 
####################################################### 
#                                                     # 
#                        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: 552 
 
 
 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 . . . . . . . . . .    75.32           53.6   140   100.0   140     ARMSMC  
     WELL ORDERED  . . . . .    75.32           53.6   140   100.0   140     ARMSMC  
     NO INTER CONTACTS . . .    75.32           53.6   140   100.0   140     ARMSMC  
     SHIFTED CHAIN . . . . .    75.39           52.3   128   100.0   128     ARMSMC  
     ALTERNATIVE PARENT  . .    56.28           66.7    15   100.0    15     ARMSMC  
     SECONDARY STRUCTURE . .    38.44           82.8    64   100.0    64     ARMSMC  
     LARGE SHIFTS/INSERTIONS    85.10           43.8    48   100.0    48     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    78.07           50.0   110   100.0   110     ARMSMC  
     BURIED  . . . . . . . .    64.19           66.7    30   100.0    30     ARMSMC  
     CORE  . . . . . . . . .    69.67           58.7    92   100.0    92     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    75.93           33.9    62   100.0    62     ARMSSC1 
     WELL ORDERED  . . . . .    75.93           33.9    62   100.0    62     ARMSSC1 
     NO INTER CONTACTS . . .    75.93           33.9    62   100.0    62     ARMSSC1 
     RELIABLE SIDE CHAINS  .    76.83           33.3    60   100.0    60     ARMSSC1 
     CHANGED ANGLES  . . . .    71.57           36.8    38   100.0    38     ARMSSC1 
     SHIFTED CHAIN . . . . .    76.97           33.3    57   100.0    57     ARMSSC1 
     ALTERNATIVE PARENT  . .    78.17           16.7     6   100.0     6     ARMSSC1 
     SECONDARY STRUCTURE . .    77.73           35.7    28   100.0    28     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    65.43           35.0    20   100.0    20     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    75.67           34.7    49   100.0    49     ARMSSC1 
     BURIED  . . . . . . . .    76.93           30.8    13   100.0    13     ARMSSC1 
     CORE  . . . . . . . . .    80.46           33.3    42   100.0    42     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    75.46           39.6    48   100.0    48     ARMSSC2 
     WELL ORDERED  . . . . .    75.46           39.6    48   100.0    48     ARMSSC2 
     NO INTER CONTACTS . . .    75.46           39.6    48   100.0    48     ARMSSC2 
     RELIABLE SIDE CHAINS  .    64.49           43.2    37   100.0    37     ARMSSC2 
     CHANGED ANGLES  . . . .    78.69           39.5    38   100.0    38     ARMSSC2 
     SHIFTED CHAIN . . . . .    76.35           39.1    46   100.0    46     ARMSSC2 
     ALTERNATIVE PARENT  . .   108.19            0.0     4   100.0     4     ARMSSC2 
     SECONDARY STRUCTURE . .    83.01           43.5    23   100.0    23     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    79.91           28.6    14   100.0    14     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    69.67           43.2    37   100.0    37     ARMSSC2 
     BURIED  . . . . . . . .    92.33           27.3    11   100.0    11     ARMSSC2 
     CORE  . . . . . . . . .    73.56           44.1    34   100.0    34     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    84.67           23.5    17   100.0    17     ARMSSC3 
     WELL ORDERED  . . . . .    84.67           23.5    17   100.0    17     ARMSSC3 
     NO INTER CONTACTS . . .    84.67           23.5    17   100.0    17     ARMSSC3 
     RELIABLE SIDE CHAINS  .    83.00           23.1    13   100.0    13     ARMSSC3 
     CHANGED ANGLES  . . . .    87.27           18.8    16   100.0    16     ARMSSC3 
     SHIFTED CHAIN . . . . .    84.67           23.5    17   100.0    17     ARMSSC3 
