
#######################################################
#                                                     #
#                        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        0.42     0.42
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.42     0.42
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.42     0.42
  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     31   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     49   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     49   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     49   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     49   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     49   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     49   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     49   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     49   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     49   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     49   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     49   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     49   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     49   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     49   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     49   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     49   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     49   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     49   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     49   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     49   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     26   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     26   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     29   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     49   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     49   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     49   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     49   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     49   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     49   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     49   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     49   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     49   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     49   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     49   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     49   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     49   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     49   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     49   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     49   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     49   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     49   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     49   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     49   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     49   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     33   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     49   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     49   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     49   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     49   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     49   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     49   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     49   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     49   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     49   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     48   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     49   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     39   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     49   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     32   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     49     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60 
GDT PERCENT_AT  81.67 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.31   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42
GDT RMS_ALL_AT   0.43   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42   0.42

# Checking swapping
#   possible swapping detected:  D     1_A      D     1_A
#   possible swapping detected:  E    18_A      E    18_A
#   possible swapping detected:  E    23_A      E    23_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    47_A      E    47_A
#   possible swapping detected:  E    50_A      E    50_A
#   possible swapping detected:  D    53_A      D    53_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_A      D     1_A     1.112     0    0.159   0.840     2.945   88.214   77.560
LGA    D     2_A      D     2_A     0.475     0    0.017   0.473     2.480   97.619   90.893
LGA    K     3_A      K     3_A     0.529     0    0.021   0.549     1.850   90.476   86.508
LGA    A     4_A      A     4_A     0.573     0    0.045   0.051     0.706   95.238   94.286
LGA    A     5_A      A     5_A     0.263     0    0.048   0.067     0.509  100.000   98.095
LGA    C     6_A      C     6_A     0.138     0    0.026   0.057     0.176  100.000  100.000
LGA    A     7_A      A     7_A     0.207     0    0.035   0.045     0.294  100.000  100.000
LGA    D     8_A      D     8_A     0.256     0    0.021   0.110     0.650  100.000   96.429
LGA    G     9_A      G     9_A     0.152     0    0.054   0.054     0.241  100.000  100.000
