 
####################################################### 
#                                                     # 
#                        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 . . . . . . . . . .    82.69           44.3   140   100.0   140     ARMSMC  
     WELL ORDERED  . . . . .    82.69           44.3   140   100.0   140     ARMSMC  
     NO INTER CONTACTS . . .    82.69           44.3   140   100.0   140     ARMSMC  
     SHIFTED CHAIN . . . . .    81.01           44.5   128   100.0   128     ARMSMC  
     ALTERNATIVE PARENT  . .    78.33           46.7    15   100.0    15     ARMSMC  
     SECONDARY STRUCTURE . .    48.54           68.8    64   100.0    64     ARMSMC  
     LARGE SHIFTS/INSERTIONS    84.11           41.7    48   100.0    48     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    85.07           42.7   110   100.0   110     ARMSMC  
     BURIED  . . . . . . . .    73.26           50.0    30   100.0    30     ARMSMC  
     CORE  . . . . . . . . .    81.93           45.7    92   100.0    92     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    87.11           29.0    62   100.0    62     ARMSSC1 
     WELL ORDERED  . . . . .    87.11           29.0    62   100.0    62     ARMSSC1 
     NO INTER CONTACTS . . .    87.11           29.0    62   100.0    62     ARMSSC1 
     RELIABLE SIDE CHAINS  .    88.21           28.3    60   100.0    60     ARMSSC1 
     CHANGED ANGLES  . . . .    80.85           31.6    38   100.0    38     ARMSSC1 
     SHIFTED CHAIN . . . . .    86.58           29.8    57   100.0    57     ARMSSC1 
     ALTERNATIVE PARENT  . .    56.88           50.0     6   100.0     6     ARMSSC1 
     SECONDARY STRUCTURE . .    92.79           17.9    28   100.0    28     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    88.22           25.0    20   100.0    20     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    86.07           30.6    49   100.0    49     ARMSSC1 
     BURIED  . . . . . . . .    90.93           23.1    13   100.0    13     ARMSSC1 
     CORE  . . . . . . . . .    86.58           31.0    42   100.0    42     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    75.56           33.3    48   100.0    48     ARMSSC2 
     WELL ORDERED  . . . . .    75.56           33.3    48   100.0    48     ARMSSC2 
     NO INTER CONTACTS . . .    75.56           33.3    48   100.0    48     ARMSSC2 
     RELIABLE SIDE CHAINS  .    69.59           35.1    37   100.0    37     ARMSSC2 
     CHANGED ANGLES  . . . .    75.20           34.2    38   100.0    38     ARMSSC2 
     SHIFTED CHAIN . . . . .    76.32           34.8    46   100.0    46     ARMSSC2 
     ALTERNATIVE PARENT  . .   110.07            0.0     4   100.0     4     ARMSSC2 
     SECONDARY STRUCTURE . .    90.61           13.0    23   100.0    23     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    63.19           50.0    14   100.0    14     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    70.31           37.8    37   100.0    37     ARMSSC2 
     BURIED  . . . . . . . .    91.04           18.2    11   100.0    11     ARMSSC2 
     CORE  . . . . . . . . .    80.11           26.5    34   100.0    34     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    97.79           23.5    17   100.0    17     ARMSSC3 
     WELL ORDERED  . . . . .    97.79           23.5    17   100.0    17     ARMSSC3 
     NO INTER CONTACTS . . .    97.79           23.5    17   100.0    17     ARMSSC3 
     RELIABLE SIDE CHAINS  .    89.69           30.8    13   100.0    13     ARMSSC3 
     CHANGED ANGLES  . . . .   100.00           25.0    16   100.0    16     ARMSSC3 
     SHIFTED CHAIN . . . . .    97.79           23.5    17   100.0    17     ARMSSC3 
