 
####################################################### 
#                                                     # 
#                        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 1102 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 . . . . . . . . . .    54.15           64.5   138    98.6   140     ARMSMC  
     WELL ORDERED  . . . . .    54.15           64.5   138    98.6   140     ARMSMC  
     NO INTER CONTACTS . . .    54.15           64.5   138    98.6   140     ARMSMC  
     SHIFTED CHAIN . . . . .    56.08           64.3   126    98.4   128     ARMSMC  
     ALTERNATIVE PARENT  . .    75.03           42.9    14    93.3    15     ARMSMC  
     SECONDARY STRUCTURE . .    37.51           75.0    64   100.0    64     ARMSMC  
     LARGE SHIFTS/INSERTIONS    73.29           43.5    46    95.8    48     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    52.90           63.9   108    98.2   110     ARMSMC  
     BURIED  . . . . . . . .    58.42           66.7    30   100.0    30     ARMSMC  
     CORE  . . . . . . . . .    41.37           75.0    92   100.0    92     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    78.93           32.8    61    98.4    62     ARMSSC1 
     WELL ORDERED  . . . . .    78.93           32.8    61    98.4    62     ARMSSC1 
     NO INTER CONTACTS . . .    78.93           32.8    61    98.4    62     ARMSSC1 
     RELIABLE SIDE CHAINS  .    79.63           32.2    59    98.3    60     ARMSSC1 
     CHANGED ANGLES  . . . .    85.49           29.7    37    97.4    38     ARMSSC1 
     SHIFTED CHAIN . . . . .    79.62           33.9    56    98.2    57     ARMSSC1 
     ALTERNATIVE PARENT  . .    53.60           60.0     5    83.3     6     ARMSSC1 
     SECONDARY STRUCTURE . .    81.21           28.6    28   100.0    28     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    90.88           21.1    19    95.0    20     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    82.22           29.2    48    98.0    49     ARMSSC1 
     BURIED  . . . . . . . .    65.37           46.2    13   100.0    13     ARMSSC1 
     CORE  . . . . . . . . .    72.88           38.1    42   100.0    42     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    79.31           39.6    48   100.0    48     ARMSSC2 
     WELL ORDERED  . . . . .    79.31           39.6    48   100.0    48     ARMSSC2 
     NO INTER CONTACTS . . .    79.31           39.6    48   100.0    48     ARMSSC2 
     RELIABLE SIDE CHAINS  .    66.01           43.2    37   100.0    37     ARMSSC2 
     CHANGED ANGLES  . . . .    83.99           39.5    38   100.0    38     ARMSSC2 
     SHIFTED CHAIN . . . . .    80.08           39.1    46   100.0    46     ARMSSC2 
     ALTERNATIVE PARENT  . .    93.52           25.0     4   100.0     4     ARMSSC2 
     SECONDARY STRUCTURE . .    81.91           43.5    23   100.0    23     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    94.84           35.7    14   100.0    14     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    76.64           40.5    37   100.0    37     ARMSSC2 
     BURIED  . . . . . . . .    87.69           36.4    11   100.0    11     ARMSSC2 
     CORE  . . . . . . . . .    71.95           41.2    34   100.0    34     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    89.69           35.3    17   100.0    17     ARMSSC3 
     WELL ORDERED  . . . . .    89.69           35.3    17   100.0    17     ARMSSC3 
     NO INTER CONTACTS . . .    89.69           35.3    17   100.0    17     ARMSSC3 
     RELIABLE SIDE CHAINS  .    78.01           38.5    13   100.0    13     ARMSSC3 
     CHANGED ANGLES  . . . .    92.35           31.2    16   100.0    16     ARMSSC3 
