 
####################################################### 
#                                                     # 
#                        ACE                          # 
#                                                     # 
#        Ab-initio protein structure prediction       # 
#                         &                           # 
#               Comparative modeling                  # 
#                                                     # 
#                     Evaluator                       # 
#                                                     # 
#                ----------------- 11/1998            # 
#                                                     # 
#                         by                          # 
#           Adam Zemla & Ceslovas Venclovas           # 
#                                                     # 
#         Protein Structure Prediction Center         # 
#      Lawrence Livermore National Laboratory, CA     # 
#                                                     # 
####################################################### 
########################## 
#                        # 
#    ACE parameters:     # 
#                        # 
########################## 
NUMBER-OF-PARENTS      4 
ALIGNMENT-DALI(1)      ../PARENTS/casp3.T0076_1.1cfd.rot 
ALIGNMENT-DALI(2)      ../PARENTS/casp3.T0076_1.1ncx.rot 
ALIGNMENT-DALI(3)      ../PARENTS/casp3.T0076_1.1a2x_A.rot 
ALIGNMENT-DALI(4)      ../PARENTS/casp3.T0076_1.5icb.rot 
# 
ITER-CUTOFF            2.5       #    DISTANCE cutoff (for CA (iter))  
# 
# 
# MEASURES: 
# 
# For AB: 0 3 9 13 14 
# For CM: 0 1 2 3 6 7 8 9 10 11 12 13 14 18 
# 
ARMSMC  0 1 2     7 8 9    11 12 13 14 18 
ARMSSC  0 1 2 3 6 7 8 9    11 12 13 14 18 
# 
CRMSCA  0 1 2     7 8 9 10 11 12 13 14 18 
CRMSMC  0 1 2     7 8 9 10 11 12 13 14 18 
CRMSSC  0 1 2 3 6     9    11 12 13 14 18 
CRMSALL 0 1 2     7 8 9    11 12 13 14 18 
# 
D-E_CA  0 1 2     7 8 9    11 12 13 14 18 
D-E_MC  0 1 2     7 8 9    11 12 13 14 18 
D-E_SC  0 1 2 3 6 7 8 9    11 12 13 14 18 
D-E_ALL 0 1 2     7 8 9    11 12 13 14 18 
# 
# Output parameters 
# 
DIHED-OUTPUT        0         #    1 - ON, 0 - OFF 
SS-OUTPUT           0         #    1 - ON, 0 - OFF  
PHI-PSI             0         #    1 - SEPARATELY, 0 - NO  
ALIGNMENT-OUTPUT    0         #    1 - ON, 0 - OFF 
# 
# Calculation parameters 
# 
TEMP-FACTOR         30.0      #    Target structure temperature factor cutoff  
ACCESS-CUTOFF       0.20      #    Solvent accessibility cutoff  
ANGLES-CORRECT      30.0      #    target-model  (diff < 30.0)  
ROTAMERS-LIMIT      30.0      #    target-parent (diff > 30.0) 
SC-SWAPPING         1         #    1 - ON, 0 - OFF  
DSSP-HELIX          6         #    Secondary Structure subset: helix cutoff  
DSSP-STRAND         3         #    Secondary Structure subset: strand cutoff 
LIGAND-DIST1        4.0       #    Ligand contact: contact with ligand cutoff 
LIGAND-DIST2        6.0       #    Ligand contact: protein neighborhood cutoff 
PARENT-DIST3        2.5       #    target-parent (dist > 2.5) 
# 
CRMS-METHOD         3         #    0 - ALL, 1 - CA, 2 - MC+CB, 3 - CA (iter)  
# 
########################## 
#                        # 
#      ACE results:      # 
#                        # 
########################## 
 
 
# Reading the coordinates set (1) 
 
 
# Evaluating the coordinates set (1) 
 
# WARNING! TARGET 1087 atoms, MODEL 1088 atoms, 552 common with TARGET 
           Number of atoms possible to evaluate: 493 
 