     ALTERNATIVE PARENT  . .    67.00           50.0     2   100.0     2     ARMSSC3 
     SECONDARY STRUCTURE . .    96.01           27.3    11   100.0    11     ARMSSC3 
     LARGE SHIFTS/INSERTIONS   107.68            0.0     3   100.0     3     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    93.40           25.0    16   100.0    16     ARMSSC3 
     BURIED  . . . . . . . .   151.56            0.0     1   100.0     1     ARMSSC3 
     CORE  . . . . . . . . .    95.53           28.6    14   100.0    14     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    84.70           16.7     6   100.0     6     ARMSSC4 
     WELL ORDERED  . . . . .    84.70           16.7     6   100.0     6     ARMSSC4 
     NO INTER CONTACTS . . .    84.70           16.7     6   100.0     6     ARMSSC4 
     RELIABLE SIDE CHAINS  .    84.70           16.7     6   100.0     6     ARMSSC4 
     CHANGED ANGLES  . . . .    92.73            0.0     5   100.0     5     ARMSSC4 
     SHIFTED CHAIN . . . . .    84.70           16.7     6   100.0     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    64.70           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 . . . . . . . .    84.70           16.7     6   100.0     6     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .    84.70           16.7     6   100.0     6     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.68263     r(1,2) =   0.57820     r(1,3) =  -0.44688 
 r(2,1) =  -0.02053     r(2,2) =   0.59611     r(2,3) =   0.80264 
 r(3,1) =   0.73048     r(3,2) =   0.55708     r(3,3) =  -0.39505 
THE OFFSET VECTOR: 
 v(1) = -14.89371     v(2) =   8.81830     v(3) = -16.88858 
 
 Number of iteration  2                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.77           (Number of atoms:   12) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   14.24         71   100.0    71     CRMSCA  
     CRN = ALL/NP  . . . . .    0.2005                            CRMSCA  
     WELL ORDERED  . . . . .   14.24         71   100.0    71     CRMSCA  
     NO INTER CONTACTS . . .   14.24         71   100.0    71     CRMSCA  
     SHIFTED CHAIN . . . . .   14.79         65   100.0    65     CRMSCA  
     ALTERNATIVE PARENT  . .    7.93          8   100.0     8     CRMSCA  
     SECONDARY STRUCTURE . .    9.31         32   100.0    32     CRMSCA  
     SHIFTED SS UNITS  . . .   10.53         16   100.0    16     CRMSCA  
     LARGE SHIFTS/INSERTIONS   18.03         25   100.0    25     CRMSCA  
     SURFACE . . . . . . . .   15.54         56   100.0    56     CRMSCA  
     BURIED  . . . . . . . .    7.62         15   100.0    15     CRMSCA  
     CORE  . . . . . . . . .   11.67         46   100.0    46     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   14.26        350   100.0   350     CRMSMC  
     WELL ORDERED  . . . . .   14.26        350   100.0   350     CRMSMC  
     NO INTER CONTACTS . . .   14.26        350   100.0   350     CRMSMC  
     SHIFTED CHAIN . . . . .   14.80        321   100.0   321     CRMSMC  
     ALTERNATIVE PARENT  . .    7.87         39   100.0    39     CRMSMC  
     SECONDARY STRUCTURE . .    9.46        159   100.0   159     CRMSMC  
     SHIFTED SS UNITS  . . .   10.92         80   100.0    80     CRMSMC  
     LARGE SHIFTS/INSERTIONS   17.96        123   100.0   123     CRMSMC  
     SURFACE . . . . . . . .   15.56        276   100.0   276     CRMSMC  
     BURIED  . . . . . . . .    7.71         74   100.0    74     CRMSMC  
     CORE  . . . . . . . . .   11.78        227   100.0   227     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   15.07        268    33.4   803     CRMSSC  
     WELL ORDERED  . . . . .   15.07        268    33.4   803     CRMSSC  