     ALTERNATIVE PARENT  . .    53.25           50.0     2   100.0     2     ARMSSC3 
     SECONDARY STRUCTURE . .    82.91           27.3    11   100.0    11     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    22.08           66.7     3   100.0     3     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    77.83           25.0    16   100.0    16     ARMSSC3 
     BURIED  . . . . . . . .   157.93            0.0     1   100.0     1     ARMSSC3 
     CORE  . . . . . . . . .    92.74           14.3    14   100.0    14     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    60.21           33.3     6   100.0     6     ARMSSC4 
     WELL ORDERED  . . . . .    60.21           33.3     6   100.0     6     ARMSSC4 
     NO INTER CONTACTS . . .    60.21           33.3     6   100.0     6     ARMSSC4 
     RELIABLE SIDE CHAINS  .    60.21           33.3     6   100.0     6     ARMSSC4 
     CHANGED ANGLES  . . . .    65.89           20.0     5   100.0     5     ARMSSC4 
     SHIFTED CHAIN . . . . .    60.21           33.3     6   100.0     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    63.26           33.3     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 . . . . . . . .    60.21           33.3     6   100.0     6     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .    60.21           33.3     6   100.0     6     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.78565     r(1,2) =  -0.61661     r(1,3) =  -0.05036 
 r(2,1) =   0.32636     r(2,2) =  -0.34392     r(2,3) =  -0.88046 
 r(3,1) =   0.52558     r(3,2) =  -0.70817     r(3,3) =   0.47144 
THE OFFSET VECTOR: 
 v(1) = -15.10661     v(2) =   4.55725     v(3) = -10.86330 
 
 Number of iteration  2                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.83           (Number of atoms:   13) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   13.18         71   100.0    71     CRMSCA  
     CRN = ALL/NP  . . . . .    0.1856                            CRMSCA  
     WELL ORDERED  . . . . .   13.18         71   100.0    71     CRMSCA  
     NO INTER CONTACTS . . .   13.18         71   100.0    71     CRMSCA  
     SHIFTED CHAIN . . . . .   13.13         65   100.0    65     CRMSCA  
     ALTERNATIVE PARENT  . .   10.19          8   100.0     8     CRMSCA  
     SECONDARY STRUCTURE . .   11.68         32   100.0    32     CRMSCA  
     SHIFTED SS UNITS  . . .   15.76         16   100.0    16     CRMSCA  
     LARGE SHIFTS/INSERTIONS   16.24         25   100.0    25     CRMSCA  
     SURFACE . . . . . . . .   13.99         56   100.0    56     CRMSCA  
     BURIED  . . . . . . . .    9.57         15   100.0    15     CRMSCA  
     CORE  . . . . . . . . .   11.17         46   100.0    46     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   13.22        350   100.0   350     CRMSMC  
     WELL ORDERED  . . . . .   13.22        350   100.0   350     CRMSMC  
     NO INTER CONTACTS . . .   13.22        350   100.0   350     CRMSMC  
     SHIFTED CHAIN . . . . .   13.19        321   100.0   321     CRMSMC  
     ALTERNATIVE PARENT  . .   10.44         39   100.0    39     CRMSMC  
     SECONDARY STRUCTURE . .   11.82        159   100.0   159     CRMSMC  
     SHIFTED SS UNITS  . . .   15.96         80   100.0    80     CRMSMC  
     LARGE SHIFTS/INSERTIONS   16.24        123   100.0   123     CRMSMC  
     SURFACE . . . . . . . .   14.01        276   100.0   276     CRMSMC  
     BURIED  . . . . . . . .    9.75         74   100.0    74     CRMSMC  
     CORE  . . . . . . . . .   11.26        227   100.0   227     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   13.91        268    33.4   803     CRMSSC  
     WELL ORDERED  . . . . .   13.91        268    33.4   803     CRMSSC  
