 
####################################################### 
#                                                     # 
#                        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: 546 
 
 
 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 . . . . . . . . . .    69.87           58.7   138    98.6   140     ARMSMC  
     WELL ORDERED  . . . . .    69.87           58.7   138    98.6   140     ARMSMC  
     NO INTER CONTACTS . . .    69.87           58.7   138    98.6   140     ARMSMC  
     SHIFTED CHAIN . . . . .    72.76           56.3   126    98.4   128     ARMSMC  
     ALTERNATIVE PARENT  . .    86.09           50.0    14    93.3    15     ARMSMC  
     SECONDARY STRUCTURE . .    59.46           81.2    64   100.0    64     ARMSMC  
     LARGE SHIFTS/INSERTIONS    89.58           34.8    46    95.8    48     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    72.30           55.6   108    98.2   110     ARMSMC  
     BURIED  . . . . . . . .    60.32           70.0    30   100.0    30     ARMSMC  
     CORE  . . . . . . . . .    57.54           70.7    92   100.0    92     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    83.09           34.4    61    98.4    62     ARMSSC1 
     WELL ORDERED  . . . . .    83.09           34.4    61    98.4    62     ARMSSC1 
     NO INTER CONTACTS . . .    83.09           34.4    61    98.4    62     ARMSSC1 
     RELIABLE SIDE CHAINS  .    82.30           35.6    59    98.3    60     ARMSSC1 
     CHANGED ANGLES  . . . .    80.09           29.7    37    97.4    38     ARMSSC1 
     SHIFTED CHAIN . . . . .    83.11           33.9    56    98.2    57     ARMSSC1 
     ALTERNATIVE PARENT  . .   104.56            0.0     5    83.3     6     ARMSSC1 
     SECONDARY STRUCTURE . .    82.11           32.1    28   100.0    28     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    81.40           31.6    19    95.0    20     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    81.04           37.5    48    98.0    49     ARMSSC1 
     BURIED  . . . . . . . .    90.27           23.1    13   100.0    13     ARMSSC1 
     CORE  . . . . . . . . .    83.85           35.7    42   100.0    42     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    72.86           35.4    48   100.0    48     ARMSSC2 
     WELL ORDERED  . . . . .    72.86           35.4    48   100.0    48     ARMSSC2 
     NO INTER CONTACTS . . .    72.86           35.4    48   100.0    48     ARMSSC2 
     RELIABLE SIDE CHAINS  .    68.72           37.8    37   100.0    37     ARMSSC2 
     CHANGED ANGLES  . . . .    73.29           31.6    38   100.0    38     ARMSSC2 
     SHIFTED CHAIN . . . . .    74.17           34.8    46   100.0    46     ARMSSC2 
     ALTERNATIVE PARENT  . .    64.83            0.0     4   100.0     4     ARMSSC2 
     SECONDARY STRUCTURE . .    77.88           43.5    23   100.0    23     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    58.41           35.7    14   100.0    14     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    69.96           40.5    37   100.0    37     ARMSSC2 
     BURIED  . . . . . . . .    81.85           18.2    11   100.0    11     ARMSSC2 
     CORE  . . . . . . . . .    78.03           35.3    34   100.0    34     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    96.38           29.4    17   100.0    17     ARMSSC3 
     WELL ORDERED  . . . . .    96.38           29.4    17   100.0    17     ARMSSC3 
     NO INTER CONTACTS . . .    96.38           29.4    17   100.0    17     ARMSSC3 
     RELIABLE SIDE CHAINS  .    84.29           30.8    13   100.0    13     ARMSSC3 
     CHANGED ANGLES  . . . .    98.73           31.2    16   100.0    16     ARMSSC3 
