 
####################################################### 
#                                                     # 
#                        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 . . . . . . . . . .    71.87           58.0   138    98.6   140     ARMSMC  
     WELL ORDERED  . . . . .    71.87           58.0   138    98.6   140     ARMSMC  
     NO INTER CONTACTS . . .    71.87           58.0   138    98.6   140     ARMSMC  
     SHIFTED CHAIN . . . . .    74.97           55.6   126    98.4   128     ARMSMC  
     ALTERNATIVE PARENT  . .    90.01           50.0    14    93.3    15     ARMSMC  
     SECONDARY STRUCTURE . .    60.05           76.6    64   100.0    64     ARMSMC  
     LARGE SHIFTS/INSERTIONS    89.49           32.6    46    95.8    48     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    73.50           54.6   108    98.2   110     ARMSMC  
     BURIED  . . . . . . . .    65.66           70.0    30   100.0    30     ARMSMC  
     CORE  . . . . . . . . .    61.18           70.7    92   100.0    92     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    86.28           34.4    61    98.4    62     ARMSSC1 
     WELL ORDERED  . . . . .    86.28           34.4    61    98.4    62     ARMSSC1 
     NO INTER CONTACTS . . .    86.28           34.4    61    98.4    62     ARMSSC1 
     RELIABLE SIDE CHAINS  .    85.66           35.6    59    98.3    60     ARMSSC1 
     CHANGED ANGLES  . . . .    82.58           35.1    37    97.4    38     ARMSSC1 
     SHIFTED CHAIN . . . . .    88.10           32.1    56    98.2    57     ARMSSC1 
     ALTERNATIVE PARENT  . .    68.91           40.0     5    83.3     6     ARMSSC1 
     SECONDARY STRUCTURE . .    86.22           35.7    28   100.0    28     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    97.95           21.1    19    95.0    20     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    84.65           35.4    48    98.0    49     ARMSSC1 
     BURIED  . . . . . . . .    92.06           30.8    13   100.0    13     ARMSSC1 
     CORE  . . . . . . . . .    80.45           40.5    42   100.0    42     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    77.28           43.8    48   100.0    48     ARMSSC2 
     WELL ORDERED  . . . . .    77.28           43.8    48   100.0    48     ARMSSC2 
     NO INTER CONTACTS . . .    77.28           43.8    48   100.0    48     ARMSSC2 
     RELIABLE SIDE CHAINS  .    68.64           51.4    37   100.0    37     ARMSSC2 
     CHANGED ANGLES  . . . .    78.75           39.5    38   100.0    38     ARMSSC2 
     SHIFTED CHAIN . . . . .    78.76           43.5    46   100.0    46     ARMSSC2 
     ALTERNATIVE PARENT  . .    91.00           25.0     4   100.0     4     ARMSSC2 
     SECONDARY STRUCTURE . .    81.96           47.8    23   100.0    23     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    67.81           35.7    14   100.0    14     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    68.71           48.6    37   100.0    37     ARMSSC2 
     BURIED  . . . . . . . .   100.88           27.3    11   100.0    11     ARMSSC2 
     CORE  . . . . . . . . .    80.85           47.1    34   100.0    34     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    99.41           17.6    17   100.0    17     ARMSSC3 
     WELL ORDERED  . . . . .    99.41           17.6    17   100.0    17     ARMSSC3 
     NO INTER CONTACTS . . .    99.41           17.6    17   100.0    17     ARMSSC3 
     RELIABLE SIDE CHAINS  .    89.82           15.4    13   100.0    13     ARMSSC3 
     CHANGED ANGLES  . . . .   102.06           18.8    16   100.0    16     ARMSSC3 
     SHIFTED CHAIN . . . . .    99.41           17.6    17   100.0    17     ARMSSC3 
