 
####################################################### 
#                                                     # 
#                        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      2 
ALIGNMENT-DALI(1)      ../PARENTS/casp2.T0004.1csp.rot 
ALIGNMENT-DALI(2)      ../PARENTS/casp2.T0004.1mjc.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 588 atoms, MODEL 645 atoms, 588 common with TARGET 
           Number of atoms possible to evaluate: 509 
 
 
 CA-RMS TARGET<->PARENT(1csp)	 2.141282 
 
 CA-RMS TARGET<->PARENT(1mjc)	 2.434782 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    88.27           28.5   130    86.7   150     ARMSMC  
     WELL ORDERED  . . . . .    88.27           28.5   130    86.7   150     ARMSMC  
     NO INTER CONTACTS . . .    88.27           28.5   130    86.7   150     ARMSMC  
     SHIFTED CHAIN . . . . .    90.08           23.7   118    85.5   138     ARMSMC  
     ALTERNATIVE PARENT  . .    85.42           50.0     8    80.0    10     ARMSMC  
     SECONDARY STRUCTURE . .    90.78           34.0    47    87.0    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS    91.91           20.8    48    77.4    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    87.08           27.0    89    84.0   106     ARMSMC  
     BURIED  . . . . . . . .    90.82           31.7    41    93.2    44     ARMSMC  
     CORE  . . . . . . . . .    86.07           32.9    82    93.2    88     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    80.61           42.6    54    87.1    62     ARMSSC1 
     WELL ORDERED  . . . . .    80.61           42.6    54    87.1    62     ARMSSC1 
     NO INTER CONTACTS . . .    80.61           42.6    54    87.1    62     ARMSSC1 
     RELIABLE SIDE CHAINS  .    80.32           38.6    44    88.0    50     ARMSSC1 
     CHANGED ANGLES  . . . .    83.50           38.1    42    85.7    49     ARMSSC1 
     SHIFTED CHAIN . . . . .    79.81           43.8    48    85.7    56     ARMSSC1 
     ALTERNATIVE PARENT  . .    40.99           75.0     4    80.0     5     ARMSSC1 
     SECONDARY STRUCTURE . .    86.25           35.0    20    87.0    23     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    62.56           61.1    18    78.3    23     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    78.72           41.0    39    84.8    46     ARMSSC1 
     BURIED  . . . . . . . .    85.32           46.7    15    93.8    16     ARMSSC1 
     CORE  . . . . . . . . .    88.26           33.3    36    92.3    39     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    61.78           42.5    40    88.9    45     ARMSSC2 
     WELL ORDERED  . . . . .    61.78           42.5    40    88.9    45     ARMSSC2 
     NO INTER CONTACTS . . .    61.78           42.5    40    88.9    45     ARMSSC2 
     RELIABLE SIDE CHAINS  .    60.99           45.7    35    87.5    40     ARMSSC2 
     CHANGED ANGLES  . . . .    60.82           47.2    36    87.8    41     ARMSSC2 
     SHIFTED CHAIN . . . . .    61.29           43.2    37    88.1    42     ARMSSC2 
     ALTERNATIVE PARENT  . .    58.32           66.7     3    75.0     4     ARMSSC2 
     SECONDARY STRUCTURE . .    53.44           41.7    12    92.3    13     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    51.15           46.2    13    76.5    17     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    61.07           41.2    34    89.5    38     ARMSSC2 
     BURIED  . . . . . . . .    65.68           50.0     6    85.7     7     ARMSSC2 
     CORE  . . . . . . . . .    66.29           40.7    27    96.4    28     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    88.85           28.6    21    87.5    24     ARMSSC3 
     WELL ORDERED  . . . . .    88.85           28.6    21    87.5    24     ARMSSC3 
     NO INTER CONTACTS . . .    88.85           28.6    21    87.5    24     ARMSSC3 
     RELIABLE SIDE CHAINS  .    89.67           29.4    17    85.0    20     ARMSSC3 
