 
####################################################### 
#                                                     # 
#                        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 500 atoms, 443 common with TARGET 
           Number of atoms possible to evaluate: 246 
 
 
 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 . . . . . . . . . .    85.48           31.5    92    61.3   150     ARMSMC  
     WELL ORDERED  . . . . .    85.48           31.5    92    61.3   150     ARMSMC  
     NO INTER CONTACTS . . .    85.48           31.5    92    61.3   150     ARMSMC  
     SHIFTED CHAIN . . . . .    87.08           30.7    88    63.8   138     ARMSMC  
     ALTERNATIVE PARENT  . .    83.60           20.0     5    50.0    10     ARMSMC  
     SECONDARY STRUCTURE . .    56.67           45.9    37    68.5    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS    92.92           27.5    40    64.5    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    87.60           29.5    61    57.5   106     ARMSMC  
     BURIED  . . . . . . . .    81.16           35.5    31    70.5    44     ARMSMC  
     CORE  . . . . . . . . .    79.29           34.6    52    59.1    88     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    62     ARMSSC1 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    62     ARMSSC1 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    62     ARMSSC1 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    50     ARMSSC1 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    49     ARMSSC1 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    56     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     5     ARMSSC1 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    23     ARMSSC1 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    23     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    46     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    16     ARMSSC1 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    39     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    45     ARMSSC2 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    45     ARMSSC2 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    45     ARMSSC2 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    40     ARMSSC2 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    41     ARMSSC2 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    42     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     4     ARMSSC2 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    13     ARMSSC2 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    17     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    38     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     7     ARMSSC2 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    28     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    24     ARMSSC3 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    24     ARMSSC3 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    24     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    20     ARMSSC3 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    24     ARMSSC3 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    23     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     2     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0     6     ARMSSC3 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    11     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    24     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    13     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    12     ARMSSC4 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    12     ARMSSC4 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    12     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    12     ARMSSC4 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    12     ARMSSC4 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    11     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     2     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0     4     ARMSSC4 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     6     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    12     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0     6     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.76316     r(1,2) =   0.61194     r(1,3) =   0.20764 
 r(2,1) =  -0.63730     r(2,2) =  -0.76589     r(2,3) =  -0.08515 
 r(3,1) =   0.10692     r(3,2) =  -0.19731     r(3,3) =   0.97449 
THE OFFSET VECTOR: 
 v(1) = -12.65178     v(2) = -11.70308     v(3) =  20.07995 
 