     SHIFTED CHAIN . . . . .    96.38           29.4    17   100.0    17     ARMSSC3 
     ALTERNATIVE PARENT  . .    79.57            0.0     2   100.0     2     ARMSSC3 
     SECONDARY STRUCTURE . .    83.04           36.4    11   100.0    11     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    98.14            0.0     3   100.0     3     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    88.73           31.2    16   100.0    16     ARMSSC3 
     BURIED  . . . . . . . .   178.77            0.0     1   100.0     1     ARMSSC3 
     CORE  . . . . . . . . .    96.01           35.7    14   100.0    14     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    59.03           16.7     6   100.0     6     ARMSSC4 
     WELL ORDERED  . . . . .    59.03           16.7     6   100.0     6     ARMSSC4 
     NO INTER CONTACTS . . .    59.03           16.7     6   100.0     6     ARMSSC4 
     RELIABLE SIDE CHAINS  .    59.03           16.7     6   100.0     6     ARMSSC4 
     CHANGED ANGLES  . . . .    60.37           20.0     5   100.0     5     ARMSSC4 
     SHIFTED CHAIN . . . . .    59.03           16.7     6   100.0     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    37.15           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 . . . . . . . .    59.03           16.7     6   100.0     6     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .    59.03           16.7     6   100.0     6     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.41679     r(1,2) =  -0.42199     r(1,3) =  -0.80512 
 r(2,1) =  -0.90102     r(2,2) =   0.07465     r(2,3) =   0.42730 
 r(3,1) =  -0.12022     r(3,2) =   0.90352     r(3,3) =  -0.41133 
THE OFFSET VECTOR: 
 v(1) =  81.92994     v(2) =  -4.48394     v(3) = -23.74212 
 
 Number of iteration  2                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.45           (Number of atoms:    9) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    8.62         70    98.6    71     CRMSCA  
     CRN = ALL/NP  . . . . .    0.1232                            CRMSCA  
     WELL ORDERED  . . . . .    8.62         70    98.6    71     CRMSCA  
     NO INTER CONTACTS . . .    8.62         70    98.6    71     CRMSCA  
     SHIFTED CHAIN . . . . .    8.76         64    98.5    65     CRMSCA  
     ALTERNATIVE PARENT  . .    9.96          7    87.5     8     CRMSCA  
     SECONDARY STRUCTURE . .    8.91         32   100.0    32     CRMSCA  
     SHIFTED SS UNITS  . . .    7.25         16   100.0    16     CRMSCA  
     LARGE SHIFTS/INSERTIONS    8.59         24    96.0    25     CRMSCA  
     SURFACE . . . . . . . .    8.64         55    98.2    56     CRMSCA  
     BURIED  . . . . . . . .    8.53         15   100.0    15     CRMSCA  
     CORE  . . . . . . . . .    8.64         46   100.0    46     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    8.63        345    98.6   350     CRMSMC  
     WELL ORDERED  . . . . .    8.63        345    98.6   350     CRMSMC  
     NO INTER CONTACTS . . .    8.63        345    98.6   350     CRMSMC  
     SHIFTED CHAIN . . . . .    8.79        316    98.4   321     CRMSMC  
     ALTERNATIVE PARENT  . .    9.75         34    87.2    39     CRMSMC  
     SECONDARY STRUCTURE . .    8.95        159   100.0   159     CRMSMC  
     SHIFTED SS UNITS  . . .    7.31         80   100.0    80     CRMSMC  
     LARGE SHIFTS/INSERTIONS    8.48        118    95.9   123     CRMSMC  
     SURFACE . . . . . . . .    8.65        271    98.2   276     CRMSMC  
     BURIED  . . . . . . . .    8.53         74   100.0    74     CRMSMC  
     CORE  . . . . . . . . .    8.71        227   100.0   227     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   10.24        266    33.1   803     CRMSSC  
     WELL ORDERED  . . . . .   10.24        266    33.1   803     CRMSSC  
