 
####################################################### 
#                                                     # 
#                        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 . . . . . . . . . .    70.37           58.7   138    98.6   140     ARMSMC  
     WELL ORDERED  . . . . .    70.37           58.7   138    98.6   140     ARMSMC  
     NO INTER CONTACTS . . .    70.37           58.7   138    98.6   140     ARMSMC  
     SHIFTED CHAIN . . . . .    73.31           56.3   126    98.4   128     ARMSMC  
     ALTERNATIVE PARENT  . .    93.18           57.1    14    93.3    15     ARMSMC  
     SECONDARY STRUCTURE . .    58.93           76.6    64   100.0    64     ARMSMC  
     LARGE SHIFTS/INSERTIONS    88.00           39.1    46    95.8    48     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    71.81           55.6   108    98.2   110     ARMSMC  
     BURIED  . . . . . . . .    64.92           70.0    30   100.0    30     ARMSMC  
     CORE  . . . . . . . . .    59.63           68.5    92   100.0    92     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    77.46           37.7    61    98.4    62     ARMSSC1 
     WELL ORDERED  . . . . .    77.46           37.7    61    98.4    62     ARMSSC1 
     NO INTER CONTACTS . . .    77.46           37.7    61    98.4    62     ARMSSC1 
     RELIABLE SIDE CHAINS  .    78.24           37.3    59    98.3    60     ARMSSC1 
     CHANGED ANGLES  . . . .    74.75           32.4    37    97.4    38     ARMSSC1 
     SHIFTED CHAIN . . . . .    78.67           35.7    56    98.2    57     ARMSSC1 
     ALTERNATIVE PARENT  . .    70.02           20.0     5    83.3     6     ARMSSC1 
     SECONDARY STRUCTURE . .    74.37           39.3    28   100.0    28     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    90.54           21.1    19    95.0    20     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    77.79           39.6    48    98.0    49     ARMSSC1 
     BURIED  . . . . . . . .    76.20           30.8    13   100.0    13     ARMSSC1 
     CORE  . . . . . . . . .    70.75           45.2    42   100.0    42     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    80.51           43.8    48   100.0    48     ARMSSC2 
     WELL ORDERED  . . . . .    80.51           43.8    48   100.0    48     ARMSSC2 
     NO INTER CONTACTS . . .    80.51           43.8    48   100.0    48     ARMSSC2 
     RELIABLE SIDE CHAINS  .    74.11           48.6    37   100.0    37     ARMSSC2 
     CHANGED ANGLES  . . . .    82.71           39.5    38   100.0    38     ARMSSC2 
     SHIFTED CHAIN . . . . .    82.03           43.5    46   100.0    46     ARMSSC2 
     ALTERNATIVE PARENT  . .    86.29           25.0     4   100.0     4     ARMSSC2 
     SECONDARY STRUCTURE . .    79.69           52.2    23   100.0    23     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    55.48           42.9    14   100.0    14     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    79.11           45.9    37   100.0    37     ARMSSC2 
     BURIED  . . . . . . . .    85.04           36.4    11   100.0    11     ARMSSC2 
     CORE  . . . . . . . . .    88.79           44.1    34   100.0    34     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    93.39           17.6    17   100.0    17     ARMSSC3 
     WELL ORDERED  . . . . .    93.39           17.6    17   100.0    17     ARMSSC3 
     NO INTER CONTACTS . . .    93.39           17.6    17   100.0    17     ARMSSC3 
     RELIABLE SIDE CHAINS  .    89.06           23.1    13   100.0    13     ARMSSC3 
     CHANGED ANGLES  . . . .    95.54           18.8    16   100.0    16     ARMSSC3 
     SHIFTED CHAIN . . . . .    93.39           17.6    17   100.0    17     ARMSSC3 
     ALTERNATIVE PARENT  . .    73.49            0.0     2   100.0     2     ARMSSC3 
     SECONDARY STRUCTURE . .    78.82           18.2    11   100.0    11     ARMSSC3 
     LARGE SHIFTS/INSERTIONS   137.31            0.0     3   100.0     3     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    94.19           18.8    16   100.0    16     ARMSSC3 
     BURIED  . . . . . . . .    79.58            0.0     1   100.0     1     ARMSSC3 
     CORE  . . . . . . . . .    80.94           21.4    14   100.0    14     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    50.88           50.0     6   100.0     6     ARMSSC4 
     WELL ORDERED  . . . . .    50.88           50.0     6   100.0     6     ARMSSC4 
     NO INTER CONTACTS . . .    50.88           50.0     6   100.0     6     ARMSSC4 
     RELIABLE SIDE CHAINS  .    50.88           50.0     6   100.0     6     ARMSSC4 
     CHANGED ANGLES  . . . .    51.65           60.0     5   100.0     5     ARMSSC4 
