
#######################################################
#                                                     #
#                        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        0.40     0.40
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.40     0.40
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.40     0.40
  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     26   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     16   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     16   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     53   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     44   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     24   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      6   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     53     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60 
GDT PERCENT_AT  88.33 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.34   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40
GDT RMS_ALL_AT   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40   0.40

# Checking swapping
#   possible swapping detected:  D     2_A      D     2_A
#   possible swapping detected:  D     8_A      D     8_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:  F    45_A      F    45_A
#   possible swapping detected:  D    46_A      D    46_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
#   possible swapping detected:  D    54_A      D    54_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_A      D     1_A     0.748     0    0.117   0.889     2.317   92.857   87.321
LGA    D     2_A      D     2_A     0.218     0    0.008   0.128     0.908  100.000   97.619
LGA    K     3_A      K     3_A     0.317     0    0.016   0.585     1.310  100.000   93.757
LGA    A     4_A      A     4_A     0.334     0    0.005   0.007     0.434  100.000  100.000
LGA    A     5_A      A     5_A     0.174     0    0.044   0.049     0.318  100.000  100.000
LGA    C     6_A      C     6_A     0.325     0    0.004   0.080     0.882  100.000   98.413
LGA    A     7_A      A     7_A     0.272     0    0.015   0.015     0.310  100.000  100.000
LGA    D     8_A      D     8_A     0.158     0    0.020   0.143     0.663  100.000   98.810
LGA    G     9_A      G     9_A     0.200     0    0.033   0.033     0.294  100.000  100.000
LGA    I    10_A      I    10_A     0.398     0    0.008   0.017     0.485  100.000  100.000
LGA    A    11_A      A    11_A     0.351     0    0.010   0.009     0.369  100.000  100.000
LGA    A    12_A      A    12_A     0.150     0    0.014   0.014     0.190  100.000  100.000
LGA    V    13_A      V    13_A     0.345     0    0.007   0.018     0.482  100.000  100.000
LGA    K    14_A      K    14_A     0.424     0    0.007   0.082     0.654  100.000   97.884
LGA    A    15_A      A    15_A     0.311     0    0.028   0.032     0.413  100.000  100.000
LGA    R    16_A      R    16_A     0.299     0    0.021   0.182     1.794  100.000   93.290
LGA    V    17_A      V    17_A     0.373     0    0.017   0.045     0.462  100.000  100.000
LGA    E    18_A      E    18_A     0.461     0    0.006   0.937     3.319  100.000   78.307
LGA    K    19_A      K    19_A     0.394     0    0.032   1.055     4.900  100.000   82.910
LGA    L    20_A      L    20_A     0.434     0    0.022   0.156     0.494  100.000  100.000
LGA    A    21_A      A    21_A     0.570     0    0.029   0.036     0.648   92.857   92.381
LGA    P    22_A      P    22_A     0.581     0    0.023   0.075     0.659   90.476   93.197
LGA    E    23_A      E    23_A     0.688     0    0.015   0.958     2.130   90.476   80.847
LGA    A    24_A      A    24_A     0.683     0    0.039   0.042     0.800   90.476   90.476
LGA    V    25_A      V    25_A     0.236     0    0.018   0.074     0.396  100.000  100.000
LGA    P    26_A      P    26_A     0.397     0    0.014   0.049     0.566  100.000   95.918
LGA    Q    27_A      Q    27_A     0.414     0    0.009   1.175     4.624  100.000   82.646