 Number of iteration  2                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.56           (Number of atoms:    5) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   14.04         52    68.4    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.2700                            CRMSCA  
     WELL ORDERED  . . . . .   14.04         52    68.4    76     CRMSCA  
     NO INTER CONTACTS . . .   14.04         52    68.4    76     CRMSCA  
     SHIFTED CHAIN . . . . .   14.14         49    70.0    70     CRMSCA  
     ALTERNATIVE PARENT  . .   15.57          3    60.0     5     CRMSCA  
     SECONDARY STRUCTURE . .   15.92         20    74.1    27     CRMSCA  
     SHIFTED SS UNITS  . . .   10.10          6   100.0     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS   11.88         23    71.9    32     CRMSCA  
     SURFACE . . . . . . . .   14.02         35    64.8    54     CRMSCA  
     BURIED  . . . . . . . .   14.08         17    77.3    22     CRMSCA  
     CORE  . . . . . . . . .   15.54         29    65.9    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   13.84        246    66.3   371     CRMSMC  
     WELL ORDERED  . . . . .   13.84        246    66.3   371     CRMSMC  
     NO INTER CONTACTS . . .   13.84        246    66.3   371     CRMSMC  
     SHIFTED CHAIN . . . . .   13.91        231    67.7   341     CRMSMC  
     ALTERNATIVE PARENT  . .   16.10         15    60.0    25     CRMSMC  
     SECONDARY STRUCTURE . .   15.44         96    72.2   133     CRMSMC  
     SHIFTED SS UNITS  . . .   10.34         30   100.0    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS   11.93        106    68.8   154     CRMSMC  
     SURFACE . . . . . . . .   14.10        166    62.9   264     CRMSMC  
     BURIED  . . . . . . . .   13.29         80    74.8   107     CRMSMC  
     CORE  . . . . . . . . .   15.13        140    64.5   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   12.82         38    13.4   284     CRMSSC  
     WELL ORDERED  . . . . .   12.82         38    13.4   284     CRMSSC  
     NO INTER CONTACTS . . .   12.82         38    13.4   284     CRMSSC  
     RELIABLE SIDE CHAINS  .   12.82         38    15.8   240     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   192     CRMSSC  
     SECONDARY STRUCTURE . .   13.26         16    16.2    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS   11.44         14    12.5   112     CRMSSC  
     SURFACE . . . . . . . .   14.14         26    11.7   222     CRMSSC  
     BURIED  . . . . . . . .    9.34         12    19.4    62     CRMSSC  
     CORE  . . . . . . . . .   13.57         24    14.0   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   13.84        246    41.8   588     CRMSALL 
     WELL ORDERED  . . . . .   13.84        246    41.8   588     CRMSALL 
     NO INTER CONTACTS . . .   13.84        246    41.8   588     CRMSALL 
     SHIFTED CHAIN . . . . .   13.91        231    42.6   542     CRMSALL 
     ALTERNATIVE PARENT  . .   16.10         15    33.3    45     CRMSALL 
     SECONDARY STRUCTURE . .   15.44         96    46.4   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS   11.93        106    44.2   240     CRMSALL 
     SURFACE . . . . . . . .   14.10        166    37.9   438     CRMSALL 
     BURIED  . . . . . . . .   13.29         80    53.3   150     CRMSALL 
     CORE  . . . . . . . . .   15.13        140    40.2   348     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1    14.57      7   100.0     7       1-AEIEVGR-7    
 CA  LOOP  2    10.12      3   100.0     3      26-GGG-28   
 CA  LOOP  3     5.77      8    80.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     0.00      0     0.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1    14.71     33    97.1    34       1-AEIEVGR-7    
 MC  LOOP  2    10.36     12   100.0    12      26-GGG-28   
 MC  LOOP  3     5.97     38    76.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     0.00      0     0.0    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1    14.71     33    62.3    53       1-AEIEVGR-7    
 ALL LOOP  2    10.36     12   100.0    12      26-GGG-28   
 ALL LOOP  3     5.97     38    43.7    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     0.00      0     0.0    35      65-RQGR-68   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.14      7   100.0     7       1-AEIEVGR-7    
 CA  LOOP  2     0.36      3   100.0     3      26-GGG-28   
 CA  LOOP  3     2.72      8    80.0    10      40-DKRVEKVTDY-49   
 WARNING! LOOP  4 cannot be considered (not enough atoms). 
 
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.82     33    97.1    34       1-AEIEVGR-7    
 MC  LOOP  2     2.10     12   100.0    12      26-GGG-28   
 MC  LOOP  3     2.98     38    76.0    50      40-DKRVEKVTDY-49   
 WARNING! LOOP  4 cannot be considered (not enough atoms). 
 
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     2.82     33    62.3    53       1-AEIEVGR-7    
 ALL LOOP  2     2.10     12   100.0    12      26-GGG-28   
 ALL LOOP  3     2.98     38    43.7    87      40-DKRVEKVTDY-49   
 WARNING! LOOP  4 cannot be considered (not enough atoms). 
 