 
 CA-RMS TARGET<->PARENT(1cfd)	 2.655663 
 
 CA-RMS TARGET<->PARENT(1ncx)	 2.782501 
 
 CA-RMS TARGET<->PARENT(1a2x-A)	 3.224615 
 
 CA-RMS TARGET<->PARENT(5icb)	 2.843657 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    33.96           75.0   120    85.7   140     ARMSMC  
     WELL ORDERED  . . . . .    33.96           75.0   120    85.7   140     ARMSMC  
     NO INTER CONTACTS . . .    33.96           75.0   120    85.7   140     ARMSMC  
     SHIFTED CHAIN . . . . .    34.50           76.9   108    84.4   128     ARMSMC  
     ALTERNATIVE PARENT  . .    40.42           75.0    12    80.0    15     ARMSMC  
     SECONDARY STRUCTURE . .    16.71           85.9    64   100.0    64     ARMSMC  
     LARGE SHIFTS/INSERTIONS    53.17           63.6    33    68.8    48     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    35.33           73.9    92    83.6   110     ARMSMC  
     BURIED  . . . . . . . .    28.99           78.6    28    93.3    30     ARMSMC  
     CORE  . . . . . . . . .    22.76           79.3    87    94.6    92     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    80.44           33.9    56    90.3    62     ARMSSC1 
     WELL ORDERED  . . . . .    80.44           33.9    56    90.3    62     ARMSSC1 
     NO INTER CONTACTS . . .    80.44           33.9    56    90.3    62     ARMSSC1 
     RELIABLE SIDE CHAINS  .    81.43           33.3    54    90.0    60     ARMSSC1 
     CHANGED ANGLES  . . . .    90.77           15.2    33    86.8    38     ARMSSC1 
     SHIFTED CHAIN . . . . .    80.93           35.3    51    89.5    57     ARMSSC1 
     ALTERNATIVE PARENT  . .   110.96           20.0     5    83.3     6     ARMSSC1 
     SECONDARY STRUCTURE . .    77.99           42.9    28   100.0    28     ARMSSC1 
     LARGE SHIFTS/INSERTIONS   104.82           13.3    15    75.0    20     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    88.46           27.9    43    87.8    49     ARMSSC1 
     BURIED  . . . . . . . .    44.63           53.8    13   100.0    13     ARMSSC1 
     CORE  . . . . . . . . .    69.41           41.5    41    97.6    42     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    82.43           21.4    42    87.5    48     ARMSSC2 
     WELL ORDERED  . . . . .    82.43           21.4    42    87.5    48     ARMSSC2 
     NO INTER CONTACTS . . .    82.43           21.4    42    87.5    48     ARMSSC2 
     RELIABLE SIDE CHAINS  .    73.12           25.0    32    86.5    37     ARMSSC2 
     CHANGED ANGLES  . . . .    85.46           21.9    32    84.2    38     ARMSSC2 
     SHIFTED CHAIN . . . . .    84.10           20.0    40    87.0    46     ARMSSC2 
     ALTERNATIVE PARENT  . .   113.63           33.3     3    75.0     4     ARMSSC2 
     SECONDARY STRUCTURE . .    86.44           34.8    23   100.0    23     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    85.50           11.1     9    64.3    14     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    79.52           19.4    31    83.8    37     ARMSSC2 
     BURIED  . . . . . . . .    90.12           27.3    11   100.0    11     ARMSSC2 
     CORE  . . . . . . . . .    81.58           24.2    33    97.1    34     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    83.78           37.5    16    94.1    17     ARMSSC3 
     WELL ORDERED  . . . . .    83.78           37.5    16    94.1    17     ARMSSC3 
     NO INTER CONTACTS . . .    83.78           37.5    16    94.1    17     ARMSSC3 
     RELIABLE SIDE CHAINS  .    77.00           50.0    12    92.3    13     ARMSSC3 
     CHANGED ANGLES  . . . .    86.47           33.3    15    93.8    16     ARMSSC3 
     SHIFTED CHAIN . . . . .    83.78           37.5    16    94.1    17     ARMSSC3 
     ALTERNATIVE PARENT  . .   106.11            0.0     2   100.0     2     ARMSSC3 
     SECONDARY STRUCTURE . .    73.54           45.5    11   100.0    11     ARMSSC3 
     LARGE SHIFTS/INSERTIONS   105.76           33.3     3   100.0     3     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    81.97           40.0    15    93.8    16     ARMSSC3 
     BURIED  . . . . . . . .   107.30            0.0     1   100.0     1     ARMSSC3 
     CORE  . . . . . . . . .    77.83           38.5    13    92.9    14     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    83.01           16.7     6   100.0     6     ARMSSC4 
     WELL ORDERED  . . . . .    83.01           16.7     6   100.0     6     ARMSSC4 
     NO INTER CONTACTS . . .    83.01           16.7     6   100.0     6     ARMSSC4 
     RELIABLE SIDE CHAINS  .    83.01           16.7     6   100.0     6     ARMSSC4 
     CHANGED ANGLES  . . . .    88.30           20.0     5   100.0     5     ARMSSC4 
     SHIFTED CHAIN . . . . .    83.01           16.7     6   100.0     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    67.03            0.0     3   100.0     3     ARMSSC4 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     0     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .    83.01           16.7     6   100.0     6     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .    83.01           16.7     6   100.0     6     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.75427     r(1,2) =   0.55997     r(1,3) =  -0.34281 
 r(2,1) =  -0.52066     r(2,2) =   0.82822     r(2,3) =   0.20728 
 r(3,1) =   0.40000     r(3,2) =   0.02214     r(3,3) =   0.91625 
THE OFFSET VECTOR: 
 v(1) = -26.56359     v(2) = -21.99263     v(3) = -33.07413 
 