     NO INTER CONTACTS . . .   15.07        268    33.4   803     CRMSSC  
     RELIABLE SIDE CHAINS  .   14.94        232    30.2   767     CRMSSC  
     CHANGED ANGLES  . . . .   16.46        156   100.0   156     CRMSSC  
     SECONDARY STRUCTURE . .   10.56        126    32.0   394     CRMSSC  
     LARGE SHIFTS/INSERTIONS   19.02         76    32.5   234     CRMSSC  
     SURFACE . . . . . . . .   16.54        211    33.8   624     CRMSSC  
     BURIED  . . . . . . . .    7.38         57    31.8   179     CRMSSC  
     CORE  . . . . . . . . .   13.18        192    33.7   569     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   14.71        552    50.8  1087     CRMSALL 
     WELL ORDERED  . . . . .   14.71        552    50.8  1087     CRMSALL 
     NO INTER CONTACTS . . .   14.71        552    50.8  1087     CRMSALL 
     SHIFTED CHAIN . . . . .   15.27        506    50.4  1003     CRMSALL 
     ALTERNATIVE PARENT  . .    8.26         55    50.5   109     CRMSALL 
     SECONDARY STRUCTURE . .   10.03        254    48.7   522     CRMSALL 
     LARGE SHIFTS/INSERTIONS   18.51        176    52.7   334     CRMSALL 
     SURFACE . . . . . . . .   16.09        435    51.3   848     CRMSALL 
     BURIED  . . . . . . . .    7.64        117    49.0   239     CRMSALL 
     CORE  . . . . . . . . .   12.53        376    49.9   753     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1    12.09      5   100.0     5       1-STDDS-5    
 CA  LOOP  2     4.94     12   100.0    12      33-ACGQNPTLAEIT-44   
 CA  LOOP  3    34.32      6   100.0     6      66-PNGFDM-71   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1    12.33     25   100.0    25       1-STDDS-5    
 MC  LOOP  2     4.98     59   100.0    59      33-ACGQNPTLAEIT-44   
 MC  LOOP  3    34.35     29   100.0    29      66-PNGFDM-71   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1    12.67     35    56.5    62       1-STDDS-5    
 ALL LOOP  2     5.24     83    50.6   164      33-ACGQNPTLAEIT-44   
 ALL LOOP  3    33.67     46    54.8    84      66-PNGFDM-71   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     1.82      5   100.0     5       1-STDDS-5    
 CA  LOOP  2     3.50     12   100.0    12      33-ACGQNPTLAEIT-44   
 CA  LOOP  3     2.17      6   100.0     6      66-PNGFDM-71   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.44     25   100.0    25       1-STDDS-5    
 MC  LOOP  2     3.51     59   100.0    59      33-ACGQNPTLAEIT-44   
 MC  LOOP  3     2.61     29   100.0    29      66-PNGFDM-71   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     2.93     35    56.5    62       1-STDDS-5    
 ALL LOOP  2     3.89     83    50.6   164      33-ACGQNPTLAEIT-44   
 ALL LOOP  3     4.43     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 . . . . . . . . . .    7.198      0.370       0.254     71   100.0    71     ERRCA  
     WELL ORDERED  . . . . .    7.198      0.370       0.254     71   100.0    71     ERRCA  
     NO INTER CONTACTS . . .    7.198      0.370       0.254     71   100.0    71     ERRCA  
     SHIFTED CHAIN . . . . .    7.577      0.372       0.245     65   100.0    65     ERRCA  
     ALTERNATIVE PARENT  . .    2.947      0.217       0.151      8   100.0     8     ERRCA  
     SECONDARY STRUCTURE . .    4.591      0.343       0.281     32   100.0    32     ERRCA  
     LARGE SHIFTS/INSERTIONS    9.119      0.339       0.203     25   100.0    25     ERRCA  
     SURFACE . . . . . . . .    8.072      0.373       0.241     56   100.0    56     ERRCA  
     BURIED  . . . . . . . .    3.935      0.358       0.305     15   100.0    15     ERRCA  