     SHIFTED CHAIN . . . . .    89.69           35.3    17   100.0    17     ARMSSC3 
     ALTERNATIVE PARENT  . .    61.54           50.0     2   100.0     2     ARMSSC3 
     SECONDARY STRUCTURE . .    84.45           36.4    11   100.0    11     ARMSSC3 
     LARGE SHIFTS/INSERTIONS   101.90           33.3     3   100.0     3     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    92.36           31.2    16   100.0    16     ARMSSC3 
     BURIED  . . . . . . . .    16.02          100.0     1   100.0     1     ARMSSC3 
     CORE  . . . . . . . . .    86.85           35.7    14   100.0    14     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    95.95           16.7     6   100.0     6     ARMSSC4 
     WELL ORDERED  . . . . .    95.95           16.7     6   100.0     6     ARMSSC4 
     NO INTER CONTACTS . . .    95.95           16.7     6   100.0     6     ARMSSC4 
     RELIABLE SIDE CHAINS  .    95.95           16.7     6   100.0     6     ARMSSC4 
     CHANGED ANGLES  . . . .    98.07           20.0     5   100.0     5     ARMSSC4 
     SHIFTED CHAIN . . . . .    95.95           16.7     6   100.0     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .   116.02            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 . . . . . . . .    95.95           16.7     6   100.0     6     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .    95.95           16.7     6   100.0     6     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.11920     r(1,2) =   0.99285     r(1,3) =  -0.00565 
 r(2,1) =   0.98189     r(2,2) =  -0.11872     r(2,3) =  -0.14766 
 r(3,1) =  -0.14728     r(3,2) =   0.01205     r(3,3) =  -0.98902 
THE OFFSET VECTOR: 
 v(1) = -10.60919     v(2) =  -4.00986     v(3) =  -8.21904 
 
 Number of iteration 75                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.60           (Number of atoms:   27) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    6.00         70    98.6    71     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0858                            CRMSCA  
     WELL ORDERED  . . . . .    6.00         70    98.6    71     CRMSCA  
     NO INTER CONTACTS . . .    6.00         70    98.6    71     CRMSCA  
     SHIFTED CHAIN . . . . .    6.05         64    98.5    65     CRMSCA  
     ALTERNATIVE PARENT  . .    7.38          7    87.5     8     CRMSCA  
     SECONDARY STRUCTURE . .    4.99         32   100.0    32     CRMSCA  
     SHIFTED SS UNITS  . . .    3.90         16   100.0    16     CRMSCA  
     LARGE SHIFTS/INSERTIONS    8.16         24    96.0    25     CRMSCA  
     SURFACE . . . . . . . .    6.50         55    98.2    56     CRMSCA  
     BURIED  . . . . . . . .    3.61         15   100.0    15     CRMSCA  
     CORE  . . . . . . . . .    4.49         46   100.0    46     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    6.05        345    98.6   350     CRMSMC  
     WELL ORDERED  . . . . .    6.05        345    98.6   350     CRMSMC  
     NO INTER CONTACTS . . .    6.05        345    98.6   350     CRMSMC  
     SHIFTED CHAIN . . . . .    6.10        316    98.4   321     CRMSMC  
     ALTERNATIVE PARENT  . .    6.90         34    87.2    39     CRMSMC  
     SECONDARY STRUCTURE . .    5.20        159   100.0   159     CRMSMC  
     SHIFTED SS UNITS  . . .    4.09         80   100.0    80     CRMSMC  
     LARGE SHIFTS/INSERTIONS    8.05        118    95.9   123     CRMSMC  
     SURFACE . . . . . . . .    6.52        271    98.2   276     CRMSMC  
     BURIED  . . . . . . . .    3.87         74   100.0    74     CRMSMC  
     CORE  . . . . . . . . .    4.69        227   100.0   227     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    6.41        266    33.1   803     CRMSSC  