     NO INTER CONTACTS . . .   10.24        266    33.1   803     CRMSSC  
     RELIABLE SIDE CHAINS  .   10.19        230    30.0   767     CRMSSC  
     CHANGED ANGLES  . . . .   10.57        155    99.4   156     CRMSSC  
     SECONDARY STRUCTURE . .   10.44        126    32.0   394     CRMSSC  
     LARGE SHIFTS/INSERTIONS    9.98         74    31.6   234     CRMSSC  
     SURFACE . . . . . . . .   10.41        209    33.5   624     CRMSSC  
     BURIED  . . . . . . . .    9.57         57    31.8   179     CRMSSC  
     CORE  . . . . . . . . .   10.34        192    33.7   569     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    9.39        546    50.2  1087     CRMSALL 
     WELL ORDERED  . . . . .    9.39        546    50.2  1087     CRMSALL 
     NO INTER CONTACTS . . .    9.39        546    50.2  1087     CRMSALL 
     SHIFTED CHAIN . . . . .    9.51        500    49.9  1003     CRMSALL 
     ALTERNATIVE PARENT  . .    8.97         49    45.0   109     CRMSALL 
     SECONDARY STRUCTURE . .    9.68        254    48.7   522     CRMSALL 
     LARGE SHIFTS/INSERTIONS    9.09        170    50.9   334     CRMSALL 
     SURFACE . . . . . . . .    9.50        429    50.6   848     CRMSALL 
     BURIED  . . . . . . . .    8.99        117    49.0   239     CRMSALL 
     CORE  . . . . . . . . .    9.53        376    49.9   753     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     4.49      4    80.0     5       1-STDDS-5    
 CA  LOOP  2     9.94     12   100.0    12      33-ACGQNPTLAEIT-44   
 CA  LOOP  3     8.28      6   100.0     6      66-PNGFDM-71   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     4.67     20    80.0    25       1-STDDS-5    
 MC  LOOP  2     9.62     59   100.0    59      33-ACGQNPTLAEIT-44   
 MC  LOOP  3     8.50     29   100.0    29      66-PNGFDM-71   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     5.82     29    46.8    62       1-STDDS-5    
 ALL LOOP  2    10.09     83    50.6   164      33-ACGQNPTLAEIT-44   
 ALL LOOP  3     9.42     46    54.8    84      66-PNGFDM-71   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     1.25      4    80.0     5       1-STDDS-5    
 CA  LOOP  2     4.92     12   100.0    12      33-ACGQNPTLAEIT-44   
 CA  LOOP  3     2.15      6   100.0     6      66-PNGFDM-71   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.19     20    80.0    25       1-STDDS-5    
 MC  LOOP  2     4.98     59   100.0    59      33-ACGQNPTLAEIT-44   
 MC  LOOP  3     2.94     29   100.0    29      66-PNGFDM-71   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     2.66     29    46.8    62       1-STDDS-5    
 ALL LOOP  2     5.84     83    50.6   164      33-ACGQNPTLAEIT-44   
 ALL LOOP  3     4.18     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 . . . . . . . . . .    3.450      0.244       0.233     70    98.6    71     ERRCA  
     WELL ORDERED  . . . . .    3.450      0.244       0.233     70    98.6    71     ERRCA  
     NO INTER CONTACTS . . .    3.450      0.244       0.233     70    98.6    71     ERRCA  
     SHIFTED CHAIN . . . . .    3.364      0.236       0.220     64    98.5    65     ERRCA  
     ALTERNATIVE PARENT  . .    5.539      0.401       0.352      7    87.5     8     ERRCA  
     SECONDARY STRUCTURE . .    3.681      0.260       0.248     32   100.0    32     ERRCA  
     LARGE SHIFTS/INSERTIONS    3.862      0.268       0.247     24    96.0    25     ERRCA  
     SURFACE . . . . . . . .    3.519      0.245       0.234     55    98.2    56     ERRCA  
     BURIED  . . . . . . . .    3.196      0.239       0.229     15   100.0    15     ERRCA  
     CORE  . . . . . . . . .    3.235      0.231       0.226     46   100.0    46     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.429      0.239       0.230    345    98.6   350     ERRMC  