 Number of iteration  3                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.50           (Number of atoms:   27) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    4.18         63    88.7    71     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0663                            CRMSCA  
     WELL ORDERED  . . . . .    4.18         63    88.7    71     CRMSCA  
     NO INTER CONTACTS . . .    4.18         63    88.7    71     CRMSCA  
     SHIFTED CHAIN . . . . .    4.27         57    87.7    65     CRMSCA  
     ALTERNATIVE PARENT  . .    5.93          7    87.5     8     CRMSCA  
     SECONDARY STRUCTURE . .    3.46         32   100.0    32     CRMSCA  
     SHIFTED SS UNITS  . . .    2.19         16   100.0    16     CRMSCA  
     LARGE SHIFTS/INSERTIONS    5.87         18    72.0    25     CRMSCA  
     SURFACE . . . . . . . .    4.45         48    85.7    56     CRMSCA  
     BURIED  . . . . . . . .    3.17         15   100.0    15     CRMSCA  
     CORE  . . . . . . . . .    3.26         45    97.8    46     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    4.20        311    88.9   350     CRMSMC  
     WELL ORDERED  . . . . .    4.20        311    88.9   350     CRMSMC  
     NO INTER CONTACTS . . .    4.20        311    88.9   350     CRMSMC  
     SHIFTED CHAIN . . . . .    4.28        282    87.9   321     CRMSMC  
     ALTERNATIVE PARENT  . .    5.67         34    87.2    39     CRMSMC  
     SECONDARY STRUCTURE . .    3.59        159   100.0   159     CRMSMC  
     SHIFTED SS UNITS  . . .    2.18         80   100.0    80     CRMSMC  
     LARGE SHIFTS/INSERTIONS    5.78         89    72.4   123     CRMSMC  
     SURFACE . . . . . . . .    4.45        237    85.9   276     CRMSMC  
     BURIED  . . . . . . . .    3.27         74   100.0    74     CRMSMC  
     CORE  . . . . . . . . .    3.36        222    97.8   227     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    4.91        241    30.0   803     CRMSSC  
     WELL ORDERED  . . . . .    4.91        241    30.0   803     CRMSSC  
     NO INTER CONTACTS . . .    4.91        241    30.0   803     CRMSSC  
     RELIABLE SIDE CHAINS  .    4.95        207    27.0   767     CRMSSC  
     CHANGED ANGLES  . . . .    5.11        138    88.5   156     CRMSSC  
     SECONDARY STRUCTURE . .    4.18        126    32.0   394     CRMSSC  
     LARGE SHIFTS/INSERTIONS    6.31         54    23.1   234     CRMSSC  
     SURFACE . . . . . . . .    5.25        184    29.5   624     CRMSSC  
     BURIED  . . . . . . . .    3.58         57    31.8   179     CRMSSC  
     CORE  . . . . . . . . .    4.42        187    32.9   569     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    4.56        493    45.4  1087     CRMSALL 
     WELL ORDERED  . . . . .    4.56        493    45.4  1087     CRMSALL 
     NO INTER CONTACTS . . .    4.56        493    45.4  1087     CRMSALL 
     SHIFTED CHAIN . . . . .    4.59        447    44.6  1003     CRMSALL 
     ALTERNATIVE PARENT  . .    5.26         48    44.0   109     CRMSALL 
     SECONDARY STRUCTURE . .    3.90        254    48.7   522     CRMSALL 
     LARGE SHIFTS/INSERTIONS    6.01        126    37.7   334     CRMSALL 
     SURFACE . . . . . . . .    4.86        376    44.3   848     CRMSALL 
     BURIED  . . . . . . . .    3.42        117    49.0   239     CRMSALL 
     CORE  . . . . . . . . .    3.94        367    48.7   753     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     5.91      5   100.0     5       1-STDDS-5    
 CA  LOOP  2     6.06     12   100.0    12      33-ACGQNPTLAEIT-44   
 CA  LOOP  3     2.33      1    16.7     6      66-PNGFDM-71   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     5.90     25   100.0    25       1-STDDS-5    
 MC  LOOP  2     5.92     59   100.0    59      33-ACGQNPTLAEIT-44   
 MC  LOOP  3     2.56      5    17.2    29      66-PNGFDM-71   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     6.76     35    56.5    62       1-STDDS-5    
 ALL LOOP  2     5.87     83    50.6   164      33-ACGQNPTLAEIT-44   
 ALL LOOP  3     3.28      8     9.5    84      66-PNGFDM-71   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.17      5   100.0     5       1-STDDS-5    
 CA  LOOP  2     0.97     12   100.0    12      33-ACGQNPTLAEIT-44   
 WARNING! LOOP  3 cannot be considered (not enough atoms). 
 
