 
####################################################### 
#                                                     # 
#                        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 . . . . . . . . . .    51.94           68.6   140   100.0   140     ARMSMC  
     WELL ORDERED  . . . . .    51.94           68.6   140   100.0   140     ARMSMC  
     NO INTER CONTACTS . . .    51.94           68.6   140   100.0   140     ARMSMC  
     SHIFTED CHAIN . . . . .    53.79           68.8   128   100.0   128     ARMSMC  
     ALTERNATIVE PARENT  . .    56.13           80.0    15   100.0    15     ARMSMC  
     SECONDARY STRUCTURE . .    14.80           93.8    64   100.0    64     ARMSMC  
     LARGE SHIFTS/INSERTIONS    69.47           54.2    48   100.0    48     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    55.17           65.5   110   100.0   110     ARMSMC  
     BURIED  . . . . . . . .    37.80           80.0    30   100.0    30     ARMSMC  
     CORE  . . . . . . . . .    39.84           76.1    92   100.0    92     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    79.08           46.8    62   100.0    62     ARMSSC1 
     WELL ORDERED  . . . . .    79.08           46.8    62   100.0    62     ARMSSC1 
     NO INTER CONTACTS . . .    79.08           46.8    62   100.0    62     ARMSSC1 
     RELIABLE SIDE CHAINS  .    77.27           46.7    60   100.0    60     ARMSSC1 
     CHANGED ANGLES  . . . .    83.43           36.8    38   100.0    38     ARMSSC1 
     SHIFTED CHAIN . . . . .    80.76           45.6    57   100.0    57     ARMSSC1 
     ALTERNATIVE PARENT  . .    57.24           50.0     6   100.0     6     ARMSSC1 
     SECONDARY STRUCTURE . .    87.21           46.4    28   100.0    28     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    75.29           35.0    20   100.0    20     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    82.99           42.9    49   100.0    49     ARMSSC1 
     BURIED  . . . . . . . .    62.17           61.5    13   100.0    13     ARMSSC1 
     CORE  . . . . . . . . .    80.82           52.4    42   100.0    42     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    71.46           39.6    48   100.0    48     ARMSSC2 
     WELL ORDERED  . . . . .    71.46           39.6    48   100.0    48     ARMSSC2 
     NO INTER CONTACTS . . .    71.46           39.6    48   100.0    48     ARMSSC2 
     RELIABLE SIDE CHAINS  .    70.45           43.2    37   100.0    37     ARMSSC2 
     CHANGED ANGLES  . . . .    75.09           34.2    38   100.0    38     ARMSSC2 
     SHIFTED CHAIN . . . . .    72.96           37.0    46   100.0    46     ARMSSC2 
     ALTERNATIVE PARENT  . .    74.17           50.0     4   100.0     4     ARMSSC2 
     SECONDARY STRUCTURE . .    69.74           52.2    23   100.0    23     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    88.03           14.3    14   100.0    14     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    69.81           37.8    37   100.0    37     ARMSSC2 
     BURIED  . . . . . . . .    76.73           45.5    11   100.0    11     ARMSSC2 
     CORE  . . . . . . . . .    63.38           50.0    34   100.0    34     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    65.39           29.4    17   100.0    17     ARMSSC3 
     WELL ORDERED  . . . . .    65.39           29.4    17   100.0    17     ARMSSC3 
     NO INTER CONTACTS . . .    65.39           29.4    17   100.0    17     ARMSSC3 
     RELIABLE SIDE CHAINS  .    66.48           38.5    13   100.0    13     ARMSSC3 
     CHANGED ANGLES  . . . .    67.22           25.0    16   100.0    16     ARMSSC3 
     SHIFTED CHAIN . . . . .    65.39           29.4    17   100.0    17     ARMSSC3 
