 
####################################################### 
#                                                     # 
#                        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:     # 
#                        # 
########################## 
# 
CONANA-INTER           ../CONANA/T0064.inter 
CONANA-PAIR            ../CONANA/T0064.pair 
# 
NUMBER-OF-PARENTS      2 
ALIGNMENT-DALI(1)      ../PARENTS/casp3.T0064.1r69.rot 
ALIGNMENT-DALI(2)      ../PARENTS/casp3.T0064.2cro.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 845 atoms, MODEL 914 atoms, 845 common with TARGET 
           Number of atoms possible to evaluate: 787 
 
 
 CA-RMS TARGET<->PARENT(1r69)	 1.473148 
 
 CA-RMS TARGET<->PARENT(2cro)	 1.394009 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    36.88           75.8   182    90.5   201     ARMSMC  
     WELL ORDERED  . . . . .    35.76           77.9   149    92.5   161     ARMSMC  
     NO INTER CONTACTS . . .    39.09           76.8    95    90.5   105     ARMSMC  
     SHIFTED CHAIN . . . . .    43.69           68.0   122    86.5   141     ARMSMC  
     ALTERNATIVE PARENT  . .    54.32           50.0     4   100.0     4     ARMSMC  
     SECONDARY STRUCTURE . .    37.48           79.8   109    85.8   127     ARMSMC  
     LARGE SHIFTS/INSERTIONS    52.03           61.4    70    78.7    89     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    39.29           74.2   132    87.4   151     ARMSMC  
     BURIED  . . . . . . . .    29.59           80.0    50   100.0    50     ARMSMC  
     CORE  . . . . . . . . .    22.78           84.8   112   100.0   112     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    81.27           44.4    81    89.0    91     ARMSSC1 
     WELL ORDERED  . . . . .    77.76           47.1    51    94.4    54     ARMSSC1 
     NO INTER CONTACTS . . .    87.10           37.5    40    88.9    45     ARMSSC1 
     RELIABLE SIDE CHAINS  .    82.52           44.6    74    88.1    84     ARMSSC1 
     CHANGED ANGLES  . . . .    91.09           32.1    56    84.8    66     ARMSSC1 
     SHIFTED CHAIN . . . . .    78.22           48.1    54    84.4    64     ARMSSC1 
     ALTERNATIVE PARENT  . .     5.83          100.0     2   100.0     2     ARMSSC1 
     SECONDARY STRUCTURE . .    84.54           39.6    48    84.2    57     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    78.24           50.0    32    76.2    42     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    79.73           49.2    59    85.5    69     ARMSSC1 
     BURIED  . . . . . . . .    85.27           31.8    22   100.0    22     ARMSSC1 
     CORE  . . . . . . . . .    83.19           40.8    49   100.0    49     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    72.96           50.0    56    87.5    64     ARMSSC2 
     WELL ORDERED  . . . . .    69.56           61.5    26    92.9    28     ARMSSC2 
     NO INTER CONTACTS . . .    66.65           51.7    29    87.9    33     ARMSSC2 
     RELIABLE SIDE CHAINS  .    73.19           42.9    42    85.7    49     ARMSSC2 
     CHANGED ANGLES  . . . .    86.72           30.8    39    83.0    47     ARMSSC2 
     SHIFTED CHAIN . . . . .    72.79           47.2    36    81.8    44     ARMSSC2 
     ALTERNATIVE PARENT  . .     3.86          100.0     1   100.0     1     ARMSSC2 
     SECONDARY STRUCTURE . .    70.47           48.6    35    83.3    42     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    75.06           40.0    20    71.4    28     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    76.58           43.9    41    83.7    49     ARMSSC2 
     BURIED  . . . . . . . .    62.01           66.7    15   100.0    15     ARMSSC2 