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.59     25   100.0    25       1-STDDS-5    
 MC  LOOP  2     1.02     59   100.0    59      33-ACGQNPTLAEIT-44   
 WARNING! LOOP  3 cannot be considered (not enough atoms). 
 
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     3.72     35    56.5    62       1-STDDS-5    
 ALL LOOP  2     2.39     83    50.6   164      33-ACGQNPTLAEIT-44   
 WARNING! LOOP  3 cannot be considered (not enough atoms). 
 
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.095      0.710       0.361     63    88.7    71     ERRCA  
     WELL ORDERED  . . . . .    3.095      0.710       0.361     63    88.7    71     ERRCA  
     NO INTER CONTACTS . . .    3.095      0.710       0.361     63    88.7    71     ERRCA  
     SHIFTED CHAIN . . . . .    3.135      0.702       0.358     57    87.7    65     ERRCA  
     ALTERNATIVE PARENT  . .    4.626      0.778       0.389      7    87.5     8     ERRCA  
     SECONDARY STRUCTURE . .    2.540      0.698       0.349     32   100.0    32     ERRCA  
     LARGE SHIFTS/INSERTIONS    4.913      0.804       0.402     18    72.0    25     ERRCA  
     SURFACE . . . . . . . .    3.291      0.709       0.362     48    85.7    56     ERRCA  
     BURIED  . . . . . . . .    2.469      0.712       0.358     15   100.0    15     ERRCA  
     CORE  . . . . . . . . .    2.368      0.672       0.345     45    97.8    46     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.124      0.708       0.355    311    88.9   350     ERRMC  
     WELL ORDERED  . . . . .    3.124      0.708       0.355    311    88.9   350     ERRMC  
     NO INTER CONTACTS . . .    3.124      0.708       0.355    311    88.9   350     ERRMC  
     SHIFTED CHAIN . . . . .    3.157      0.701       0.352    282    87.9   321     ERRMC  
     ALTERNATIVE PARENT  . .    4.410      0.775       0.387     34    87.2    39     ERRMC  
     SECONDARY STRUCTURE . .    2.620      0.698       0.349    159   100.0   159     ERRMC  
     LARGE SHIFTS/INSERTIONS    4.805      0.795       0.397     89    72.4   123     ERRMC  
     SURFACE . . . . . . . .    3.310      0.707       0.355    237    85.9   276     ERRMC  
     BURIED  . . . . . . . .    2.530      0.711       0.356     74   100.0    74     ERRMC  
     CORE  . . . . . . . . .    2.451      0.673       0.338    222    97.8   227     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.778      0.756       0.378    241    30.0   803     ERRSC  
     WELL ORDERED  . . . . .    3.778      0.756       0.378    241    30.0   803     ERRSC  
     NO INTER CONTACTS . . .    3.778      0.756       0.378    241    30.0   803     ERRSC  
     RELIABLE SIDE CHAINS  .    3.750      0.746       0.373    207    27.0   767     ERRSC  
     CHANGED ANGLES  . . . .    3.963      0.776       0.388    138    88.5   156     ERRSC  