     ALTERNATIVE PARENT  . .    60.87            0.0     2   100.0     2     ARMSSC3 
     SECONDARY STRUCTURE . .    66.50           36.4    11   100.0    11     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    43.65           33.3     3   100.0     3     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    63.32           31.2    16   100.0    16     ARMSSC3 
     BURIED  . . . . . . . .    92.37            0.0     1   100.0     1     ARMSSC3 
     CORE  . . . . . . . . .    69.16           28.6    14   100.0    14     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    78.24           33.3     6   100.0     6     ARMSSC4 
     WELL ORDERED  . . . . .    78.24           33.3     6   100.0     6     ARMSSC4 
     NO INTER CONTACTS . . .    78.24           33.3     6   100.0     6     ARMSSC4 
     RELIABLE SIDE CHAINS  .    78.24           33.3     6   100.0     6     ARMSSC4 
     CHANGED ANGLES  . . . .    79.88           40.0     5   100.0     5     ARMSSC4 
     SHIFTED CHAIN . . . . .    78.24           33.3     6   100.0     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    89.93            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 . . . . . . . .    78.24           33.3     6   100.0     6     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .    78.24           33.3     6   100.0     6     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.18751     r(1,2) =  -0.79549     r(1,3) =  -0.57622 
 r(2,1) =  -0.92285     r(2,2) =  -0.05824     r(2,3) =   0.38072 
 r(3,1) =  -0.33642     r(3,2) =   0.60316     r(3,3) =  -0.72320 
THE OFFSET VECTOR: 
 v(1) =  78.05226     v(2) =   2.99041     v(3) =  20.68418 
 
 Number of iteration  5                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.56           (Number of atoms:   34) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    5.42         71   100.0    71     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0763                            CRMSCA  
     WELL ORDERED  . . . . .    5.42         71   100.0    71     CRMSCA  
     NO INTER CONTACTS . . .    5.42         71   100.0    71     CRMSCA  
     SHIFTED CHAIN . . . . .    5.59         65   100.0    65     CRMSCA  
     ALTERNATIVE PARENT  . .    6.48          8   100.0     8     CRMSCA  
     SECONDARY STRUCTURE . .    3.80         32   100.0    32     CRMSCA  
     SHIFTED SS UNITS  . . .    2.14         16   100.0    16     CRMSCA  
     LARGE SHIFTS/INSERTIONS    8.18         25   100.0    25     CRMSCA  
     SURFACE . . . . . . . .    5.89         56   100.0    56     CRMSCA  
     BURIED  . . . . . . . .    3.07         15   100.0    15     CRMSCA  
     CORE  . . . . . . . . .    2.99         46   100.0    46     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    5.45        350   100.0   350     CRMSMC  
     WELL ORDERED  . . . . .    5.45        350   100.0   350     CRMSMC  
     NO INTER CONTACTS . . .    5.45        350   100.0   350     CRMSMC  
     SHIFTED CHAIN . . . . .    5.62        321   100.0   321     CRMSMC  
     ALTERNATIVE PARENT  . .    6.02         39   100.0    39     CRMSMC  
     SECONDARY STRUCTURE . .    3.94        159   100.0   159     CRMSMC  
     SHIFTED SS UNITS  . . .    2.18         80   100.0    80     CRMSMC  
     LARGE SHIFTS/INSERTIONS    8.13        123   100.0   123     CRMSMC  
     SURFACE . . . . . . . .    5.91        276   100.0   276     CRMSMC  
     BURIED  . . . . . . . .    3.17         74   100.0    74     CRMSMC  
     CORE  . . . . . . . . .    3.16        227   100.0   227     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    5.85        268    33.4   803     CRMSSC  