     SHIFTED CHAIN . . . . .    50.88           50.0     6   100.0     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    69.43            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 . . . . . . . .    50.88           50.0     6   100.0     6     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .    50.88           50.0     6   100.0     6     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.43790     r(1,2) =  -0.40232     r(1,3) =  -0.80398 
 r(2,1) =  -0.89532     r(2,2) =   0.11403     r(2,3) =   0.43059 
 r(3,1) =  -0.08156     r(3,2) =   0.90837     r(3,3) =  -0.41013 
THE OFFSET VECTOR: 
 v(1) =  81.36689     v(2) =  -7.14406     v(3) = -24.93202 
 
 Number of iteration  2                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.56           (Number of atoms:    9) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    8.58         70    98.6    71     CRMSCA  
     CRN = ALL/NP  . . . . .    0.1225                            CRMSCA  
     WELL ORDERED  . . . . .    8.58         70    98.6    71     CRMSCA  
     NO INTER CONTACTS . . .    8.58         70    98.6    71     CRMSCA  
     SHIFTED CHAIN . . . . .    8.71         64    98.5    65     CRMSCA  
     ALTERNATIVE PARENT  . .    9.89          7    87.5     8     CRMSCA  
     SECONDARY STRUCTURE . .    8.83         32   100.0    32     CRMSCA  
     SHIFTED SS UNITS  . . .    7.11         16   100.0    16     CRMSCA  
     LARGE SHIFTS/INSERTIONS    8.82         24    96.0    25     CRMSCA  
     SURFACE . . . . . . . .    8.68         55    98.2    56     CRMSCA  
     BURIED  . . . . . . . .    8.20         15   100.0    15     CRMSCA  
     CORE  . . . . . . . . .    8.45         46   100.0    46     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    8.60        345    98.6   350     CRMSMC  
     WELL ORDERED  . . . . .    8.60        345    98.6   350     CRMSMC  
     NO INTER CONTACTS . . .    8.60        345    98.6   350     CRMSMC  
     SHIFTED CHAIN . . . . .    8.76        316    98.4   321     CRMSMC  
     ALTERNATIVE PARENT  . .    9.70         34    87.2    39     CRMSMC  
     SECONDARY STRUCTURE . .    8.87        159   100.0   159     CRMSMC  
     SHIFTED SS UNITS  . . .    7.18         80   100.0    80     CRMSMC  
     LARGE SHIFTS/INSERTIONS    8.73        118    95.9   123     CRMSMC  
     SURFACE . . . . . . . .    8.71        271    98.2   276     CRMSMC  
     BURIED  . . . . . . . .    8.18         74   100.0    74     CRMSMC  
     CORE  . . . . . . . . .    8.52        227   100.0   227     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   10.20        266    33.1   803     CRMSSC  
     WELL ORDERED  . . . . .   10.20        266    33.1   803     CRMSSC  
     NO INTER CONTACTS . . .   10.20        266    33.1   803     CRMSSC  
     RELIABLE SIDE CHAINS  .   10.17        230    30.0   767     CRMSSC  
     CHANGED ANGLES  . . . .   10.50        155    99.4   156     CRMSSC  
     SECONDARY STRUCTURE . .   10.35        126    32.0   394     CRMSSC  
     LARGE SHIFTS/INSERTIONS   10.15         74    31.6   234     CRMSSC  
     SURFACE . . . . . . . .   10.47        209    33.5   624     CRMSSC  
     BURIED  . . . . . . . .    9.12         57    31.8   179     CRMSSC  
     CORE  . . . . . . . . .   10.21        192    33.7   569     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    9.35        546    50.2  1087     CRMSALL 
     WELL ORDERED  . . . . .    9.35        546    50.2  1087     CRMSALL 
     NO INTER CONTACTS . . .    9.35        546    50.2  1087     CRMSALL 
     SHIFTED CHAIN . . . . .    9.47        500    49.9  1003     CRMSALL 
     ALTERNATIVE PARENT  . .    8.87         49    45.0   109     CRMSALL 
     SECONDARY STRUCTURE . .    9.59        254    48.7   522     CRMSALL 
     LARGE SHIFTS/INSERTIONS    9.29        170    50.9   334     CRMSALL 
     SURFACE . . . . . . . .    9.55        429    50.6   848     CRMSALL 
     BURIED  . . . . . . . .    8.59        117    49.0   239     CRMSALL 
     CORE  . . . . . . . . .    9.38        376    49.9   753     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     4.43      4    80.0     5       1-STDDS-5    
 CA  LOOP  2     9.89     12   100.0    12      33-ACGQNPTLAEIT-44   
 CA  LOOP  3     8.92      6   100.0     6      66-PNGFDM-71   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     4.60     20    80.0    25       1-STDDS-5    
 MC  LOOP  2     9.57     59   100.0    59      33-ACGQNPTLAEIT-44   
 MC  LOOP  3     9.06     29   100.0    29      66-PNGFDM-71   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     5.76     29    46.8    62       1-STDDS-5    
 ALL LOOP  2     9.97     83    50.6   164      33-ACGQNPTLAEIT-44   
 ALL LOOP  3     9.99     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     4.89     12   100.0    12      33-ACGQNPTLAEIT-44   
 CA  LOOP  3     2.16      6   100.0     6      66-PNGFDM-71   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.20     20    80.0    25       1-STDDS-5    