     CORE  . . . . . . . . .    71.78           55.6    36   100.0    36     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    90.50           28.0    25    80.6    31     ARMSSC3 
     WELL ORDERED  . . . . .    75.44           25.0     8    80.0    10     ARMSSC3 
     NO INTER CONTACTS . . .    85.44           33.3    12    80.0    15     ARMSSC3 
     RELIABLE SIDE CHAINS  .    85.15           33.3    21    80.8    26     ARMSSC3 
     CHANGED ANGLES  . . . .    96.54           20.0    20    83.3    24     ARMSSC3 
     SHIFTED CHAIN . . . . .    84.44           21.4    14    70.0    20     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    88.17           33.3    18    78.3    23     ARMSSC3 
     LARGE SHIFTS/INSERTIONS   100.69            0.0     8    57.1    14     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    92.21           27.3    22    78.6    28     ARMSSC3 
     BURIED  . . . . . . . .    76.80           33.3     3   100.0     3     ARMSSC3 
     CORE  . . . . . . . . .    85.28           41.2    17   100.0    17     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .   117.33           30.0    10    83.3    12     ARMSSC4 
     WELL ORDERED  . . . . .   105.00           33.3     3   100.0     3     ARMSSC4 
     NO INTER CONTACTS . . .   107.95           40.0     5    83.3     6     ARMSSC4 
     RELIABLE SIDE CHAINS  .   117.33           30.0    10    83.3    12     ARMSSC4 
     CHANGED ANGLES  . . . .   123.67           22.2     9    81.8    11     ARMSSC4 
     SHIFTED CHAIN . . . . .   128.11           25.0     4    66.7     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .   119.91           28.6     7    77.8     9     ARMSSC4 
     LARGE SHIFTS/INSERTIONS   139.44            0.0     1    33.3     3     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .   124.07           25.0     8    80.0    10     ARMSSC4 
     BURIED  . . . . . . . .    85.22           50.0     2   100.0     2     ARMSSC4 
     CORE  . . . . . . . . .   114.61           33.3     9   100.0     9     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.00974     r(1,2) =  -0.88182     r(1,3) =   0.47148 
 r(2,1) =  -0.78867     r(2,2) =  -0.28309     r(2,3) =  -0.54576 
 r(3,1) =   0.61473     r(3,2) =  -0.37716     r(3,3) =  -0.69272 
THE OFFSET VECTOR: 
 v(1) =  42.28182     v(2) = 144.62997     v(3) = 131.37540 
 
 Number of iteration 44                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.18           (Number of atoms:   59) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   13.83         97    94.2   103     CRMSCA  
     CRN = ALL/NP  . . . . .    0.1426                            CRMSCA  
     WELL ORDERED  . . . . .   14.20         83    97.6    85     CRMSCA  
     NO INTER CONTACTS . . .    8.79         50    92.6    54     CRMSCA  
     SHIFTED CHAIN . . . . .   16.64         67    91.8    73     CRMSCA  
     ALTERNATIVE PARENT  . .    2.65          2   100.0     2     CRMSCA  
     SECONDARY STRUCTURE . .   15.60         60    92.3    65     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS   21.24         41    87.2    47     CRMSCA  
     SURFACE . . . . . . . .   16.04         72    92.3    78     CRMSCA  
     BURIED  . . . . . . . .    1.26         25   100.0    25     CRMSCA  
     CORE  . . . . . . . . .    1.12         56   100.0    56     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   13.83        481    94.1   511     CRMSMC  
     WELL ORDERED  . . . . .   14.11        410    97.6   420     CRMSMC  
     NO INTER CONTACTS . . .    8.60        247    92.5   267     CRMSMC  
     SHIFTED CHAIN . . . . .   16.62        333    91.7   363     CRMSMC  
     ALTERNATIVE PARENT  . .    2.95         10   100.0    10     CRMSMC  
     SECONDARY STRUCTURE . .   15.58        299    92.3   324     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS   21.20        204    87.2   234     CRMSMC  