     WELL ORDERED  . . . . .    5.85        268    33.4   803     CRMSSC  
     NO INTER CONTACTS . . .    5.85        268    33.4   803     CRMSSC  
     RELIABLE SIDE CHAINS  .    5.98        232    30.2   767     CRMSSC  
     CHANGED ANGLES  . . . .    6.13        156   100.0   156     CRMSSC  
     SECONDARY STRUCTURE . .    4.29        126    32.0   394     CRMSSC  
     LARGE SHIFTS/INSERTIONS    9.26         76    32.5   234     CRMSSC  
     SURFACE . . . . . . . .    6.37        211    33.8   624     CRMSSC  
     BURIED  . . . . . . . .    3.30         57    31.8   179     CRMSSC  
     CORE  . . . . . . . . .    3.73        192    33.7   569     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    5.65        552    50.8  1087     CRMSALL 
     WELL ORDERED  . . . . .    5.65        552    50.8  1087     CRMSALL 
     NO INTER CONTACTS . . .    5.65        552    50.8  1087     CRMSALL 
     SHIFTED CHAIN . . . . .    5.83        506    50.4  1003     CRMSALL 
     ALTERNATIVE PARENT  . .    5.46         55    50.5   109     CRMSALL 
     SECONDARY STRUCTURE . .    4.14        254    48.7   522     CRMSALL 
     LARGE SHIFTS/INSERTIONS    8.63        176    52.7   334     CRMSALL 
     SURFACE . . . . . . . .    6.14        435    51.3   848     CRMSALL 
     BURIED  . . . . . . . .    3.25        117    49.0   239     CRMSALL 
     CORE  . . . . . . . . .    3.47        376    49.9   753     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     5.32      5   100.0     5       1-STDDS-5    
 CA  LOOP  2     7.04     12   100.0    12      33-ACGQNPTLAEIT-44   
 CA  LOOP  3    12.10      6   100.0     6      66-PNGFDM-71   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     5.38     25   100.0    25       1-STDDS-5    
 MC  LOOP  2     6.81     59   100.0    59      33-ACGQNPTLAEIT-44   
 MC  LOOP  3    12.29     29   100.0    29      66-PNGFDM-71   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     6.47     35    56.5    62       1-STDDS-5    
 ALL LOOP  2     6.54     83    50.6   164      33-ACGQNPTLAEIT-44   
 ALL LOOP  3    12.97     46    54.8    84      66-PNGFDM-71   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.66      5   100.0     5       1-STDDS-5    
 CA  LOOP  2     1.18     12   100.0    12      33-ACGQNPTLAEIT-44   
 CA  LOOP  3     2.40      6   100.0     6      66-PNGFDM-71   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     3.04     25   100.0    25       1-STDDS-5    
 MC  LOOP  2     1.22     59   100.0    59      33-ACGQNPTLAEIT-44   
 MC  LOOP  3     3.17     29   100.0    29      66-PNGFDM-71   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     3.77     35    56.5    62       1-STDDS-5    
 ALL LOOP  2     2.22     83    50.6   164      33-ACGQNPTLAEIT-44   
 ALL LOOP  3     4.22     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 . . . . . . . . . .    5.707      0.497       0.528     71   100.0    71     ERRCA  
     WELL ORDERED  . . . . .    5.707      0.497       0.528     71   100.0    71     ERRCA  
     NO INTER CONTACTS . . .    5.707      0.497       0.528     71   100.0    71     ERRCA  
     SHIFTED CHAIN . . . . .    5.649      0.491       0.517     65   100.0    65     ERRCA  
     ALTERNATIVE PARENT  . .    5.414      0.450       0.497      8   100.0     8     ERRCA  
     SECONDARY STRUCTURE . .    6.134      0.554       0.600     32   100.0    32     ERRCA  
     LARGE SHIFTS/INSERTIONS    4.043      0.287       0.290     25   100.0    25     ERRCA  
     SURFACE . . . . . . . .    5.534      0.477       0.502     56   100.0    56     ERRCA  
     BURIED  . . . . . . . .    6.353      0.571       0.625     15   100.0    15     ERRCA  