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   11.953      1.000       0.500     52    68.4    76     ERRCA  
     WELL ORDERED  . . . . .   11.953      1.000       0.500     52    68.4    76     ERRCA  
     NO INTER CONTACTS . . .   11.953      1.000       0.500     52    68.4    76     ERRCA  
     SHIFTED CHAIN . . . . .   11.982      1.000       0.500     49    70.0    70     ERRCA  
     ALTERNATIVE PARENT  . .   15.419      1.000       0.500      3    60.0     5     ERRCA  
     SECONDARY STRUCTURE . .   14.443      1.000       0.500     20    74.1    27     ERRCA  
     LARGE SHIFTS/INSERTIONS   10.154      1.000       0.500     23    71.9    32     ERRCA  
     SURFACE . . . . . . . .   12.297      1.000       0.500     35    64.8    54     ERRCA  
     BURIED  . . . . . . . .   11.244      1.000       0.500     17    77.3    22     ERRCA  
     CORE  . . . . . . . . .   13.380      1.000       0.500     29    65.9    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   11.812      1.000       0.500    246    66.3   371     ERRMC  
     WELL ORDERED  . . . . .   11.812      1.000       0.500    246    66.3   371     ERRMC  
     NO INTER CONTACTS . . .   11.812      1.000       0.500    246    66.3   371     ERRMC  
     SHIFTED CHAIN . . . . .   11.821      1.000       0.500    231    67.7   341     ERRMC  
     ALTERNATIVE PARENT  . .   15.879      1.000       0.500     15    60.0    25     ERRMC  
     SECONDARY STRUCTURE . .   14.041      1.000       0.500     96    72.2   133     ERRMC  
     LARGE SHIFTS/INSERTIONS   10.226      1.000       0.500    106    68.8   154     ERRMC  
     SURFACE . . . . . . . .   12.319      1.000       0.500    166    62.9   264     ERRMC  
     BURIED  . . . . . . . .   10.761      1.000       0.500     80    74.8   107     ERRMC  
     CORE  . . . . . . . . .   13.013      1.000       0.500    140    64.5   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   11.083      1.000       0.500     38    13.4   284     ERRSC  
     WELL ORDERED  . . . . .   11.083      1.000       0.500     38    13.4   284     ERRSC  
     NO INTER CONTACTS . . .   11.083      1.000       0.500     38    13.4   284     ERRSC  
     RELIABLE SIDE CHAINS  .   11.083      1.000       0.500     38    15.8   240     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   192     ERRSC  
     SHIFTED CHAIN . . . . .   11.075      1.000       0.500     35    13.4   262     ERRSC  
     ALTERNATIVE PARENT  . .   16.187      1.000       0.500      3    12.0    25     ERRSC  
     SECONDARY STRUCTURE . .   12.459      1.000       0.500     16    16.2    99     ERRSC  
     LARGE SHIFTS/INSERTIONS    9.873      1.000       0.500     14    12.5   112     ERRSC  
     SURFACE . . . . . . . .   12.354      1.000       0.500     26    11.7   222     ERRSC  
     BURIED  . . . . . . . .    8.328      1.000       0.500     12    19.4    62     ERRSC  
     CORE  . . . . . . . . .   11.789      1.000       0.500     24    14.0   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   11.812      1.000       0.500    246    41.8   588     ERRALL 
     WELL ORDERED  . . . . .   11.812      1.000       0.500    246    41.8   588     ERRALL 
     NO INTER CONTACTS . . .   11.812      1.000       0.500    246    41.8   588     ERRALL 
     SHIFTED CHAIN . . . . .   11.821      1.000       0.500    231    42.6   542     ERRALL 
     ALTERNATIVE PARENT  . .   15.879      1.000       0.500     15    33.3    45     ERRALL 
     SECONDARY STRUCTURE . .   14.041      1.000       0.500     96    46.4   207     ERRALL 
     LARGE SHIFTS/INSERTIONS   10.226      1.000       0.500    106    44.2   240     ERRALL 
     SURFACE . . . . . . . .   12.319      1.000       0.500    166    37.9   438     ERRALL 
     BURIED  . . . . . . . .   10.761      1.000       0.500     80    53.3   150     ERRALL 
     CORE  . . . . . . . . .   13.013      1.000       0.500    140    40.2   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)         0         4         5         8        22      52      76   DISTCA 
CA  (P)      0.00      5.26      6.58     10.53     28.95              76   DISTCA 
CA  (RMS)    0.00      1.36      1.56      3.03      6.28                   DISTCA 
 
ALL (N)         2        13        23        42       104     246     588   DISTALL 
ALL (P)      0.34      2.21      3.91      7.14     17.69             588   DISTALL 
ALL (RMS)    0.58      1.39      2.00      3.17      6.23                   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            29            23          RMSLSI 
CA  (P)       57.89         38.16         30.26          RMSLSI 
CA  (RMS)      1.67         15.54         11.88          RMSLSI 
 
 
 
END of the results output 
