_A     0.339     0    0.019   0.082     0.519  100.000   98.268
LGA    D    46_A      D    46_A     0.417     0    0.011   1.125     4.007  100.000   84.167
LGA    E    47_A      E    47_A     0.236     0    0.010   1.003     3.129  100.000   85.608
LGA    C    48_A      C    48_A     0.174     0    0.038   0.075     0.321  100.000  100.000
LGA    L    49_A      L    49_A     0.223     0    0.009   0.049     0.545  100.000   98.810
LGA    E    50_A      E    50_A     0.166     0    0.012   0.214     0.673  100.000   97.884
LGA    A    51_A      A    51_A     0.186     0    0.006   0.007     0.279  100.000  100.000
LGA    L    52_A      L    52_A     0.346     0    0.030   0.035     0.641  100.000   96.429
LGA    D    53_A      D    53_A     0.267     0    0.009   0.055     0.567  100.000   98.810
LGA    D    54_A      D    54_A     0.230     0    0.003   0.077     0.260  100.000  100.000
LGA    A    55_A      A    55_A     0.372     0    0.018   0.025     0.443  100.000  100.000
LGA    K    56_A      K    56_A     0.588     0    0.019   0.632     1.320   97.619   90.635
LGA    R    57_A      R    57_A     0.221     0    0.008   1.116     4.455  100.000   82.771
LGA    A    58_A      A    58_A     0.404     0    0.032   0.031     0.554   97.619   96.190
LGA    L    59_A      L    59_A     0.408     0    0.030   0.166     1.220  100.000   92.976
LGA    P    60_A      P    60_A     0.869     0    0.023   0.292     1.206   90.476   87.891

# 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):     0.338          0.329                  1.072           99.603   94.709

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   61   60    4.0     60    0.34   100.000   100.000    13.701

LGA_LOCAL      RMSD:   0.338  Number of atoms:   60  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.338  Number of assigned atoms:   60 
Std_ASGN_ATOMS RMSD:   0.338  Standard rmsd on all 60 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.227611 * X  +  -0.341697 * Y  +   0.911832 * Z  +  13.541066
  Y_new =  -0.570084 * X  +   0.805915 * Y  +   0.159702 * Z  +   5.794795
  Z_new =  -0.789428 * X  +  -0.483471 * Y  +  -0.378231 * Z  +   8.155982 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.950663  0.909877 -2.234665   [DEG: -111.7647   52.1321 -128.0369 ]
ZXZ:  1.744182  1.958681 -2.120307   [DEG:   99.9343  112.2241 -121.4846 ]
 
# END of job