     ALTERNATIVE PARENT  . .    75.56            0.0     2   100.0     2     ARMSSC3 
     SECONDARY STRUCTURE . .    85.30           27.3    11   100.0    11     ARMSSC3 
     LARGE SHIFTS/INSERTIONS   132.75            0.0     3   100.0     3     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    92.32           18.8    16   100.0    16     ARMSSC3 
     BURIED  . . . . . . . .   177.85            0.0     1   100.0     1     ARMSSC3 
     CORE  . . . . . . . . .    90.68           21.4    14   100.0    14     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    70.50           33.3     6   100.0     6     ARMSSC4 
     WELL ORDERED  . . . . .    70.50           33.3     6   100.0     6     ARMSSC4 
     NO INTER CONTACTS . . .    70.50           33.3     6   100.0     6     ARMSSC4 
     RELIABLE SIDE CHAINS  .    70.50           33.3     6   100.0     6     ARMSSC4 
     CHANGED ANGLES  . . . .    72.14           40.0     5   100.0     5     ARMSSC4 
     SHIFTED CHAIN . . . . .    70.50           33.3     6   100.0     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    74.08            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 . . . . . . . .    70.50           33.3     6   100.0     6     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .    70.50           33.3     6   100.0     6     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.41970     r(1,2) =  -0.46865     r(1,3) =  -0.77732 
 r(2,1) =  -0.88265     r(2,2) =   0.01108     r(2,3) =   0.46990 
 r(3,1) =  -0.21160     r(3,2) =   0.88332     r(3,3) =  -0.41830 
THE OFFSET VECTOR: 
 v(1) =  82.81757     v(2) =  -4.96188     v(3) = -20.04876 
 
 Number of iteration  3                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.66           (Number of atoms:    9) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    8.68         70    98.6    71     CRMSCA  
     CRN = ALL/NP  . . . . .    0.1239                            CRMSCA  
     WELL ORDERED  . . . . .    8.68         70    98.6    71     CRMSCA  
     NO INTER CONTACTS . . .    8.68         70    98.6    71     CRMSCA  
     SHIFTED CHAIN . . . . .    8.85         64    98.5    65     CRMSCA  
     ALTERNATIVE PARENT  . .    9.79          7    87.5     8     CRMSCA  
     SECONDARY STRUCTURE . .    8.84         32   100.0    32     CRMSCA  
     SHIFTED SS UNITS  . . .    7.52         16   100.0    16     CRMSCA  
     LARGE SHIFTS/INSERTIONS    8.74         24    96.0    25     CRMSCA  
     SURFACE . . . . . . . .    8.74         55    98.2    56     CRMSCA  
     BURIED  . . . . . . . .    8.45         15   100.0    15     CRMSCA  
     CORE  . . . . . . . . .    8.64         46   100.0    46     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    8.68        345    98.6   350     CRMSMC  
     WELL ORDERED  . . . . .    8.68        345    98.6   350     CRMSMC  
     NO INTER CONTACTS . . .    8.68        345    98.6   350     CRMSMC  
     SHIFTED CHAIN . . . . .    8.88        316    98.4   321     CRMSMC  
     ALTERNATIVE PARENT  . .    9.55         34    87.2    39     CRMSMC  
     SECONDARY STRUCTURE . .    8.89        159   100.0   159     CRMSMC  
     SHIFTED SS UNITS  . . .    7.56         80   100.0    80     CRMSMC  
     LARGE SHIFTS/INSERTIONS    8.63        118    95.9   123     CRMSMC  
     SURFACE . . . . . . . .    8.74        271    98.2   276     CRMSMC  
     BURIED  . . . . . . . .    8.45         74   100.0    74     CRMSMC  
     CORE  . . . . . . . . .    8.71        227   100.0   227     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   10.41        266    33.1   803     CRMSSC  