     WELL ORDERED  . . . . .    3.429      0.239       0.230    345    98.6   350     ERRMC  
     NO INTER CONTACTS . . .    3.429      0.239       0.230    345    98.6   350     ERRMC  
     SHIFTED CHAIN . . . . .    3.336      0.229       0.217    316    98.4   321     ERRMC  
     ALTERNATIVE PARENT  . .    4.969      0.341       0.308     34    87.2    39     ERRMC  
     SECONDARY STRUCTURE . .    3.686      0.259       0.247    159   100.0   159     ERRMC  
     LARGE SHIFTS/INSERTIONS    3.789      0.260       0.253    118    95.9   123     ERRMC  
     SURFACE . . . . . . . .    3.481      0.240       0.230    271    98.2   276     ERRMC  
     BURIED  . . . . . . . .    3.240      0.235       0.228     74   100.0    74     ERRMC  
     CORE  . . . . . . . . .    3.242      0.227       0.218    227   100.0   227     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.104      0.176       0.139    266    33.1   803     ERRSC  
     WELL ORDERED  . . . . .    3.104      0.176       0.139    266    33.1   803     ERRSC  
     NO INTER CONTACTS . . .    3.104      0.176       0.139    266    33.1   803     ERRSC  
     RELIABLE SIDE CHAINS  .    3.138      0.181       0.146    230    30.0   767     ERRSC  
     CHANGED ANGLES  . . . .    3.161      0.172       0.130    155    99.4   156     ERRSC  
     SHIFTED CHAIN . . . . .    3.129      0.177       0.138    244    32.8   743     ERRSC  
     ALTERNATIVE PARENT  . .    3.144      0.224       0.221     21    27.3    77     ERRSC  
     SECONDARY STRUCTURE . .    3.155      0.180       0.136    126    32.0   394     ERRSC  
     LARGE SHIFTS/INSERTIONS    3.234      0.185       0.159     74    31.6   234     ERRSC  
     SURFACE . . . . . . . .    3.280      0.185       0.146    209    33.5   624     ERRSC  
     BURIED  . . . . . . . .    2.460      0.146       0.113     57    31.8   179     ERRSC  
     CORE  . . . . . . . . .    3.054      0.173       0.131    192    33.7   569     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.307      0.213       0.191    546    50.2  1087     ERRALL 
     WELL ORDERED  . . . . .    3.307      0.213       0.191    546    50.2  1087     ERRALL 
     NO INTER CONTACTS . . .    3.307      0.213       0.191    546    50.2  1087     ERRALL 
     SHIFTED CHAIN . . . . .    3.263      0.208       0.183    500    49.9  1003     ERRALL 
     ALTERNATIVE PARENT  . .    4.293      0.296       0.273     49    45.0   109     ERRALL 
     SECONDARY STRUCTURE . .    3.476      0.225       0.200    254    48.7   522     ERRALL 
     LARGE SHIFTS/INSERTIONS    3.622      0.235       0.218    170    50.9   334     ERRALL 
     SURFACE . . . . . . . .    3.414      0.217       0.194    429    50.6   848     ERRALL 
     BURIED  . . . . . . . .    2.916      0.197       0.180    117    49.0   239     ERRALL 
     CORE  . . . . . . . . .    3.164      0.202       0.179    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)         3         8         9        19        49      70      71   DISTCA 
CA  (P)      4.23     11.27     12.68     26.76     69.01              71   DISTCA 
CA  (RMS)    0.75      1.31      1.45      3.17      6.28                   DISTCA 
 
ALL (N)         9        34        50       107       342     546    1087   DISTALL 
ALL (P)      0.83      3.13      4.60      9.84     31.46            1087   DISTALL 
ALL (RMS)    0.73      1.40      1.86      3.17      6.55                   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            24          RMSLSI 
CA  (P)       64.79         64.79         33.80          RMSLSI 
CA  (RMS)      1.65          8.64          8.59          RMSLSI 
 
 
 
END of the results output 