     CORE  . . . . . . . . .    6.611      0.612       0.657     46   100.0    46     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    5.656      0.491       0.524    350   100.0   350     ERRMC  
     WELL ORDERED  . . . . .    5.656      0.491       0.524    350   100.0   350     ERRMC  
     NO INTER CONTACTS . . .    5.656      0.491       0.524    350   100.0   350     ERRMC  
     SHIFTED CHAIN . . . . .    5.597      0.484       0.514    321   100.0   321     ERRMC  
     ALTERNATIVE PARENT  . .    5.370      0.459       0.498     39   100.0    39     ERRMC  
     SECONDARY STRUCTURE . .    6.099      0.549       0.595    159   100.0   159     ERRMC  
     LARGE SHIFTS/INSERTIONS    4.074      0.292       0.298    123   100.0   123     ERRMC  
     SURFACE . . . . . . . .    5.484      0.470       0.499    276   100.0   276     ERRMC  
     BURIED  . . . . . . . .    6.298      0.567       0.617     74   100.0    74     ERRMC  
     CORE  . . . . . . . . .    6.514      0.598       0.646    227   100.0   227     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    5.453      0.452       0.493    268    33.4   803     ERRSC  
     WELL ORDERED  . . . . .    5.453      0.452       0.493    268    33.4   803     ERRSC  
     NO INTER CONTACTS . . .    5.453      0.452       0.493    268    33.4   803     ERRSC  
     RELIABLE SIDE CHAINS  .    5.531      0.459       0.499    232    30.2   767     ERRSC  
     CHANGED ANGLES  . . . .    5.409      0.443       0.484    156   100.0   156     ERRSC  
     SHIFTED CHAIN . . . . .    5.395      0.445       0.482    246    33.1   743     ERRSC  
     ALTERNATIVE PARENT  . .    5.483      0.473       0.525     23    29.9    77     ERRSC  
     SECONDARY STRUCTURE . .    5.644      0.490       0.543    126    32.0   394     ERRSC  
     LARGE SHIFTS/INSERTIONS    4.106      0.266       0.251     76    32.5   234     ERRSC  
     SURFACE . . . . . . . .    5.255      0.424       0.463    211    33.8   624     ERRSC  
     BURIED  . . . . . . . .    6.186      0.553       0.606     57    31.8   179     ERRSC  
     CORE  . . . . . . . . .    5.986      0.525       0.589    192    33.7   569     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    5.574      0.473       0.511    552    50.8  1087     ERRALL 
     WELL ORDERED  . . . . .    5.574      0.473       0.511    552    50.8  1087     ERRALL 
     NO INTER CONTACTS . . .    5.574      0.473       0.511    552    50.8  1087     ERRALL 
     SHIFTED CHAIN . . . . .    5.518      0.467       0.501    506    50.4  1003     ERRALL 
     ALTERNATIVE PARENT  . .    5.463      0.467       0.515     55    50.5   109     ERRALL 
     SECONDARY STRUCTURE . .    5.875      0.520       0.569    254    48.7   522     ERRALL 
     LARGE SHIFTS/INSERTIONS    4.133      0.284       0.283    176    52.7   334     ERRALL 
     SURFACE . . . . . . . .    5.397      0.450       0.484    435    51.3   848     ERRALL 
     BURIED  . . . . . . . .    6.233      0.559       0.610    117    49.0   239     ERRALL 
     CORE  . . . . . . . . .    6.249      0.562       0.617    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)         8        27        40        51        63      71      71   DISTCA 
CA  (P)     11.27     38.03     56.34     71.83     88.73              71   DISTCA 
CA  (RMS)    0.82      1.34      1.80      2.39      3.66                   DISTCA 
 
ALL (N)        35       178       284       394       491     552    1087   DISTALL 
ALL (P)      3.22     16.38     26.13     36.25     45.17            1087   DISTALL 
ALL (RMS)    0.82      1.40      1.90      2.64      3.85                   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          2.99          8.18          RMSLSI 
 
 
 
END of the results output 