     CHANGED ANGLES  . . . .    88.85           28.6    21    87.5    24     ARMSSC3 
     SHIFTED CHAIN . . . . .    89.91           30.0    20    87.0    23     ARMSSC3 
     ALTERNATIVE PARENT  . .   112.01            0.0     1    50.0     2     ARMSSC3 
     SECONDARY STRUCTURE . .    90.63           16.7     6   100.0     6     ARMSSC3 
     LARGE SHIFTS/INSERTIONS   102.93           37.5     8    72.7    11     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    88.85           28.6    21    87.5    24     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     CORE  . . . . . . . . .    78.94           23.1    13   100.0    13     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    84.81            9.1    11    91.7    12     ARMSSC4 
     WELL ORDERED  . . . . .    84.81            9.1    11    91.7    12     ARMSSC4 
     NO INTER CONTACTS . . .    84.81            9.1    11    91.7    12     ARMSSC4 
     RELIABLE SIDE CHAINS  .    84.81            9.1    11    91.7    12     ARMSSC4 
     CHANGED ANGLES  . . . .    84.81            9.1    11    91.7    12     ARMSSC4 
     SHIFTED CHAIN . . . . .    86.85           10.0    10    90.9    11     ARMSSC4 
     ALTERNATIVE PARENT  . .   148.63            0.0     1    50.0     2     ARMSSC4 
     SECONDARY STRUCTURE . .    45.19            0.0     4   100.0     4     ARMSSC4 
     LARGE SHIFTS/INSERTIONS   100.98           20.0     5    83.3     6     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .    84.81            9.1    11    91.7    12     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .    68.47            0.0     6   100.0     6     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.60610     r(1,2) =   0.61258     r(1,3) =  -0.50734 
 r(2,1) =   0.74273     r(2,2) =  -0.66411     r(2,3) =   0.08544 
 r(3,1) =  -0.28459     r(3,2) =  -0.42860     r(3,3) =  -0.85750 
THE OFFSET VECTOR: 
 v(1) =   4.78490     v(2) =  -7.15062     v(3) =  51.39725 
 
 Number of iteration  2                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.57           (Number of atoms:   11) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   14.51         66    86.8    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.2198                            CRMSCA  
     WELL ORDERED  . . . . .   14.51         66    86.8    76     CRMSCA  
     NO INTER CONTACTS . . .   14.51         66    86.8    76     CRMSCA  
     SHIFTED CHAIN . . . . .   13.79         60    85.7    70     CRMSCA  
     ALTERNATIVE PARENT  . .    6.83          4    80.0     5     CRMSCA  
     SECONDARY STRUCTURE . .   15.98         24    88.9    27     CRMSCA  
     SHIFTED SS UNITS  . . .    8.85          6   100.0     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS   12.95         25    78.1    32     CRMSCA  
     SURFACE . . . . . . . .   14.82         45    83.3    54     CRMSCA  
     BURIED  . . . . . . . .   13.82         21    95.5    22     CRMSCA  
     CORE  . . . . . . . . .   15.38         41    93.2    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   14.54        322    86.8   371     CRMSMC  
     WELL ORDERED  . . . . .   14.54        322    86.8   371     CRMSMC  
     NO INTER CONTACTS . . .   14.54        322    86.8   371     CRMSMC  
     SHIFTED CHAIN . . . . .   13.81        292    85.6   341     CRMSMC  
     ALTERNATIVE PARENT  . .    7.05         20    80.0    25     CRMSMC  
     SECONDARY STRUCTURE . .   15.98        118    88.7   133     CRMSMC  
     SHIFTED SS UNITS  . . .    8.83         30   100.0    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS   13.00        120    77.9   154     CRMSMC  
     SURFACE . . . . . . . .   14.76        220    83.3   264     CRMSMC  
     BURIED  . . . . . . . .   14.06        102    95.3   107     CRMSMC  
     CORE  . . . . . . . . .   15.39        202    93.1   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   16.61        245    86.3   284     CRMSSC  
