 
####################################################### 
#                                                     # 
#                        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 408 atoms, 368 common with TARGET 
           Number of atoms possible to evaluate: 368 
 
 
 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 . . . . . . . . . .    66.26           47.3   150   100.0   150     ARMSMC  
     WELL ORDERED  . . . . .    66.26           47.3   150   100.0   150     ARMSMC  
     NO INTER CONTACTS . . .    66.26           47.3   150   100.0   150     ARMSMC  
     SHIFTED CHAIN . . . . .    66.12           45.7   138   100.0   138     ARMSMC  
     ALTERNATIVE PARENT  . .    65.47           50.0    10   100.0    10     ARMSMC  
     SECONDARY STRUCTURE . .    59.67           51.9    54   100.0    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS    78.66           37.1    62   100.0    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    72.08           46.2   106   100.0   106     ARMSMC  
     BURIED  . . . . . . . .    49.51           50.0    44   100.0    44     ARMSMC  
     CORE  . . . . . . . . .    55.90           54.5    88   100.0    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) =   0.70750     r(1,2) =  -0.59621     r(1,3) =  -0.37944 
 r(2,1) =  -0.45523     r(2,2) =  -0.79516     r(2,3) =   0.40062 
 r(3,1) =  -0.54057     r(3,2) =  -0.11070     r(3,3) =  -0.83398 
THE OFFSET VECTOR: 
 v(1) =  70.35883     v(2) = 126.12115     v(3) = 161.38980 
 