 MC  LOOP  2     4.96     59   100.0    59      33-ACGQNPTLAEIT-44   
 MC  LOOP  3     2.86     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     5.81     83    50.6   164      33-ACGQNPTLAEIT-44   
 ALL LOOP  3     4.05     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 . . . . . . . . . .    3.345      0.236       0.228     70    98.6    71     ERRCA  
     WELL ORDERED  . . . . .    3.345      0.236       0.228     70    98.6    71     ERRCA  
     NO INTER CONTACTS . . .    3.345      0.236       0.228     70    98.6    71     ERRCA  
     SHIFTED CHAIN . . . . .    3.253      0.227       0.215     64    98.5    65     ERRCA  
     ALTERNATIVE PARENT  . .    5.492      0.386       0.365      7    87.5     8     ERRCA  
     SECONDARY STRUCTURE . .    3.640      0.256       0.247     32   100.0    32     ERRCA  
     LARGE SHIFTS/INSERTIONS    3.835      0.268       0.257     24    96.0    25     ERRCA  
     SURFACE . . . . . . . .    3.384      0.235       0.227     55    98.2    56     ERRCA  
     BURIED  . . . . . . . .    3.203      0.240       0.231     15   100.0    15     ERRCA  
     CORE  . . . . . . . . .    3.090      0.220       0.213     46   100.0    46     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.356      0.233       0.225    345    98.6   350     ERRMC  
     WELL ORDERED  . . . . .    3.356      0.233       0.225    345    98.6   350     ERRMC  
     NO INTER CONTACTS . . .    3.356      0.233       0.225    345    98.6   350     ERRMC  
     SHIFTED CHAIN . . . . .    3.257      0.223       0.211    316    98.4   321     ERRMC  
     ALTERNATIVE PARENT  . .    4.934      0.336       0.309     34    87.2    39     ERRMC  
     SECONDARY STRUCTURE . .    3.667      0.256       0.245    159   100.0   159     ERRMC  
     LARGE SHIFTS/INSERTIONS    3.813      0.262       0.255    118    95.9   123     ERRMC  
     SURFACE . . . . . . . .    3.390      0.232       0.223    271    98.2   276     ERRMC  
     BURIED  . . . . . . . .    3.232      0.239       0.234     74   100.0    74     ERRMC  
     CORE  . . . . . . . . .    3.119      0.218       0.210    227   100.0   227     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.058      0.174       0.140    266    33.1   803     ERRSC  
     WELL ORDERED  . . . . .    3.058      0.174       0.140    266    33.1   803     ERRSC  
     NO INTER CONTACTS . . .    3.058      0.174       0.140    266    33.1   803     ERRSC  
     RELIABLE SIDE CHAINS  .    3.117      0.179       0.147    230    30.0   767     ERRSC  
     CHANGED ANGLES  . . . .    3.127      0.171       0.133    155    99.4   156     ERRSC  
     SHIFTED CHAIN . . . . .    3.067      0.173       0.138    244    32.8   743     ERRSC  
     ALTERNATIVE PARENT  . .    3.332      0.241       0.253     21    27.3    77     ERRSC  
     SECONDARY STRUCTURE . .    3.120      0.176       0.136    126    32.0   394     ERRSC  
     LARGE SHIFTS/INSERTIONS    3.188      0.182       0.158     74    31.6   234     ERRSC  
     SURFACE . . . . . . . .    3.246      0.180       0.142    209    33.5   624     ERRSC  
     BURIED  . . . . . . . .    2.371      0.151       0.133     57    31.8   179     ERRSC  
     CORE  . . . . . . . . .    3.008      0.171       0.134    192    33.7   569     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.246      0.209       0.189    546    50.2  1087     ERRALL 
     WELL ORDERED  . . . . .    3.246      0.209       0.189    546    50.2  1087     ERRALL 
     NO INTER CONTACTS . . .    3.246      0.209       0.189    546    50.2  1087     ERRALL 
     SHIFTED CHAIN . . . . .    3.191      0.203       0.180    500    49.9  1003     ERRALL 
     ALTERNATIVE PARENT  . .    4.331      0.298       0.286     49    45.0   109     ERRALL 
     SECONDARY STRUCTURE . .    3.450      0.222       0.198    254    48.7   522     ERRALL 
     LARGE SHIFTS/INSERTIONS    3.605      0.234       0.219    170    50.9   334     ERRALL 
     SURFACE . . . . . . . .    3.345      0.210       0.188    429    50.6   848     ERRALL 
     BURIED  . . . . . . . .    2.883      0.202       0.192    117    49.0   239     ERRALL 
     CORE  . . . . . . . . .    3.083      0.197       0.175    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         7        10        20        50      70      71   DISTCA 
CA  (P)      2.82      9.86     14.08     28.17     70.42              71   DISTCA 
CA  (RMS)    0.72      1.21      1.74      3.38      6.35                   DISTCA 
 
ALL (N)         3        30        53       111       352     546    1087   DISTALL 
ALL (P)      0.28      2.76      4.88     10.21     32.38            1087   DISTALL 
ALL (RMS)    0.74      1.44      2.00      3.26      6.65                   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          8.45          8.82          RMSLSI 
 
 
 
END of the results output 