     CORE  . . . . . . . . .    6.154      0.386       0.282     46   100.0    46     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.199      0.368       0.255    350   100.0   350     ERRMC  
     WELL ORDERED  . . . . .    7.199      0.368       0.255    350   100.0   350     ERRMC  
     NO INTER CONTACTS . . .    7.199      0.368       0.255    350   100.0   350     ERRMC  
     SHIFTED CHAIN . . . . .    7.613      0.375       0.250    321   100.0   321     ERRMC  
     ALTERNATIVE PARENT  . .    3.189      0.251       0.179     39   100.0    39     ERRMC  
     SECONDARY STRUCTURE . .    4.682      0.349       0.285    159   100.0   159     ERRMC  
     LARGE SHIFTS/INSERTIONS    9.176      0.352       0.213    123   100.0   123     ERRMC  
     SURFACE . . . . . . . .    8.089      0.375       0.245    276   100.0   276     ERRMC  
     BURIED  . . . . . . . .    3.880      0.341       0.290     74   100.0    74     ERRMC  
     CORE  . . . . . . . . .    6.128      0.376       0.277    227   100.0   227     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.866      0.368       0.228    268    33.4   803     ERRSC  
     WELL ORDERED  . . . . .    7.866      0.368       0.228    268    33.4   803     ERRSC  
     NO INTER CONTACTS . . .    7.866      0.368       0.228    268    33.4   803     ERRSC  
     RELIABLE SIDE CHAINS  .    7.690      0.362       0.226    232    30.2   767     ERRSC  
     CHANGED ANGLES  . . . .    9.124      0.399       0.235    156   100.0   156     ERRSC  
     SHIFTED CHAIN . . . . .    8.331      0.376       0.224    246    33.1   743     ERRSC  
     ALTERNATIVE PARENT  . .    3.307      0.214       0.118     23    29.9    77     ERRSC  
     SECONDARY STRUCTURE . .    4.952      0.308       0.210    126    32.0   394     ERRSC  
     LARGE SHIFTS/INSERTIONS   10.483      0.389       0.219     76    32.5   234     ERRSC  
     SURFACE . . . . . . . .    9.080      0.388       0.228    211    33.8   624     ERRSC  
     BURIED  . . . . . . . .    3.372      0.293       0.230     57    31.8   179     ERRSC  
     CORE  . . . . . . . . .    6.830      0.360       0.232    192    33.7   569     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.564      0.370       0.245    552    50.8  1087     ERRALL 
     WELL ORDERED  . . . . .    7.564      0.370       0.245    552    50.8  1087     ERRALL 
     NO INTER CONTACTS . . .    7.564      0.370       0.245    552    50.8  1087     ERRALL 
     SHIFTED CHAIN . . . . .    8.010      0.377       0.240    506    50.4  1003     ERRALL 
     ALTERNATIVE PARENT  . .    3.289      0.243       0.161     55    50.5   109     ERRALL 
     SECONDARY STRUCTURE . .    4.849      0.333       0.253    254    48.7   522     ERRALL 
     LARGE SHIFTS/INSERTIONS    9.828      0.373       0.221    176    52.7   334     ERRALL 
     SURFACE . . . . . . . .    8.603      0.383       0.240    435    51.3   848     ERRALL 
     BURIED  . . . . . . . .    3.704      0.322       0.264    117    49.0   239     ERRALL 
     CORE  . . . . . . . . .    6.505      0.369       0.256    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)         0         8        14        26        44      71      71   DISTCA 
CA  (P)      0.00     11.27     19.72     36.62     61.97              71   DISTCA 
CA  (RMS)    0.00      1.54      1.97      2.99      5.20                   DISTCA 
 
ALL (N)         1        43        98       186       330     552    1087   DISTALL 
ALL (P)      0.09      3.96      9.02     17.11     30.36            1087   DISTALL 
ALL (RMS)    0.33      1.55      2.17      3.16      5.50                   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         11.67         18.03          RMSLSI 
 
 
 
END of the results output 