LGA    K    28_A      K    28_A     0.232     0    0.011   0.823     2.960  100.000   85.397
LGA    L    29_A      L    29_A     0.246     0    0.012   1.163     3.001  100.000   89.345
LGA    K    30_A      K    30_A     0.410     0    0.008   0.053     0.460  100.000  100.000
LGA    R    31_A      R    31_A     0.460     0    0.014   1.259     6.507  100.000   71.212
LGA    A    32_A      A    32_A     0.379     0    0.009   0.009     0.406  100.000  100.000
LGA    L    33_A      L    33_A     0.328     0    0.009   0.081     0.508  100.000   98.810
LGA    K    34_A      K    34_A     0.385     0    0.008   0.665     2.942  100.000   90.106
LGA    I    35_A      I    35_A     0.346     0    0.015   0.064     0.415  100.000  100.000
LGA    A    36_A      A    36_A     0.278     0    0.003   0.008     0.302  100.000  100.000
LGA    E    37_A      E    37_A     0.260     0    0.022   0.111     0.429  100.000  100.000
LGA    R    38_A      R    38_A     0.362     0    0.015   0.543     1.504  100.000   95.801
LGA    E    39_A      E    39_A     0.358     0    0.019   1.013     3.755  100.000   85.714
LGA    Q    40_A      Q    40_A     0.355     0    0.010   0.327     1.335  100.000   96.878
LGA    G    41_A      G    41_A     0.367     0    0.053   0.053     0.378  100.000  100.000
LGA    E    42_A      E    42_A     0.466     0    0.039   0.220     1.054  100.000   95.820
LGA    G    43_A      G    43_A     0.385     0    0.028   0.028     0.485  100.000  100.000
LGA    E    44_A      E    44_A     0.165     0    0.021   0.886     4.246  100.000   83.492
LGA    F    45_A      F    45_A     0.339     0    0.027   0.058     0.379  100.000  100.000
LGA    D    46_A      D    46_A     0.439     0    0.015   1.119     3.878  100.000   84.940
LGA    E    47_A      E    47_A     0.355     0    0.007   0.438     1.414  100.000   93.757
LGA    C    48_A      C    48_A     0.147     0    0.038   0.083     0.266  100.000  100.000
LGA    L    49_A      L    49_A     0.240     0    0.008   0.050     0.516  100.000   98.810
LGA    E    50_A      E    50_A     0.174     0    0.010   0.218     0.766  100.000   97.884
LGA    A    51_A      A    51_A     0.193     0    0.007   0.007     0.259  100.000  100.000
LGA    L    52_A      L    52_A     0.322     0    0.031   0.042     0.541  100.000   97.619
LGA    D    53_A      D    53_A     0.279     0    0.010   0.154     0.729  100.000   98.810
LGA    D    54_A      D    54_A     0.282     0    0.004   0.076     0.302  100.000  100.000
LGA    A    55_A      A    55_A     0.394     0    0.024   0.032     0.498  100.000  100.000
LGA    K    56_A      K    56_A     0.577     0    0.011   0.642     1.532   95.238   88.624
LGA    R    57_A      R    57_A     0.257     0    0.008   0.596     2.819  100.000   92.727
LGA    A    58_A      A    58_A     0.546     0    0.026   0.026     0.676   92.857   92.381
LGA    L    59_A      L    59_A     0.620     0    0.023   0.153     1.110   92.857   89.405
LGA    P    60_A      P    60_A     0.862     0    0.013   0.097     1.118   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):     0.397          0.381                  1.004           98.810   94.653

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   61   60    4.0     60    0.40   100.000   100.000    12.072

LGA_LOCAL      RMSD:   0.397  Number of atoms:   60  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.397  Number of assigned atoms:   60 
Std_ASGN_ATOMS RMSD:   0.397  Standard rmsd on all 60 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.838437 * X  +   0.138368 * Y  +   0.527142 * Z  +  12.954569
  Y_new =   0.289663 * X  +  -0.706171 * Y  +   0.646079 * Z  +   6.814232
  Z_new =   0.461649 * X  +   0.694389 * Y  +   0.552000 * Z  +   8.108017 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.808950 -0.479853  0.899147   [DEG:  160.9410  -27.4936   51.5173 ]
ZXZ:  2.457226  0.986036  0.586728   [DEG:  140.7887   56.4957   33.6170 ]
 
# END of job