     WELL ORDERED  . . . . .   16.61        245    86.3   284     CRMSSC  
     NO INTER CONTACTS . . .   16.61        245    86.3   284     CRMSSC  
     RELIABLE SIDE CHAINS  .   17.10        205    85.4   240     CRMSSC  
     CHANGED ANGLES  . . . .   17.64        165    85.9   192     CRMSSC  
     SECONDARY STRUCTURE . .   17.90         85    85.9    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS   14.20         87    77.7   112     CRMSSC  
     SURFACE . . . . . . . .   17.33        191    86.0   222     CRMSSC  
     BURIED  . . . . . . . .   13.72         54    87.1    62     CRMSSC  
     CORE  . . . . . . . . .   17.79        158    91.9   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   15.54        509    86.6   588     CRMSALL 
     WELL ORDERED  . . . . .   15.54        509    86.6   588     CRMSALL 
     NO INTER CONTACTS . . .   15.54        509    86.6   588     CRMSALL 
     SHIFTED CHAIN . . . . .   14.90        463    85.4   542     CRMSALL 
     ALTERNATIVE PARENT  . .    8.97         34    75.6    45     CRMSALL 
     SECONDARY STRUCTURE . .   16.91        181    87.4   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS   13.59        187    77.9   240     CRMSALL 
     SURFACE . . . . . . . .   16.06        371    84.7   438     CRMSALL 
     BURIED  . . . . . . . .   14.04        138    92.0   150     CRMSALL 
     CORE  . . . . . . . . .   16.56        322    92.5   348     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     0.00      0     0.0     7       1-AEIEVGR-7    
 CA  LOOP  2    12.80      3   100.0     3      26-GGG-28   
 CA  LOOP  3    12.81     10   100.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     6.41      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     0.00      0     0.0    34       1-AEIEVGR-7    
 MC  LOOP  2    12.40     12   100.0    12      26-GGG-28   
 MC  LOOP  3    13.12     50   100.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     6.53     19   100.0    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     0.00      0     0.0    53       1-AEIEVGR-7    
 ALL LOOP  2    12.40     12   100.0    12      26-GGG-28   
 ALL LOOP  3    14.01     87   100.0    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     8.74     35   100.0    35      65-RQGR-68   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 CA  LOOP  2     0.06      3   100.0     3      26-GGG-28   
 CA  LOOP  3     4.82     10   100.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     1.03      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 MC  LOOP  2     1.05     12   100.0    12      26-GGG-28   
 MC  LOOP  3     5.14     50   100.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     1.64     19   100.0    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 ALL LOOP  2     1.05     12   100.0    12      26-GGG-28   
 ALL LOOP  3     7.04     87   100.0    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     2.84     35   100.0    35      65-RQGR-68   
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   10.553      0.628       0.329     66    86.8    76     ERRCA  
     WELL ORDERED  . . . . .   10.553      0.628       0.329     66    86.8    76     ERRCA  
     NO INTER CONTACTS . . .   10.553      0.628       0.329     66    86.8    76     ERRCA  
     SHIFTED CHAIN . . . . .    9.889      0.617       0.325     60    85.7    70     ERRCA  
     ALTERNATIVE PARENT  . .    4.520      0.486       0.243      4    80.0     5     ERRCA  
     SECONDARY STRUCTURE . .   11.817      0.620       0.324     24    88.9    27     ERRCA  
     LARGE SHIFTS/INSERTIONS    9.287      0.617       0.309     25    78.1    32     ERRCA  
     SURFACE . . . . . . . .   10.794      0.626       0.327     45    83.3    54     ERRCA  
     BURIED  . . . . . . . .   10.038      0.632       0.332     21    95.5    22     ERRCA  