     WELL ORDERED  . . . . .    6.41        266    33.1   803     CRMSSC  
     NO INTER CONTACTS . . .    6.41        266    33.1   803     CRMSSC  
     RELIABLE SIDE CHAINS  .    6.27        230    30.0   767     CRMSSC  
     CHANGED ANGLES  . . . .    6.77        155    99.4   156     CRMSSC  
     SECONDARY STRUCTURE . .    5.73        126    32.0   394     CRMSSC  
     LARGE SHIFTS/INSERTIONS    8.76         74    31.6   234     CRMSSC  
     SURFACE . . . . . . . .    6.93        209    33.5   624     CRMSSC  
     BURIED  . . . . . . . .    4.01         57    31.8   179     CRMSSC  
     CORE  . . . . . . . . .    5.23        192    33.7   569     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    6.24        546    50.2  1087     CRMSALL 
     WELL ORDERED  . . . . .    6.24        546    50.2  1087     CRMSALL 
     NO INTER CONTACTS . . .    6.24        546    50.2  1087     CRMSALL 
     SHIFTED CHAIN . . . . .    6.30        500    49.9  1003     CRMSALL 
     ALTERNATIVE PARENT  . .    6.17         49    45.0   109     CRMSALL 
     SECONDARY STRUCTURE . .    5.49        254    48.7   522     CRMSALL 
     LARGE SHIFTS/INSERTIONS    8.38        170    50.9   334     CRMSALL 
     SURFACE . . . . . . . .    6.72        429    50.6   848     CRMSALL 
     BURIED  . . . . . . . .    3.96        117    49.0   239     CRMSALL 
     CORE  . . . . . . . . .    4.98        376    49.9   753     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     5.24      4    80.0     5       1-STDDS-5    
 CA  LOOP  2     8.20     12   100.0    12      33-ACGQNPTLAEIT-44   
 CA  LOOP  3    10.60      6   100.0     6      66-PNGFDM-71   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     5.15     20    80.0    25       1-STDDS-5    
 MC  LOOP  2     7.93     59   100.0    59      33-ACGQNPTLAEIT-44   
 MC  LOOP  3    10.79     29   100.0    29      66-PNGFDM-71   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     6.04     29    46.8    62       1-STDDS-5    
 ALL LOOP  2     7.71     83    50.6   164      33-ACGQNPTLAEIT-44   
 ALL LOOP  3    11.33     46    54.8    84      66-PNGFDM-71   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.12      4    80.0     5       1-STDDS-5    
 CA  LOOP  2     1.33     12   100.0    12      33-ACGQNPTLAEIT-44   
 CA  LOOP  3     0.77      6   100.0     6      66-PNGFDM-71   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.49     20    80.0    25       1-STDDS-5    
 MC  LOOP  2     1.46     59   100.0    59      33-ACGQNPTLAEIT-44   
 MC  LOOP  3     1.63     29   100.0    29      66-PNGFDM-71   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     3.62     29    46.8    62       1-STDDS-5    
 ALL LOOP  2     2.58     83    50.6   164      33-ACGQNPTLAEIT-44   
 ALL LOOP  3     2.28     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 . . . . . . . . . .    3.847      0.515       0.258     70    98.6    71     ERRCA  
     WELL ORDERED  . . . . .    3.847      0.515       0.258     70    98.6    71     ERRCA  
     NO INTER CONTACTS . . .    3.847      0.515       0.258     70    98.6    71     ERRCA  
     SHIFTED CHAIN . . . . .    3.847      0.509       0.255     64    98.5    65     ERRCA  
     ALTERNATIVE PARENT  . .    4.358      0.464       0.232      7    87.5     8     ERRCA  
     SECONDARY STRUCTURE . .    3.261      0.527       0.263     32   100.0    32     ERRCA  
     LARGE SHIFTS/INSERTIONS    5.999      0.636       0.318     24    96.0    25     ERRCA  
     SURFACE . . . . . . . .    4.338      0.552       0.277     55    98.2    56     ERRCA  
     BURIED  . . . . . . . .    2.046      0.378       0.189     15   100.0    15     ERRCA  