     SURFACE . . . . . . . .   16.04        357    92.2   387     CRMSMC  
     BURIED  . . . . . . . .    1.33        124   100.0   124     CRMSMC  
     CORE  . . . . . . . . .    1.16        277   100.0   277     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   15.19        399    92.1   433     CRMSSC  
     WELL ORDERED  . . . . .   15.44        238    96.0   248     CRMSSC  
     NO INTER CONTACTS . . .    9.67        186    88.6   210     CRMSSC  
     RELIABLE SIDE CHAINS  .   15.62        339    91.4   371     CRMSSC  
     CHANGED ANGLES  . . . .   17.03        253    90.0   281     CRMSSC  
     SECONDARY STRUCTURE . .   17.40        268    90.2   297     CRMSSC  
     LARGE SHIFTS/INSERTIONS   22.49        179    84.0   213     CRMSSC  
     SURFACE . . . . . . . .   17.18        310    90.1   344     CRMSSC  
     BURIED  . . . . . . . .    2.48         89   100.0    89     CRMSSC  
     CORE  . . . . . . . . .    2.63        220   100.0   220     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   14.50        787    93.1   845     CRMSALL 
     WELL ORDERED  . . . . .   14.63        574    96.8   593     CRMSALL 
     NO INTER CONTACTS . . .    9.17        386    90.6   426     CRMSALL 
     SHIFTED CHAIN . . . . .   17.42        543    90.3   601     CRMSALL 
     ALTERNATIVE PARENT  . .    3.11         14   100.0    14     CRMSALL 
     SECONDARY STRUCTURE . .   16.51        508    91.2   557     CRMSALL 
     LARGE SHIFTS/INSERTIONS   21.85        343    85.5   401     CRMSALL 
     SURFACE . . . . . . . .   16.60        598    91.2   656     CRMSALL 
     BURIED  . . . . . . . .    1.93        189   100.0   189     CRMSALL 
     CORE  . . . . . . . . .    2.01        444   100.0   444     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     3.74      6   100.0     6      40-TNPSIQ-45   
 CA  LOOP  2    23.26     34    85.0    40      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     4.01     30   100.0    30      40-TNPSIQ-45   
 MC  LOOP  2    23.22    169    84.9   199      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     5.29     45   100.0    45      40-TNPSIQ-45   
 ALL LOOP  2    23.66    290    83.3   348      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     1.99      6   100.0     6      40-TNPSIQ-45   
 CA  LOOP  2     5.88     34    85.0    40      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.63     30   100.0    30      40-TNPSIQ-45   
 MC  LOOP  2     6.00    169    84.9   199      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     3.55     45   100.0    45      40-TNPSIQ-45   
 ALL LOOP  2     7.41    290    83.3   348      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   10.249      0.650       0.602     97    94.2   103     ERRCA  
     WELL ORDERED  . . . . .   10.785      0.685       0.631     83    97.6    85     ERRCA  
     NO INTER CONTACTS . . .    9.259      0.725       0.718     50    92.6    54     ERRCA  
     SHIFTED CHAIN . . . . .   10.660      0.549       0.475     67    91.8    73     ERRCA  
     ALTERNATIVE PARENT  . .    7.362      0.583       0.655      2   100.0     2     ERRCA  
     SECONDARY STRUCTURE . .   11.195      0.662       0.591     60    92.3    65     ERRCA  
     LARGE SHIFTS/INSERTIONS   11.907      0.407       0.270     41    87.2    47     ERRCA  
     SURFACE . . . . . . . .   10.713      0.595       0.523     72    92.3    78     ERRCA  
     BURIED  . . . . . . . .    8.913      0.810       0.830     25   100.0    25     ERRCA  
     CORE  . . . . . . . . .    9.035      0.829       0.845     56   100.0    56     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   10.186      0.643       0.597    481    94.1   511     ERRMC  