 Number of iteration  2                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.87           (Number of atoms:   19) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    7.99         76   100.0    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.1051                            CRMSCA  
     WELL ORDERED  . . . . .    7.99         76   100.0    76     CRMSCA  
     NO INTER CONTACTS . . .    7.99         76   100.0    76     CRMSCA  
     SHIFTED CHAIN . . . . .    7.65         70   100.0    70     CRMSCA  
     ALTERNATIVE PARENT  . .    8.05          5   100.0     5     CRMSCA  
     SECONDARY STRUCTURE . .    8.92         27   100.0    27     CRMSCA  
     SHIFTED SS UNITS  . . .    2.85          6   100.0     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS    8.55         32   100.0    32     CRMSCA  
     SURFACE . . . . . . . .    8.35         54   100.0    54     CRMSCA  
     BURIED  . . . . . . . .    7.01         22   100.0    22     CRMSCA  
     CORE  . . . . . . . . .    7.54         44   100.0    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    8.00        368    99.2   371     CRMSMC  
     WELL ORDERED  . . . . .    8.00        368    99.2   371     CRMSMC  
     NO INTER CONTACTS . . .    8.00        368    99.2   371     CRMSMC  
     SHIFTED CHAIN . . . . .    7.62        338    99.1   341     CRMSMC  
     ALTERNATIVE PARENT  . .    7.82         25   100.0    25     CRMSMC  
     SECONDARY STRUCTURE . .    8.98        131    98.5   133     CRMSMC  
     SHIFTED SS UNITS  . . .    3.02         29    96.7    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS    8.54        153    99.4   154     CRMSMC  
     SURFACE . . . . . . . .    8.36        261    98.9   264     CRMSMC  
     BURIED  . . . . . . . .    7.07        107   100.0   107     CRMSMC  
     CORE  . . . . . . . . .    7.60        215    99.1   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    8.52         64    22.5   284     CRMSSC  
     WELL ORDERED  . . . . .    8.52         64    22.5   284     CRMSSC  
     NO INTER CONTACTS . . .    8.52         64    22.5   284     CRMSSC  
     RELIABLE SIDE CHAINS  .    8.52         64    26.7   240     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   192     CRMSSC  
     SECONDARY STRUCTURE . .    9.30         23    23.2    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS    9.28         25    22.3   112     CRMSSC  
     SURFACE . . . . . . . .    9.01         45    20.3   222     CRMSSC  
     BURIED  . . . . . . . .    7.24         19    30.6    62     CRMSSC  
     CORE  . . . . . . . . .    8.00         39    22.7   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    8.00        368    62.6   588     CRMSALL 
     WELL ORDERED  . . . . .    8.00        368    62.6   588     CRMSALL 
     NO INTER CONTACTS . . .    8.00        368    62.6   588     CRMSALL 
     SHIFTED CHAIN . . . . .    7.62        338    62.4   542     CRMSALL 
     ALTERNATIVE PARENT  . .    7.82         25    55.6    45     CRMSALL 
     SECONDARY STRUCTURE . .    8.98        131    63.3   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS    8.54        153    63.8   240     CRMSALL 
     SURFACE . . . . . . . .    8.36        261    59.6   438     CRMSALL 
     BURIED  . . . . . . . .    7.07        107    71.3   150     CRMSALL 
     CORE  . . . . . . . . .    7.60        215    61.8   348     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1    15.31      7   100.0     7       1-AEIEVGR-7    
 CA  LOOP  2     4.52      3   100.0     3      26-GGG-28   
 CA  LOOP  3     5.48     10   100.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     3.92      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1    15.05     34   100.0    34       1-AEIEVGR-7    
 MC  LOOP  2     4.38     12   100.0    12      26-GGG-28   
 MC  LOOP  3     5.62     49    98.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     3.86     19   100.0    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1    15.05     34    64.2    53       1-AEIEVGR-7    
 ALL LOOP  2     4.38     12   100.0    12      26-GGG-28   
 ALL LOOP  3     5.62     49    56.3    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     3.86     19    54.3    35      65-RQGR-68   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     3.01      7   100.0     7       1-AEIEVGR-7    
 CA  LOOP  2     0.78      3   100.0     3      26-GGG-28   
 CA  LOOP  3     4.15     10   100.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     0.37      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     3.43     34   100.0    34       1-AEIEVGR-7    
 MC  LOOP  2     1.42     12   100.0    12      26-GGG-28   
 MC  LOOP  3     4.28     49    98.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     0.60     19   100.0    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     3.43     34    64.2    53       1-AEIEVGR-7    
 ALL LOOP  2     1.42     12   100.0    12      26-GGG-28   
 ALL LOOP  3     4.28     49    56.3    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     0.60     19    54.3    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 . . . . . . . . . .    6.518      1.000       0.500     76   100.0    76     ERRCA  
     WELL ORDERED  . . . . .    6.518      1.000       0.500     76   100.0    76     ERRCA  
     NO INTER CONTACTS . . .    6.518      1.000       0.500     76   100.0    76     ERRCA  
     SHIFTED CHAIN . . . . .    6.220      1.000       0.500     70   100.0    70     ERRCA  
     ALTERNATIVE PARENT  . .    5.791      1.000       0.500      5   100.0     5     ERRCA  
     SECONDARY STRUCTURE . .    7.445      1.000       0.500     27   100.0    27     ERRCA  
     LARGE SHIFTS/INSERTIONS    7.010      1.000       0.500     32   100.0    32     ERRCA  
     SURFACE . . . . . . . .    6.665      1.000       0.500     54   100.0    54     ERRCA  
     BURIED  . . . . . . . .    6.156      1.000       0.500     22   100.0    22     ERRCA  
     CORE  . . . . . . . . .    6.160      1.000       0.500     44   100.0    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    6.564      1.000       0.500    368    99.2   371     ERRMC  
     WELL ORDERED  . . . . .    6.564      1.000       0.500    368    99.2   371     ERRMC  
     NO INTER CONTACTS . . .    6.564      1.000       0.500    368    99.2   371     ERRMC  
     SHIFTED CHAIN . . . . .    6.231      1.000       0.500    338    99.1   341     ERRMC  
     ALTERNATIVE PARENT  . .    5.648      1.000       0.500     25   100.0    25     ERRMC  
     SECONDARY STRUCTURE . .    7.464      1.000       0.500    131    98.5   133     ERRMC  
     LARGE SHIFTS/INSERTIONS    7.044      1.000       0.500    153    99.4   154     ERRMC  
     SURFACE . . . . . . . .    6.749      1.000       0.500    261    98.9   264     ERRMC  
     BURIED  . . . . . . . .    6.110      1.000       0.500    107   100.0   107     ERRMC  
     CORE  . . . . . . . . .    6.222      1.000       0.500    215    99.1   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.226      1.000       0.500     64    22.5   284     ERRSC  
     WELL ORDERED  . . . . .    7.226      1.000       0.500     64    22.5   284     ERRSC  
     NO INTER CONTACTS . . .    7.226      1.000       0.500     64    22.5   284     ERRSC  
     RELIABLE SIDE CHAINS  .    7.226      1.000       0.500     64    26.7   240     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   192     ERRSC  
     SHIFTED CHAIN . . . . .    6.877      1.000       0.500     58    22.1   262     ERRSC  
     ALTERNATIVE PARENT  . .    7.380      1.000       0.500      5    20.0    25     ERRSC  
     SECONDARY STRUCTURE . .    7.881      1.000       0.500     23    23.2    99     ERRSC  
     LARGE SHIFTS/INSERTIONS    7.990      1.000       0.500     25    22.3   112     ERRSC  
     SURFACE . . . . . . . .    7.593      1.000       0.500     45    20.3   222     ERRSC  
     BURIED  . . . . . . . .    6.355      1.000       0.500     19    30.6    62     ERRSC  
     CORE  . . . . . . . . .    6.735      1.000       0.500     39    22.7   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    6.564      1.000       0.500    368    62.6   588     ERRALL 
     WELL ORDERED  . . . . .    6.564      1.000       0.500    368    62.6   588     ERRALL 
     NO INTER CONTACTS . . .    6.564      1.000       0.500    368    62.6   588     ERRALL 
     SHIFTED CHAIN . . . . .    6.231      1.000       0.500    338    62.4   542     ERRALL 
     ALTERNATIVE PARENT  . .    5.648      1.000       0.500     25    55.6    45     ERRALL 
     SECONDARY STRUCTURE . .    7.464      1.000       0.500    131    63.3   207     ERRALL 
     LARGE SHIFTS/INSERTIONS    7.044      1.000       0.500    153    63.8   240     ERRALL 
     SURFACE . . . . . . . .    6.749      1.000       0.500    261    59.6   438     ERRALL 
     BURIED  . . . . . . . .    6.110      1.000       0.500    107    71.3   150     ERRALL 
     CORE  . . . . . . . . .    6.222      1.000       0.500    215    61.8   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)         2        11        19        37        60      76      76   DISTCA 
CA  (P)      2.63     14.47     25.00     48.68     78.95              76   DISTCA 
CA  (RMS)    0.66      1.53      1.87      3.10      5.11                   DISTCA 
 
ALL (N)         8        54        83       182       291     368     588   DISTALL 
ALL (P)      1.36      9.18     14.12     30.95     49.49             588   DISTALL 
ALL (RMS)    0.77      1.48      1.85      3.20      5.17                   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            44            32          RMSLSI 
CA  (P)       57.89         57.89         42.11          RMSLSI 
CA  (RMS)      1.67          7.54          8.55          RMSLSI 
 
 
 
END of the results output 