     NO INTER CONTACTS . . .   13.91        268    33.4   803     CRMSSC  
     RELIABLE SIDE CHAINS  .   14.10        232    30.2   767     CRMSSC  
     CHANGED ANGLES  . . . .   14.06        156   100.0   156     CRMSSC  
     SECONDARY STRUCTURE . .   12.49        126    32.0   394     CRMSSC  
     LARGE SHIFTS/INSERTIONS   17.06         76    32.5   234     CRMSSC  
     SURFACE . . . . . . . .   14.85        211    33.8   624     CRMSSC  
     BURIED  . . . . . . . .    9.65         57    31.8   179     CRMSSC  
     CORE  . . . . . . . . .   12.44        192    33.7   569     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   13.53        552    50.8  1087     CRMSALL 
     WELL ORDERED  . . . . .   13.53        552    50.8  1087     CRMSALL 
     NO INTER CONTACTS . . .   13.53        552    50.8  1087     CRMSALL 
     SHIFTED CHAIN . . . . .   13.60        506    50.4  1003     CRMSALL 
     ALTERNATIVE PARENT  . .   10.66         55    50.5   109     CRMSALL 
     SECONDARY STRUCTURE . .   12.13        254    48.7   522     CRMSALL 
     LARGE SHIFTS/INSERTIONS   16.55        176    52.7   334     CRMSALL 
     SURFACE . . . . . . . .   14.38        435    51.3   848     CRMSALL 
     BURIED  . . . . . . . .    9.74        117    49.0   239     CRMSALL 
     CORE  . . . . . . . . .   11.85        376    49.9   753     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     9.05      5   100.0     5       1-STDDS-5    
 CA  LOOP  2    13.34     12   100.0    12      33-ACGQNPTLAEIT-44   
 CA  LOOP  3    24.00      6   100.0     6      66-PNGFDM-71   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     9.06     25   100.0    25       1-STDDS-5    
 MC  LOOP  2    13.65     59   100.0    59      33-ACGQNPTLAEIT-44   
 MC  LOOP  3    23.95     29   100.0    29      66-PNGFDM-71   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     9.14     35    56.5    62       1-STDDS-5    
 ALL LOOP  2    13.64     83    50.6   164      33-ACGQNPTLAEIT-44   
 ALL LOOP  3    24.05     46    54.8    84      66-PNGFDM-71   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.62      5   100.0     5       1-STDDS-5    
 CA  LOOP  2     3.91     12   100.0    12      33-ACGQNPTLAEIT-44   
 CA  LOOP  3     3.07      6   100.0     6      66-PNGFDM-71   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.99     25   100.0    25       1-STDDS-5    
 MC  LOOP  2     3.89     59   100.0    59      33-ACGQNPTLAEIT-44   
 MC  LOOP  3     3.67     29   100.0    29      66-PNGFDM-71   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     3.71     35    56.5    62       1-STDDS-5    
 ALL LOOP  2     4.25     83    50.6   164      33-ACGQNPTLAEIT-44   
 ALL LOOP  3     5.86     46    54.8    84      66-PNGFDM-71   
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.204      0.397       0.266     71   100.0    71     ERRCA  
     WELL ORDERED  . . . . .    7.204      0.397       0.266     71   100.0    71     ERRCA  
     NO INTER CONTACTS . . .    7.204      0.397       0.266     71   100.0    71     ERRCA  
     SHIFTED CHAIN . . . . .    7.180      0.396       0.257     65   100.0    65     ERRCA  
     ALTERNATIVE PARENT  . .    5.512      0.394       0.326      8   100.0     8     ERRCA  
     SECONDARY STRUCTURE . .    6.137      0.375       0.280     32   100.0    32     ERRCA  
     LARGE SHIFTS/INSERTIONS   10.393      0.510       0.316     25   100.0    25     ERRCA  
     SURFACE . . . . . . . .    8.048      0.434       0.288     56   100.0    56     ERRCA  
     BURIED  . . . . . . . .    4.053      0.257       0.187     15   100.0    15     ERRCA  
     CORE  . . . . . . . . .    5.471      0.335       0.239     46   100.0    46     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.204      0.392       0.257    350   100.0   350     ERRMC  