     WELL ORDERED  . . . . .   10.41        266    33.1   803     CRMSSC  
     NO INTER CONTACTS . . .   10.41        266    33.1   803     CRMSSC  
     RELIABLE SIDE CHAINS  .   10.33        230    30.0   767     CRMSSC  
     CHANGED ANGLES  . . . .   10.84        155    99.4   156     CRMSSC  
     SECONDARY STRUCTURE . .   10.40        126    32.0   394     CRMSSC  
     LARGE SHIFTS/INSERTIONS   10.39         74    31.6   234     CRMSSC  
     SURFACE . . . . . . . .   10.63        209    33.5   624     CRMSSC  
     BURIED  . . . . . . . .    9.52         57    31.8   179     CRMSSC  
     CORE  . . . . . . . . .   10.41        192    33.7   569     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    9.51        546    50.2  1087     CRMSALL 
     WELL ORDERED  . . . . .    9.51        546    50.2  1087     CRMSALL 
     NO INTER CONTACTS . . .    9.51        546    50.2  1087     CRMSALL 
     SHIFTED CHAIN . . . . .    9.66        500    49.9  1003     CRMSALL 
     ALTERNATIVE PARENT  . .    8.89         49    45.0   109     CRMSALL 
     SECONDARY STRUCTURE . .    9.63        254    48.7   522     CRMSALL 
     LARGE SHIFTS/INSERTIONS    9.36        170    50.9   334     CRMSALL 
     SURFACE . . . . . . . .    9.66        429    50.6   848     CRMSALL 
     BURIED  . . . . . . . .    8.91        117    49.0   239     CRMSALL 
     CORE  . . . . . . . . .    9.57        376    49.9   753     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     4.33      4    80.0     5       1-STDDS-5    
 CA  LOOP  2     9.76     12   100.0    12      33-ACGQNPTLAEIT-44   
 CA  LOOP  3     9.69      6   100.0     6      66-PNGFDM-71   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     4.53     20    80.0    25       1-STDDS-5    
 MC  LOOP  2     9.45     59   100.0    59      33-ACGQNPTLAEIT-44   
 MC  LOOP  3     9.76     29   100.0    29      66-PNGFDM-71   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     5.71     29    46.8    62       1-STDDS-5    
 ALL LOOP  2     9.87     83    50.6   164      33-ACGQNPTLAEIT-44   
 ALL LOOP  3    10.92     46    54.8    84      66-PNGFDM-71   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     1.22      4    80.0     5       1-STDDS-5    
 CA  LOOP  2     4.89     12   100.0    12      33-ACGQNPTLAEIT-44   
 CA  LOOP  3     2.04      6   100.0     6      66-PNGFDM-71   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.18     20    80.0    25       1-STDDS-5    
 MC  LOOP  2     4.96     59   100.0    59      33-ACGQNPTLAEIT-44   
 MC  LOOP  3     2.78     29   100.0    29      66-PNGFDM-71   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     2.64     29    46.8    62       1-STDDS-5    
 ALL LOOP  2     5.84     83    50.6   164      33-ACGQNPTLAEIT-44   
 ALL LOOP  3     4.25     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 . . . . . . . . . .    3.402      0.241       0.236     70    98.6    71     ERRCA  
     WELL ORDERED  . . . . .    3.402      0.241       0.236     70    98.6    71     ERRCA  
     NO INTER CONTACTS . . .    3.402      0.241       0.236     70    98.6    71     ERRCA  
     SHIFTED CHAIN . . . . .    3.270      0.228       0.219     64    98.5    65     ERRCA  
     ALTERNATIVE PARENT  . .    5.154      0.360       0.342      7    87.5     8     ERRCA  
     SECONDARY STRUCTURE . .    3.544      0.250       0.248     32   100.0    32     ERRCA  
     LARGE SHIFTS/INSERTIONS    3.970      0.277       0.258     24    96.0    25     ERRCA  
     SURFACE . . . . . . . .    3.516      0.247       0.239     55    98.2    56     ERRCA  
     BURIED  . . . . . . . .    2.986      0.216       0.227     15   100.0    15     ERRCA  
