
#######################################################
#                                                     #
#                        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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     53   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     53   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     53   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     54   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     38   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     54   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     37   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     54   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     44   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     54     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60 
GDT PERCENT_AT  90.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.27   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   0.35   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     0.251     0    0.458   0.977     5.835   91.190   63.571
LGA    D     2_A      D     2_A     0.076     0    0.042   0.358     1.890  100.000   95.417
LGA    K     3_A      K     3_A     0.243     0    0.035   0.537     1.317  100.000   93.757
LGA    A     4_A      A     4_A     0.117     0    0.074   0.087     0.200  100.000  100.000
LGA    A     5_A      A     5_A     0.145     0    0.043   0.059     0.285  100.000  100.000
LGA    C     6_A      C     6_A     0.118     0    0.010   0.041     0.169  100.000  100.000
LGA    A     7_A      A     7_A     0.127     0    0.036   0.042     0.259  100.000  100.000
LGA    D     8_A      D     8_A     0.160     0    0.040   0.078     0.459  100.000  100.000
LGA    G     9_A      G     9_A     0.134     0    0.020   0.020     0.211  100.000  100.000
LGA    I    10_A      I    10_A     0.123     0    0.013   0.028     0.221  100.000  100.000
LGA    A    11_A      A    11_A     0.181     0    0.027   0.032     0.227  100.000  100.000
LGA    A    12_A      A    12_A     0.172     0    0.020   0.020     0.222  100.000  100.000
LGA    V    13_A      V    13_A     0.121     0    0.023   0.061     0.280  100.000  100.000
LGA    K    14_A      K    14_A     0.139     0    0.079   0.203     0.663  100.000   97.884
LGA    A    15_A      A    15_A     0.114     0    0.015   0.025     0.243  100.000  100.000
LGA    R    16_A      R    16_A     0.211     0    0.030   0.250     1.215  100.000   96.580
LGA    V    17_A      V    17_A     0.237     0    0.037   0.043     0.264  100.000  100.000
LGA    E    18_A      E    18_A     0.160     0    0.017   0.886     3.213  100.000   80.212
LGA    K    19_A      K    19_A     0.191     0    0.061   1.052     5.201  100.000   81.481
LGA    L    20_A      L    20_A     0.311     0    0.009   0.167     0.586  100.000   96.429
LGA    A    21_A      A    21_A     0.343     0    0.023   0.022     0.517   97.619   98.095
LGA    P    22_A      P    22_A     0.562     0    0.050   0.053     0.913   90.476   91.837
LGA    E    23_A      E    23_A     0.604     0    0.030   0.790     3.280   90.476   81.164
LGA    A    24_A      A    24_A     0.613     0    0.042   0.045     0.765   90.476   90.476
LGA    V    25_A      V    25_A     0.332     0    0.022   0.032     0.407  100.000  100.000
LGA    P    26_A      P    26_A     0.324     0    0.014   0.087     0.468  100.000  100.000
LGA    Q    27_A      Q    27_A     0.246     0    0.015   1.175     4.658  100.000   82.646
LGA    K    28_A      K    28_A     0.073     0    0.036   0.831     3.339  100.000   82.857
LGA    L    29_A      L    29_A     0.245     0    0.015   1.156     2.867  100.000   89.286
LGA    K    30_A      K    30_A     0.345     0    0.012   0.094     0.707  100.000   98.942
LGA    R    31_A      R    31_A     0.352     0    0.030   1.569     6.988  100.000   66.883
LGA    A    32_A      A    32_A     0.371     0    0.023   0.027     0.398  100.000  100.000
LGA    L    33_A      L    33_A     0.337     0    0.051   0.072     0.382  100.000  100.000
LGA    K    34_A      K    34_A     0.263     0    0.048   1.038     4.946  100.000   76.720
LGA    I    35_A      I    35_A     0.400     0    0.060   0.062     0.622  100.000   97.619
LGA    A    36_A      A    36_A     0.379     0    0.018   0.017     0.470  100.000  100.000
LGA    E    37_A      E    37_A     0.331     0    0.042   0.323     0.880  100.000   97.884
LGA    R    38_A      R    38_A     0.272     0    0.056   0.162     1.140  100.000   96.580
LGA    E    39_A      E    39_A     0.260     0    0.020   1.082     3.803  100.000   85.714
LGA    Q    40_A      Q    40_A     0.247     0    0.020   0.869     3.121  100.000   89.259
LGA    G    41_A      G    41_A     0.231     0    0.030   0.030     0.328  100.000  100.000
LGA    E    42_A      E    42_A     0.498     0    0.132   0.209     0.924   97.619   93.651
LGA    G    43_A      G    43_A     0.372     0    0.083   0.083     0.471  100.000  100.000
LGA    E    44_A      E    44_A     0.245     0    0.080   0.996     4.388  100.000   84.339
LGA    F    45_A      F    45_A     0.368     0    0.012   0.110     0.426  100.000  100.000
LGA    D    46_A      D    46_A     0.335     0    0.068   0.488     1.616  100.000   95.417
LGA    E    47_A      E    47_A     0.305     0    0.037   1.050     3.232  100.000   85.608
LGA    C    48_A      C    48_A     0.109     0    0.034   0.104     0.231  100.000  100.000
LGA    L    49_A      L    49_A     0.326     0    0.049   0.061     0.506  100.000   97.619
LGA    E    50_A      E    50_A     0.218     0    0.017   0.208     0.773  100.000   98.942
LGA    A    51_A      A    51_A     0.218     0    0.023   0.028     0.358  100.000  100.000
LGA    L    52_A      L    52_A     0.371     0    0.039   0.046     0.593  100.000   95.238
LGA    D    53_A      D    53_A     0.311     0    0.021   0.747     3.340  100.000   84.940
LGA    D    54_A      D    54_A     0.298     0    0.014   0.360     1.300  100.000   95.298
LGA    A    55_A      A    55_A     0.492     0    0.032   0.032     0.642   95.238   94.286
LGA    K    56_A      K    56_A     0.850     0    0.034   0.565     1.899   90.476   83.545
LGA    R    57_A      R    57_A     0.453     0    0.039   1.194     4.859   92.857   77.273
LGA    A    58_A      A    58_A     0.589     0    0.067   0.063     1.064   90.595   90.571
LGA    L    59_A      L    59_A     0.498     0    0.028   0.141     1.478   92.857   89.405
LGA    P    60_A      P    60_A     0.803     0    0.022   0.333     1.073   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):     0.344          0.385                  1.258           98.506   93.110

#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    13.514

LGA_LOCAL      RMSD:   0.344  Number of atoms:   60  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.344  Number of assigned atoms:   60 
Std_ASGN_ATOMS RMSD:   0.344  Standard rmsd on all 60 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.188392 * X  +   0.738437 * Y  +   0.647471 * Z  +  12.690032
  Y_new =  -0.910130 * X  +  -0.378991 * Y  +   0.167420 * Z  +   6.446262
  Z_new =   0.369014 * X  +  -0.557742 * Y  +   0.743473 * Z  +   9.377536 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.774909 -0.377948 -0.643620   [DEG: -101.6948  -21.6548  -36.8767 ]
ZXZ:  1.823829  0.732548  2.557091   [DEG:  104.4977   41.9719  146.5105 ]
 
# END of job
