
#######################################################
#                                                     #
#                        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   34 (  238),  selected   34 , name one
# Molecule2: number of CA atoms   34 (  235),  selected   34 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    34       1_A - 34_A        0.96     0.96
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    34       1_A - 34_A        0.96     0.96
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    34       1_A - 34_A        0.96     0.96
  LCS_AVERAGE:    100.00

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   34
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     S     1_B     S     1_A     34   34   34     18   30   32   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G     2_B     G     2_A     34   34   34     18   30   32   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     P     3_B     P     3_A     34   34   34     12   30   32   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     N     4_B     N     4_A     34   34   34      5   30   32   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G     5_B     G     5_A     34   34   34      3    8   16   26   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G     6_B     G     6_A     34   34   34      4    9   32   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     V     7_B     V     7_A     34   34   34      9   30   32   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C     8_B     C     8_A     34   34   34     11   30   32   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     P     9_B     P     9_A     34   34   34     11   30   32   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     V    10_B     V    10_A     34   34   34     13   30   32   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     L    11_B     L    11_A     34   34   34      5   14   32   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     I    12_B     I    12_A     34   34   34      6   30   32   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     Y    13_B     Y    13_A     34   34   34     13   30   32   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     L    14_B     L    14_A     34   34   34     18   30   32   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    15_B     C    15_A     34   34   34     18   30   32   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     R    16_B     R    16_A     34   34   34     18   30   32   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     R    17_B     R    17_A     34   34   34     18   30   32   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     D    18_B     D    18_A     34   34   34     18   30   32   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     S    19_B     S    19_A     34   34   34     18   30   32   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     D    20_B     D    20_A     34   34   34     18   30   32   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    21_B     C    21_A     34   34   34     18   30   32   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     P    22_B     P    22_A     34   34   34     18   30   32   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    23_B     G    23_A     34   34   34     18   30   32   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     E    24_B     E    24_A     34   34   34      3   30   32   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    25_B     C    25_A     34   34   34     18   30   32   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     I    26_B     I    26_A     34   34   34     18   30   32   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    27_B     C    27_A     34   34   34     18   30   32   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     L    28_B     L    28_A     34   34   34     13   30   32   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    29_B     G    29_A     34   34   34     11   30   32   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     N    30_B     N    30_A     34   34   34      5   12   31   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    31_B     G    31_A     34   34   34      9   30   32   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     Y    32_B     Y    32_A     34   34   34     18   30   32   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    33_B     C    33_A     34   34   34     18   30   32   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    34_B     G    34_A     34   34   34     18   30   32   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
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     18     30     32     33     34     34     34     34     34     34     34     34     34     34     34     34     34     34     34     34 
GDT PERCENT_AT  52.94  88.24  94.12  97.06 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.35   0.62   0.78   0.83   0.96   0.96   0.96   0.96   0.96   0.96   0.96   0.96   0.96   0.96   0.96   0.96   0.96   0.96   0.96   0.96
GDT RMS_ALL_AT   1.15   1.00   0.97   0.98   0.96   0.96   0.96   0.96   0.96   0.96   0.96   0.96   0.96   0.96   0.96   0.96   0.96   0.96   0.96   0.96