     CORE  . . . . . . . . .    2.724      0.452       0.227     46   100.0    46     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.909      0.524       0.263    345    98.6   350     ERRMC  
     WELL ORDERED  . . . . .    3.909      0.524       0.263    345    98.6   350     ERRMC  
     NO INTER CONTACTS . . .    3.909      0.524       0.263    345    98.6   350     ERRMC  
     SHIFTED CHAIN . . . . .    3.930      0.522       0.262    316    98.4   321     ERRMC  
     ALTERNATIVE PARENT  . .    4.149      0.480       0.240     34    87.2    39     ERRMC  
     SECONDARY STRUCTURE . .    3.445      0.544       0.272    159   100.0   159     ERRMC  
     LARGE SHIFTS/INSERTIONS    5.909      0.641       0.321    118    95.9   123     ERRMC  
     SURFACE . . . . . . . .    4.360      0.555       0.279    271    98.2   276     ERRMC  
     BURIED  . . . . . . . .    2.259      0.412       0.206     74   100.0    74     ERRMC  
     CORE  . . . . . . . . .    2.870      0.464       0.233    227   100.0   227     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.434      0.601       0.301    266    33.1   803     ERRSC  
     WELL ORDERED  . . . . .    4.434      0.601       0.301    266    33.1   803     ERRSC  
     NO INTER CONTACTS . . .    4.434      0.601       0.301    266    33.1   803     ERRSC  
     RELIABLE SIDE CHAINS  .    4.343      0.594       0.297    230    30.0   767     ERRSC  
     CHANGED ANGLES  . . . .    4.729      0.613       0.306    155    99.4   156     ERRSC  
     SHIFTED CHAIN . . . . .    4.464      0.599       0.299    244    32.8   743     ERRSC  
     ALTERNATIVE PARENT  . .    3.006      0.533       0.267     21    27.3    77     ERRSC  
     SECONDARY STRUCTURE . .    4.083      0.614       0.307    126    32.0   394     ERRSC  
     LARGE SHIFTS/INSERTIONS    6.810      0.711       0.355     74    31.6   234     ERRSC  
     SURFACE . . . . . . . .    4.936      0.628       0.314    209    33.5   624     ERRSC  
     BURIED  . . . . . . . .    2.594      0.501       0.251     57    31.8   179     ERRSC  
     CORE  . . . . . . . . .    3.518      0.559       0.279    192    33.7   569     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.156      0.557       0.279    546    50.2  1087     ERRALL 
     WELL ORDERED  . . . . .    4.156      0.557       0.279    546    50.2  1087     ERRALL 
     NO INTER CONTACTS . . .    4.156      0.557       0.279    546    50.2  1087     ERRALL 
     SHIFTED CHAIN . . . . .    4.190      0.556       0.279    500    49.9  1003     ERRALL 
     ALTERNATIVE PARENT  . .    3.761      0.503       0.251     49    45.0   109     ERRALL 
     SECONDARY STRUCTURE . .    3.776      0.577       0.289    254    48.7   522     ERRALL 
     LARGE SHIFTS/INSERTIONS    6.299      0.669       0.334    170    50.9   334     ERRALL 
     SURFACE . . . . . . . .    4.627      0.587       0.294    429    50.6   848     ERRALL 
     BURIED  . . . . . . . .    2.426      0.450       0.225    117    49.0   239     ERRALL 
     CORE  . . . . . . . . .    3.186      0.507       0.255    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        21        28        41        63      70      71   DISTCA 
CA  (P)      4.23     29.58     39.44     57.75     88.73              71   DISTCA 
CA  (RMS)    0.85      1.40      1.67      2.69      4.75                   DISTCA 
 
ALL (N)        14       117       182       317       490     546    1087   DISTALL 
ALL (P)      1.29     10.76     16.74     29.16     45.08            1087   DISTALL 
ALL (RMS)    0.86      1.46      1.87      2.99      4.99                   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          4.49          8.16          RMSLSI 
 
 
 
END of the results output 