     CORE  . . . . . . . . .    3.106      0.222       0.225     46   100.0    46     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.406      0.237       0.234    345    98.6   350     ERRMC  
     WELL ORDERED  . . . . .    3.406      0.237       0.234    345    98.6   350     ERRMC  
     NO INTER CONTACTS . . .    3.406      0.237       0.234    345    98.6   350     ERRMC  
     SHIFTED CHAIN . . . . .    3.270      0.223       0.216    316    98.4   321     ERRMC  
     ALTERNATIVE PARENT  . .    4.679      0.321       0.306     34    87.2    39     ERRMC  
     SECONDARY STRUCTURE . .    3.559      0.249       0.245    159   100.0   159     ERRMC  
     LARGE SHIFTS/INSERTIONS    3.855      0.264       0.264    118    95.9   123     ERRMC  
     SURFACE . . . . . . . .    3.497      0.242       0.237    271    98.2   276     ERRMC  
     BURIED  . . . . . . . .    3.073      0.220       0.222     74   100.0    74     ERRMC  
     CORE  . . . . . . . . .    3.172      0.223       0.218    227   100.0   227     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.079      0.173       0.135    266    33.1   803     ERRSC  
     WELL ORDERED  . . . . .    3.079      0.173       0.135    266    33.1   803     ERRSC  
     NO INTER CONTACTS . . .    3.079      0.173       0.135    266    33.1   803     ERRSC  
     RELIABLE SIDE CHAINS  .    3.093      0.176       0.142    230    30.0   767     ERRSC  
     CHANGED ANGLES  . . . .    3.124      0.166       0.121    155    99.4   156     ERRSC  
     SHIFTED CHAIN . . . . .    3.077      0.170       0.130    244    32.8   743     ERRSC  
     ALTERNATIVE PARENT  . .    2.578      0.183       0.187     21    27.3    77     ERRSC  
     SECONDARY STRUCTURE . .    3.071      0.173       0.130    126    32.0   394     ERRSC  
     LARGE SHIFTS/INSERTIONS    3.518      0.198       0.169     74    31.6   234     ERRSC  
     SURFACE . . . . . . . .    3.310      0.184       0.145    209    33.5   624     ERRSC  
     BURIED  . . . . . . . .    2.232      0.129       0.098     57    31.8   179     ERRSC  
     CORE  . . . . . . . . .    2.910      0.163       0.122    192    33.7   569     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.287      0.211       0.192    546    50.2  1087     ERRALL 
     WELL ORDERED  . . . . .    3.287      0.211       0.192    546    50.2  1087     ERRALL 
     NO INTER CONTACTS . . .    3.287      0.211       0.192    546    50.2  1087     ERRALL 
     SHIFTED CHAIN . . . . .    3.207      0.202       0.179    500    49.9  1003     ERRALL 
     ALTERNATIVE PARENT  . .    3.917      0.270       0.261     49    45.0   109     ERRALL 
     SECONDARY STRUCTURE . .    3.374      0.218       0.197    254    48.7   522     ERRALL 
     LARGE SHIFTS/INSERTIONS    3.774      0.242       0.229    170    50.9   334     ERRALL 
     SURFACE . . . . . . . .    3.437      0.218       0.197    429    50.6   848     ERRALL 
     BURIED  . . . . . . . .    2.738      0.183       0.172    117    49.0   239     ERRALL 
     CORE  . . . . . . . . .    3.067      0.196       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)         1         6        11        21        47      70      71   DISTCA 
CA  (P)      1.41      8.45     15.49     29.58     66.20              71   DISTCA 
CA  (RMS)    0.71      1.30      1.95      3.18      6.25                   DISTCA 
 
ALL (N)         5        28        55       118       330     546    1087   DISTALL 
ALL (P)      0.46      2.58      5.06     10.86     30.36            1087   DISTALL 
ALL (RMS)    0.78      1.45      2.09      3.23      6.60                   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          8.74          RMSLSI 
 
 
 
END of the results output 