     CORE  . . . . . . . . .   11.325      0.634       0.341     41    93.2    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   10.614      0.636       0.326    322    86.8   371     ERRMC  
     WELL ORDERED  . . . . .   10.614      0.636       0.326    322    86.8   371     ERRMC  
     NO INTER CONTACTS . . .   10.614      0.636       0.326    322    86.8   371     ERRMC  
     SHIFTED CHAIN . . . . .    9.935      0.625       0.321    292    85.6   341     ERRMC  
     ALTERNATIVE PARENT  . .    4.745      0.508       0.255     20    80.0    25     ERRMC  
     SECONDARY STRUCTURE . .   11.784      0.626       0.321    118    88.7   133     ERRMC  
     LARGE SHIFTS/INSERTIONS    9.401      0.632       0.316    120    77.9   154     ERRMC  
     SURFACE . . . . . . . .   10.834      0.638       0.327    220    83.3   264     ERRMC  
     BURIED  . . . . . . . .   10.140      0.633       0.324    102    95.3   107     ERRMC  
     CORE  . . . . . . . . .   11.335      0.639       0.332    202    93.1   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   12.781      0.701       0.351    245    86.3   284     ERRSC  
     WELL ORDERED  . . . . .   12.781      0.701       0.351    245    86.3   284     ERRSC  
     NO INTER CONTACTS . . .   12.781      0.701       0.351    245    86.3   284     ERRSC  
     RELIABLE SIDE CHAINS  .   13.403      0.717       0.358    205    85.4   240     ERRSC  
     CHANGED ANGLES  . . . .   14.054      0.744       0.373    165    85.9   192     ERRSC  
     SHIFTED CHAIN . . . . .   12.199      0.694       0.348    223    85.1   262     ERRSC  
     ALTERNATIVE PARENT  . .    8.288      0.684       0.342     18    72.0    25     ERRSC  
     SECONDARY STRUCTURE . .   13.915      0.689       0.346     85    85.9    99     ERRSC  
     LARGE SHIFTS/INSERTIONS   10.967      0.714       0.357     87    77.7   112     ERRSC  
     SURFACE . . . . . . . .   13.511      0.714       0.357    191    86.0   222     ERRSC  
     BURIED  . . . . . . . .   10.201      0.657       0.330     54    87.1    62     ERRSC  
     CORE  . . . . . . . . .   13.780      0.694       0.348    158    91.9   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   11.623      0.667       0.339    509    86.6   588     ERRALL 
     WELL ORDERED  . . . . .   11.623      0.667       0.339    509    86.6   588     ERRALL 
     NO INTER CONTACTS . . .   11.623      0.667       0.339    509    86.6   588     ERRALL 
     SHIFTED CHAIN . . . . .   11.003      0.658       0.334    463    85.4   542     ERRALL 
     ALTERNATIVE PARENT  . .    6.506      0.592       0.296     34    75.6    45     ERRALL 
     SECONDARY STRUCTURE . .   12.792      0.657       0.334    181    87.4   207     ERRALL 
     LARGE SHIFTS/INSERTIONS   10.118      0.667       0.334    187    77.9   240     ERRALL 
     SURFACE . . . . . . . .   12.127      0.675       0.342    371    84.7   438     ERRALL 
     BURIED  . . . . . . . .   10.265      0.645       0.329    138    92.0   150     ERRALL 
     CORE  . . . . . . . . .   12.497      0.667       0.342    322    92.5   348     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         9        11        14        28      66      76   DISTCA 
CA  (P)      3.95     11.84     14.47     18.42     36.84              76   DISTCA 
CA  (RMS)    0.72      1.37      1.57      2.37      5.94                   DISTCA 
 
ALL (N)        10        32        57        99       201     509     588   DISTALL 
ALL (P)      1.70      5.44      9.69     16.84     34.18             588   DISTALL 
ALL (RMS)    0.77      1.36      1.87      3.04      6.06                   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)          44            41            25          RMSLSI 
CA  (P)       57.89         53.95         32.89          RMSLSI 
CA  (RMS)      1.67         15.38         12.95          RMSLSI 
 
 
 
END of the results output 