     WELL ORDERED  . . . . .    7.204      0.392       0.257    350   100.0   350     ERRMC  
     NO INTER CONTACTS . . .    7.204      0.392       0.257    350   100.0   350     ERRMC  
     SHIFTED CHAIN . . . . .    7.182      0.390       0.249    321   100.0   321     ERRMC  
     ALTERNATIVE PARENT  . .    5.648      0.394       0.312     39   100.0    39     ERRMC  
     SECONDARY STRUCTURE . .    6.276      0.383       0.278    159   100.0   159     ERRMC  
     LARGE SHIFTS/INSERTIONS   10.278      0.492       0.296    123   100.0   123     ERRMC  
     SURFACE . . . . . . . .    7.991      0.424       0.275    276   100.0   276     ERRMC  
     BURIED  . . . . . . . .    4.268      0.271       0.190     74   100.0    74     ERRMC  
     CORE  . . . . . . . . .    5.538      0.338       0.235    227   100.0   227     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.688      0.391       0.235    268    33.4   803     ERRSC  
     WELL ORDERED  . . . . .    7.688      0.391       0.235    268    33.4   803     ERRSC  
     NO INTER CONTACTS . . .    7.688      0.391       0.235    268    33.4   803     ERRSC  
     RELIABLE SIDE CHAINS  .    7.827      0.395       0.238    232    30.2   767     ERRSC  
     CHANGED ANGLES  . . . .    7.849      0.393       0.235    156   100.0   156     ERRSC  
     SHIFTED CHAIN . . . . .    7.852      0.393       0.229    246    33.1   743     ERRSC  
     ALTERNATIVE PARENT  . .    5.373      0.310       0.187     23    29.9    77     ERRSC  
     SECONDARY STRUCTURE . .    6.702      0.379       0.254    126    32.0   394     ERRSC  
     LARGE SHIFTS/INSERTIONS   10.954      0.495       0.282     76    32.5   234     ERRSC  
     SURFACE . . . . . . . .    8.599      0.419       0.243    211    33.8   624     ERRSC  
     BURIED  . . . . . . . .    4.315      0.286       0.206     57    31.8   179     ERRSC  
     CORE  . . . . . . . . .    6.395      0.350       0.216    192    33.7   569     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.418      0.392       0.247    552    50.8  1087     ERRALL 
     WELL ORDERED  . . . . .    7.418      0.392       0.247    552    50.8  1087     ERRALL 
     NO INTER CONTACTS . . .    7.418      0.392       0.247    552    50.8  1087     ERRALL 
     SHIFTED CHAIN . . . . .    7.494      0.392       0.241    506    50.4  1003     ERRALL 
     ALTERNATIVE PARENT  . .    5.548      0.363       0.265     55    50.5   109     ERRALL 
     SECONDARY STRUCTURE . .    6.467      0.380       0.266    254    48.7   522     ERRALL 
     LARGE SHIFTS/INSERTIONS   10.515      0.491       0.289    176    52.7   334     ERRALL 
     SURFACE . . . . . . . .    8.255      0.422       0.261    435    51.3   848     ERRALL 
     BURIED  . . . . . . . .    4.306      0.278       0.197    117    49.0   239     ERRALL 
     CORE  . . . . . . . . .    5.968      0.345       0.228    376    49.9   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)         2         8        13        20        38      71      71   DISTCA 
CA  (P)      2.82     11.27     18.31     28.17     53.52              71   DISTCA 
CA  (RMS)    0.84      1.43      1.83      2.81      5.53                   DISTCA 
 
ALL (N)         8        46        77       145       283     552    1087   DISTALL 
ALL (P)      0.74      4.23      7.08     13.34     26.03            1087   DISTALL 
ALL (RMS)    0.84      1.41      1.87      3.05      5.71                   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            46            25          RMSLSI 
CA  (P)       64.79         64.79         35.21          RMSLSI 
CA  (RMS)      1.65         11.17         16.24          RMSLSI 
 
 
 
END of the results output 
