
#######################################################
#                                                     #
#                        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        0.36     0.36
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.36     0.36
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.36     0.36
  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     51   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     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     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     41   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     55   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     39   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    0.31   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36
GDT RMS_ALL_AT   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36

# 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
#   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     0.617     0    0.248   0.821     1.450   90.595   89.464
LGA    D     2_A      D     2_A     0.256     0    0.009   0.506     2.208  100.000   94.405
LGA    K     3_A      K     3_A     0.383     0    0.020   0.579     1.620  100.000   90.794
LGA    A     4_A      A     4_A     0.362     0    0.047   0.055     0.438  100.000  100.000
LGA    A     5_A      A     5_A     0.219     0    0.041   0.058     0.442  100.000  100.000
LGA    C     6_A      C     6_A     0.143     0    0.027   0.054     0.194  100.000  100.000
LGA    A     7_A      A     7_A     0.145     0    0.035   0.047     0.225  100.000  100.000
LGA    D     8_A      D     8_A     0.177     0    0.022   0.128     0.580  100.000   97.619
LGA    G     9_A      G     9_A     0.178     0    0.049   0.049     0.269  100.000  100.000
LGA    I    10_A      I    10_A     0.248     0    0.021   0.045     0.422  100.000  100.000
LGA    A    11_A      A    11_A     0.207     0    0.034   0.046     0.249  100.000  100.000
LGA    A    12_A      A    12_A     0.078     0    0.014   0.018     0.237  100.000  100.000
LGA    V    13_A      V    13_A     0.246     0    0.022   0.049     0.405  100.000  100.000
LGA    K    14_A      K    14_A     0.264     0    0.082   0.177     0.656   97.619   96.825
LGA    A    15_A      A    15_A     0.160     0    0.059   0.055     0.306  100.000  100.000
LGA    R    16_A      R    16_A     0.305     0    0.019   0.236     1.834  100.000   93.290
LGA    V    17_A      V    17_A     0.331     0    0.040   0.050     0.381  100.000  100.000
LGA    E    18_A      E    18_A     0.250     0    0.022   0.667     3.417  100.000   83.598
LGA    K    19_A      K    19_A     0.262     0    0.049   1.069     4.758  100.000   83.704
LGA    L    20_A      L    20_A     0.359     0    0.034   0.151     0.463  100.000  100.000
LGA    A    21_A      A    21_A     0.358     0    0.015   0.022     0.457  100.000  100.000
LGA    P    22_A      P    22_A     0.530     0    0.037   0.053     0.811   92.857   94.558
LGA    E    23_A      E    23_A     0.485     0    0.055   0.712     1.994  100.000   86.878
LGA    A    24_A      A    24_A     0.490     0    0.083   0.095     0.623   97.619   96.190
LGA    V    25_A      V    25_A     0.306     0    0.033   0.066     0.352  100.000  100.000
LGA    P    26_A      P    26_A     0.325     0    0.041   0.086     0.470  100.000  100.000
LGA    Q    27_A      Q    27_A     0.311     0    0.017   1.153     4.378  100.000   84.339
LGA    K    28_A      K    28_A     0.193     0    0.043   0.826     3.374  100.000   82.857
LGA    L    29_A      L    29_A     0.299     0    0.024   1.131     2.804  100.000   89.286
LGA    K    30_A      K    30_A     0.445     0    0.014   0.075     0.606  100.000   98.942
LGA    R    31_A      R    31_A     0.433     0    0.035   1.274     7.047  100.000   68.485
LGA    A    32_A      A    32_A     0.417     0    0.041   0.053     0.443  100.000  100.000
LGA    L    33_A      L    33_A     0.436     0    0.038   0.059     0.478  100.000  100.000
LGA    K    34_A      K    34_A     0.405     0    0.059   0.647     2.673  100.000   90.000
LGA    I    35_A      I    35_A     0.419     0    0.090   0.089     0.521   97.619   98.810
LGA    A    36_A      A    36_A     0.421     0    0.016   0.020     0.441  100.000  100.000
LGA    E    37_A      E    37_A     0.326     0    0.023   0.304     0.802  100.000   97.884
LGA    R    38_A      R    38_A     0.332     0    0.064   1.137     4.511  100.000   81.602
LGA    E    39_A      E    39_A     0.322     0    0.042   1.063     3.899  100.000   83.968
LGA    Q    40_A      Q    40_A     0.307     0    0.042   0.239     0.937  100.000   98.942
LGA    G    41_A      G    41_A     0.191     0    0.038   0.038     0.219  100.000  100.000
LGA    E    42_A      E    42_A     0.364     0    0.133   0.426     1.294  100.000   95.820
LGA    G    43_A      G    43_A     0.224     0    0.055   0.055     0.348  100.000  100.000
LGA    E    44_A      E    44_A     0.196     0    0.065   0.919     3.922  100.000   84.233
LGA    F    45_A      F    45_A     0.324     0    0.019   0.059     0.411  100.000  100.000
LGA    D    46_A      D    46_A     0.394     0    0.066   1.191     4.249  100.000   83.333
LGA    E    47_A      E    47_A     0.297     0    0.034   1.075     3.431  100.000   86.667
LGA    C    48_A      C    48_A     0.078     0    0.016   0.077     0.199  100.000  100.000
LGA    L    49_A      L    49_A     0.225     0    0.028   0.091     0.429  100.000  100.000
LGA    E    50_A      E    50_A     0.140     0    0.025   0.330     1.215  100.000   97.937
LGA    A    51_A      A    51_A     0.162     0    0.014   0.023     0.290  100.000  100.000
LGA    L    52_A      L    52_A     0.366     0    0.016   0.055     0.629  100.000   98.810
LGA    D    53_A      D    53_A     0.287     0    0.048   0.321     0.750  100.000   97.619
LGA    D    54_A      D    54_A     0.200     0    0.018   0.256     0.870  100.000   97.619
LGA    A    55_A      A    55_A     0.405     0    0.009   0.017     0.514   97.619   98.095
LGA    K    56_A      K    56_A     0.705     0    0.047   0.648     1.501   92.857   86.561
LGA    R    57_A      R    57_A     0.360     0    0.015   1.122     4.793  100.000   81.602
LGA    A    58_A      A    58_A     0.586     0    0.041   0.043     0.935   92.857   92.381
LGA    L    59_A      L    59_A     0.475     0    0.047   0.171     1.346  100.000   92.976
LGA    P    60_A      P    60_A     0.851     0    0.031   0.336     1.071   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):     0.357          0.366                  1.127           99.169   94.421

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   61   60    4.0     60    0.36   100.000   100.000    13.133

LGA_LOCAL      RMSD:   0.357  Number of atoms:   60  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.357  Number of assigned atoms:   60 
Std_ASGN_ATOMS RMSD:   0.357  Standard rmsd on all 60 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.822697 * X  +   0.520794 * Y  +  -0.227910 * Z  +  10.233323
  Y_new =   0.329151 * X  +  -0.763260 * Y  +  -0.555962 * Z  +  10.627962
  Z_new =  -0.463496 * X  +   0.382372 * Y  +  -0.799352 * Z  +   6.115358 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.380582  0.481936  2.695413   [DEG:   21.8058   27.6129  154.4358 ]
ZXZ: -0.389044  2.497012 -0.881013   [DEG:  -22.2906  143.0683  -50.4783 ]
 
# END of job