     SHIFTED CHAIN . . . . .    3.773      0.756       0.378    219    29.5   743     ERRSC  
     ALTERNATIVE PARENT  . .    3.513      0.770       0.385     20    26.0    77     ERRSC  
     SECONDARY STRUCTURE . .    3.121      0.732       0.366    126    32.0   394     ERRSC  
     LARGE SHIFTS/INSERTIONS    5.300      0.816       0.408     54    23.1   234     ERRSC  
     SURFACE . . . . . . . .    4.128      0.767       0.384    184    29.5   624     ERRSC  
     BURIED  . . . . . . . .    2.647      0.718       0.359     57    31.8   179     ERRSC  
     CORE  . . . . . . . . .    3.338      0.738       0.369    187    32.9   569     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.441      0.731       0.366    493    45.4  1087     ERRALL 
     WELL ORDERED  . . . . .    3.441      0.731       0.366    493    45.4  1087     ERRALL 
     NO INTER CONTACTS . . .    3.441      0.731       0.366    493    45.4  1087     ERRALL 
     SHIFTED CHAIN . . . . .    3.454      0.727       0.364    447    44.6  1003     ERRALL 
     ALTERNATIVE PARENT  . .    4.098      0.775       0.388     48    44.0   109     ERRALL 
     SECONDARY STRUCTURE . .    2.873      0.715       0.358    254    48.7   522     ERRALL 
     LARGE SHIFTS/INSERTIONS    5.007      0.803       0.402    126    37.7   334     ERRALL 
     SURFACE . . . . . . . .    3.707      0.737       0.369    376    44.3   848     ERRALL 
     BURIED  . . . . . . . .    2.586      0.713       0.357    117    49.0   239     ERRALL 
     CORE  . . . . . . . . .    2.904      0.706       0.354    367    48.7   753     ERRALL 
 
 
 
DISTANCES: Percent of total atoms where distance (target <-> model) in global 
           superposition is less than: 1 , 2 , 3 , 5 , 10 Angstroms 
            D < 1     D < 2     D < 3     D < 5    D < 10      NP      TN 
CA  (N)         5        23        30        47        62      63      71   DISTCA 
CA  (P)      7.04     32.39     42.25     66.20     87.32              71   DISTCA 
CA  (RMS)    0.69      1.32      1.66      2.67      4.00                   DISTCA 
 
ALL (N)        37       145       219       356       484     493    1087   DISTALL 
ALL (P)      3.40     13.34     20.15     32.75     44.53            1087   DISTALL 
ALL (RMS)    0.78      1.39      1.84      2.89      4.35                   DISTALL 
 
CA RMS: P<->T (parent <-> target), and T<->M (target <-> model) calculated using 
        CA positions for which there exists an alignment with principal parent, 
        and for which does not (LARGE SHIFTS/INSERTIONS): 
              P<->T         T<->M         T<->M (LSI) 
CA  (N)          46            45            18          RMSLSI 
CA  (P)       64.79         63.38         25.35          RMSLSI 
CA  (RMS)      1.65          3.26          5.87          RMSLSI 
 
 
 
END of the results output 