     WELL ORDERED  . . . . .   10.683      0.677       0.627    410    97.6   420     ERRMC  
     NO INTER CONTACTS . . .    9.149      0.718       0.715    247    92.5   267     ERRMC  
     SHIFTED CHAIN . . . . .   10.597      0.545       0.473    333    91.7   363     ERRMC  
     ALTERNATIVE PARENT  . .    7.079      0.550       0.633     10   100.0    10     ERRMC  
     SECONDARY STRUCTURE . .   11.149      0.659       0.589    299    92.3   324     ERRMC  
     LARGE SHIFTS/INSERTIONS   11.797      0.399       0.266    204    87.2   234     ERRMC  
     SURFACE . . . . . . . .   10.640      0.587       0.517    357    92.2   387     ERRMC  
     BURIED  . . . . . . . .    8.881      0.806       0.827    124   100.0   124     ERRMC  
     CORE  . . . . . . . . .    9.000      0.823       0.841    277   100.0   277     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    9.857      0.541       0.495    399    92.1   433     ERRSC  
     WELL ORDERED  . . . . .   10.659      0.601       0.551    238    96.0   248     ERRSC  
     NO INTER CONTACTS . . .    8.307      0.591       0.596    186    88.6   210     ERRSC  
     RELIABLE SIDE CHAINS  .   10.125      0.546       0.496    339    91.4   371     ERRSC  
     CHANGED ANGLES  . . . .   10.035      0.466       0.403    253    90.0   281     ERRSC  
     SHIFTED CHAIN . . . . .   10.667      0.469       0.384    275    89.0   309     ERRSC  
     ALTERNATIVE PARENT  . .    6.683      0.505       0.604      6   100.0     6     ERRSC  
     SECONDARY STRUCTURE . .   11.273      0.562       0.490    268    90.2   297     ERRSC  
     LARGE SHIFTS/INSERTIONS   12.262      0.373       0.218    179    84.0   213     ERRSC  
     SURFACE . . . . . . . .   10.394      0.499       0.428    310    90.1   344     ERRSC  
     BURIED  . . . . . . . .    7.986      0.686       0.730     89   100.0    89     ERRSC  
     CORE  . . . . . . . . .    7.901      0.677       0.720    220   100.0   220     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   10.025      0.594       0.547    787    93.1   845     ERRALL 
     WELL ORDERED  . . . . .   10.670      0.648       0.598    574    96.8   593     ERRALL 
     NO INTER CONTACTS . . .    8.774      0.659       0.659    386    90.6   426     ERRALL 
     SHIFTED CHAIN . . . . .   10.641      0.509       0.430    543    90.3   601     ERRALL 
     ALTERNATIVE PARENT  . .    6.929      0.532       0.622     14   100.0    14     ERRALL 
     SECONDARY STRUCTURE . .   11.196      0.609       0.538    508    91.2   557     ERRALL 
     LARGE SHIFTS/INSERTIONS   12.036      0.387       0.242    343    85.5   401     ERRALL 
     SURFACE . . . . . . . .   10.513      0.543       0.472    598    91.2   656     ERRALL 
     BURIED  . . . . . . . .    8.479      0.752       0.783    189   100.0   189     ERRALL 
     CORE  . . . . . . . . .    8.471      0.753       0.783    444   100.0   444     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)        35        53        60        63        67      97     103   DISTCA 
CA  (P)     33.98     51.46     58.25     61.17     65.05             103   DISTCA 
CA  (RMS)    0.66      0.97      1.23      1.44      2.32                   DISTCA 
 
ALL (N)       206       340       414       473       524     787     845   DISTALL 
ALL (P)     24.38     40.24     48.99     55.98     62.01             845   DISTALL 
ALL (RMS)    0.70      1.05      1.43      1.89      2.94                   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)          56            56            41          RMSLSI 
CA  (P)       54.37         54.37         39.81          RMSLSI 
CA  (RMS)      1.04          1.12         21.24          RMSLSI 
 
 
 
END of the results output 