# Checking swapping
#   possible swapping detected:  Y    13_B      Y    13_A
#   possible swapping detected:  E    24_B      E    24_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     1_B      S     1_A     0.775     0    0.112   0.754     3.097   90.476   80.794
LGA    G     2_B      G     2_A     0.956     0    0.046   0.046     0.956   95.238   95.238
LGA    P     3_B      P     3_A     0.215     0    0.314   0.419     1.860   88.452   89.320
LGA    N     4_B      N     4_A     0.601     0    0.614   0.776     2.366   84.048   82.857
LGA    G     5_B      G     5_A     2.774     0    0.640   0.640     3.007   59.167   59.167
LGA    G     6_B      G     6_A     1.794     0    0.079   0.079     2.520   73.214   73.214
LGA    V     7_B      V     7_A     0.688     0    0.100   0.180     0.892   90.476   90.476
LGA    C     8_B      C     8_A     0.455     0    0.047   0.061     0.572   97.619   98.413
LGA    P     9_B      P     9_A     0.602     0    0.035   0.331     1.489   95.238   91.905
LGA    V    10_B      V    10_A     0.820     0    0.546   0.983     4.356   84.048   71.905
LGA    L    11_B      L    11_A     1.737     3    0.079   0.093     1.844   75.000   46.607
LGA    I    12_B      I    12_A     0.843     0    0.042   0.987     2.144   92.976   80.952
LGA    Y    13_B      Y    13_A     0.486     0    0.051   0.430     4.051  100.000   74.008
LGA    L    14_B      L    14_A     0.674     0    0.049   0.235     0.764   90.476   91.667
LGA    C    15_B      C    15_A     0.603     0    0.036   0.091     0.662   90.476   93.651
LGA    R    16_B      R    16_A     0.448     0    0.164   1.357     7.062   95.238   69.437
LGA    R    17_B      R    17_A     0.846     0    0.032   1.180     7.294   90.476   64.416
LGA    D    18_B      D    18_A     0.905     0    0.024   0.930     3.563   90.476   74.226
LGA    S    19_B      S    19_A     1.172     0    0.051   0.625     1.656   83.690   81.508
LGA    D    20_B      D    20_A     0.802     0    0.040   0.196     1.181   88.214   89.405
LGA    C    21_B      C    21_A     0.185     0    0.023   0.079     0.367  100.000  100.000
LGA    P    22_B      P    22_A     0.363     0    0.053   0.067     0.519   97.619   98.639
LGA    G    23_B      G    23_A     0.294     0    0.025   0.025     0.383  100.000  100.000
LGA    E    24_B      E    24_A     0.843     0    0.204   1.578     7.491   95.238   61.376
LGA    C    25_B      C    25_A     0.313     0    0.016   0.075     0.711   95.238   96.825
LGA    I    26_B      I    26_A     0.843     0    0.044   0.056     1.809   92.857   85.000
LGA    C    27_B      C    27_A     0.525     0    0.026   0.054     0.699   90.476   93.651
LGA    L    28_B      L    28_A     0.853     0    0.043   0.149     1.994   92.857   83.929
LGA    G    29_B      G    29_A     0.837     0    0.103   0.103     1.234   85.952   85.952
LGA    N    30_B      N    30_A     1.874     0    0.191   0.340     2.945   77.143   70.000
LGA    G    31_B      G    31_A     0.960     0    0.070   0.070     1.124   88.214   88.214
LGA    Y    32_B      Y    32_A     0.192     0    0.064   0.129     0.658  100.000   97.619
LGA    C    33_B      C    33_A     0.268     0    0.038   0.043     0.364  100.000  100.000
LGA    G    34_B      G    34_A     0.533     0    0.337   0.337     1.402   90.595   90.595

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       34     136    136  100.00     235    235  100.00                34
SUMMARY(RMSD_GDC):     0.961          0.958                  1.715           90.035   83.852

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   34    4.0     34    0.96    96.324    98.426     3.205

LGA_LOCAL      RMSD:   0.961  Number of atoms:   34  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.961  Number of assigned atoms:   34 
Std_ASGN_ATOMS RMSD:   0.961  Standard rmsd on all 34 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.746682 * X  +   0.054374 * Y  +  -0.662955 * Z  + -22.440088
  Y_new =  -0.330030 * X  +  -0.835048 * Y  +  -0.440200 * Z  +  10.187407
  Z_new =  -0.577534 * X  +   0.547484 * Y  +  -0.605570 * Z  +  12.256503 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.416177  0.615705  2.406528   [DEG:  -23.8452   35.2773  137.8839 ]
ZXZ: -0.984644  2.221278 -0.812102   [DEG:  -56.4160  127.2699  -46.5300 ]
 
# END of job