LGA    I    10_A      I    10_A     0.245     0    0.027   0.055     0.401  100.000  100.000
LGA    A    11_A      A    11_A     0.278     0    0.031   0.043     0.334  100.000  100.000
LGA    A    12_A      A    12_A     0.068     0    0.015   0.016     0.312  100.000  100.000
LGA    V    13_A      V    13_A     0.293     0    0.023   0.049     0.455  100.000  100.000
LGA    K    14_A      K    14_A     0.323     0    0.082   0.185     0.658   97.619   96.825
LGA    A    15_A      A    15_A     0.248     0    0.055   0.052     0.446  100.000  100.000
LGA    R    16_A      R    16_A     0.339     0    0.015   0.209     1.233  100.000   95.758
LGA    V    17_A      V    17_A     0.343     0    0.036   0.050     0.384  100.000  100.000
LGA    E    18_A      E    18_A     0.268     0    0.023   0.717     3.521  100.000   82.857
LGA    K    19_A      K    19_A     0.410     0    0.043   1.058     5.118   97.619   80.423
LGA    L    20_A      L    20_A     0.353     0    0.033   0.163     0.439  100.000  100.000
LGA    A    21_A      A    21_A     0.459     0    0.017   0.024     0.534  100.000   98.095
LGA    P    22_A      P    22_A     0.592     0    0.047   0.061     0.917   90.476   91.837
LGA    E    23_A      E    23_A     0.657     0    0.082   1.142     3.314   90.476   80.106
LGA    A    24_A      A    24_A     0.598     0    0.076   0.089     0.744   92.857   92.381
LGA    V    25_A      V    25_A     0.313     0    0.029   0.063     0.389  100.000  100.000
LGA    P    26_A      P    26_A     0.308     0    0.040   0.087     0.467  100.000  100.000
LGA    Q    27_A      Q    27_A     0.394     0    0.009   1.161     4.480  100.000   84.339
LGA    K    28_A      K    28_A     0.278     0    0.055   0.821     3.430  100.000   82.857
LGA    L    29_A      L    29_A     0.304     0    0.025   1.119     2.767   97.619   88.095
LGA    K    30_A      K    30_A     0.522     0    0.014   0.091     0.865   90.476   90.476
LGA    R    31_A      R    31_A     0.484     0    0.043   0.857     2.036   97.619   88.398
LGA    A    32_A      A    32_A     0.383     0    0.038   0.054     0.446  100.000  100.000
LGA    L    33_A      L    33_A     0.460     0    0.033   0.049     0.479  100.000  100.000
LGA    K    34_A      K    34_A     0.456     0    0.059   0.641     2.399  100.000   90.847
LGA    I    35_A      I    35_A     0.404     0    0.086   0.096     0.456  100.000  100.000
LGA    A    36_A      A    36_A     0.389     0    0.016   0.017     0.462  100.000  100.000
LGA    E    37_A      E    37_A     0.319     0    0.020   0.246     0.676  100.000   97.884
LGA    R    38_A      R    38_A     0.344     0    0.072   0.284     0.835   97.619   94.805
LGA    E    39_A      E    39_A     0.388     0    0.015   1.198     4.078  100.000   85.026
LGA    Q    40_A      Q    40_A     0.324     0    0.039   0.246     0.867  100.000   98.942
LGA    G    41_A      G    41_A     0.169     0    0.054   0.054     0.229  100.000  100.000
LGA    E    42_A      E    42_A     0.426     0    0.123   0.179     0.695  100.000   94.709
LGA    G    43_A      G    43_A     0.330     0    0.036   0.036     0.464  100.000  100.000
LGA    E    44_A      E    44_A     0.290     0    0.034   0.300     1.837  100.000   92.857
LGA    F    45_A      F    45_A     0.487     0    0.013   0.048     0.782  100.000   93.939
LGA    D    46_A      D    46_A     0.606     0    0.078   1.182     4.154   92.857   79.583
LGA    E    47_A      E    47_A     0.439     0    0.036   0.360     1.683   97.619   93.810
LGA    C    48_A      C    48_A     0.089     0    0.017   0.077     0.233  100.000  100.000
LGA    L    49_A      L    49_A     0.181     0    0.026   0.126     0.423  100.000  100.000
LGA    E    50_A      E    50_A     0.141     0    0.025   0.248     1.036  100.000   97.937
LGA    A    51_A      A    51_A     0.086     0    0.011   0.026     0.230  100.000  100.000
LGA    L    52_A      L    52_A     0.269     0    0.017   0.054     0.548  100.000   98.810
LGA    D    53_A      D    53_A     0.233     0    0.036   0.203     0.775  100.000   98.810
LGA    D    54_A      D    54_A     0.206     0    0.017   0.368     1.197  100.000   94.167
LGA    A    55_A      A    55_A     0.322     0    0.010   0.018     0.406  100.000  100.000
LGA    K    56_A      K    56_A     0.604     0    0.047   0.638     1.416   97.619   90.635
LGA    R    57_A      R    57_A     0.300     0    0.016   1.139     4.828  100.000   80.866
LGA    A    58_A      A    58_A     0.581     0    0.032   0.037     0.919   92.857   92.381
LGA    L    59_A      L    59_A     0.480     0    0.060   0.166     1.247   97.619   91.786
LGA    P    60_A      P    60_A     0.875     0    0.030   0.338     1.151   90.476   89.184

# 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):     0.415          0.409                  0.967           98.216   94.220

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   61   60    4.0     60    0.42   100.000   100.000    11.648

LGA_LOCAL      RMSD:   0.415  Number of atoms:   60  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.415  Number of assigned atoms:   60 
Std_ASGN_ATOMS RMSD:   0.415  Standard rmsd on all 60 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.358285 * X  +   0.191718 * Y  +   0.913716 * Z  +  13.633397
  Y_new =  -0.789003 * X  +  -0.585380 * Y  +  -0.186557 * Z  +   5.754813
  Z_new =   0.499105 * X  +  -0.787765 * Y  +   0.360999 * Z  +  10.698771 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.997053 -0.522566 -1.141097   [DEG: -114.4227  -29.9408  -65.3801 ]
ZXZ:  1.369390  1.201458  2.576854   [DEG:   78.4603   68.8384  147.6429 ]
 
# END of job
