 
####################################################### 
#                                                     # 
#                        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 416 atoms, 377 common with TARGET 
           Number of atoms possible to evaluate: 334 
 
 
 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 . . . . . . . . . .    77.87           47.0   134    89.3   150     ARMSMC  
     WELL ORDERED  . . . . .    77.87           47.0   134    89.3   150     ARMSMC  
     NO INTER CONTACTS . . .    77.87           47.0   134    89.3   150     ARMSMC  
     SHIFTED CHAIN . . . . .    79.82           46.4   125    90.6   138     ARMSMC  
     ALTERNATIVE PARENT  . .    73.13           30.0    10   100.0    10     ARMSMC  
     SECONDARY STRUCTURE . .    79.56           36.0    50    92.6    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS    89.51           40.0    50    80.6    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    73.80           51.6    93    87.7   106     ARMSMC  
     BURIED  . . . . . . . .    86.39           36.6    41    93.2    44     ARMSMC  
     CORE  . . . . . . . . .    70.03           51.2    84    95.5    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) =   0.86475     r(1,2) =  -0.18195     r(1,3) =   0.46808 
 r(2,1) =  -0.09309     r(2,2) =  -0.97398     r(2,3) =  -0.20663 
 r(3,1) =   0.49349     r(3,2) =   0.13511     r(3,3) =  -0.85919 
THE OFFSET VECTOR: 
 v(1) = -94.63953     v(2) =  -2.74574     v(3) =  -6.80497 
 
 Number of iteration  3                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.65           (Number of atoms:    8) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    9.21         70    92.1    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.1315                            CRMSCA  
     WELL ORDERED  . . . . .    9.21         70    92.1    76     CRMSCA  
     NO INTER CONTACTS . . .    9.21         70    92.1    76     CRMSCA  
     SHIFTED CHAIN . . . . .    9.32         65    92.9    70     CRMSCA  
     ALTERNATIVE PARENT  . .   10.89          5   100.0     5     CRMSCA  
     SECONDARY STRUCTURE . .    9.86         26    96.3    27     CRMSCA  
     SHIFTED SS UNITS  . . .   11.09          6   100.0     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS   10.33         27    84.4    32     CRMSCA  
     SURFACE . . . . . . . .    9.57         49    90.7    54     CRMSCA  
     BURIED  . . . . . . . .    8.29         21    95.5    22     CRMSCA  
     CORE  . . . . . . . . .    8.42         43    97.7    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    9.28        334    90.0   371     CRMSMC  
     WELL ORDERED  . . . . .    9.28        334    90.0   371     CRMSMC  
     NO INTER CONTACTS . . .    9.28        334    90.0   371     CRMSMC  
     SHIFTED CHAIN . . . . .    9.37        309    90.6   341     CRMSMC  
     ALTERNATIVE PARENT  . .   10.92         25   100.0    25     CRMSMC  
     SECONDARY STRUCTURE . .    9.97        123    92.5   133     CRMSMC  
     SHIFTED SS UNITS  . . .   11.20         29    96.7    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS   10.34        129    83.8   154     CRMSMC  
     SURFACE . . . . . . . .    9.56        236    89.4   264     CRMSMC  
     BURIED  . . . . . . . .    8.58         98    91.6   107     CRMSMC  
     CORE  . . . . . . . . .    8.55        205    94.5   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    9.67         54    19.0   284     CRMSSC  
     WELL ORDERED  . . . . .    9.67         54    19.0   284     CRMSSC  
     NO INTER CONTACTS . . .    9.67         54    19.0   284     CRMSSC  
     RELIABLE SIDE CHAINS  .    9.67         54    22.5   240     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   192     CRMSSC  
     SECONDARY STRUCTURE . .   10.39         19    19.2    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS   11.14         21    18.8   112     CRMSSC  
     SURFACE . . . . . . . .   10.02         40    18.0   222     CRMSSC  
     BURIED  . . . . . . . .    8.61         14    22.6    62     CRMSSC  
     CORE  . . . . . . . . .    8.61         33    19.2   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    9.28        334    56.8   588     CRMSALL 
     WELL ORDERED  . . . . .    9.28        334    56.8   588     CRMSALL 
     NO INTER CONTACTS . . .    9.28        334    56.8   588     CRMSALL 
     SHIFTED CHAIN . . . . .    9.37        309    57.0   542     CRMSALL 
     ALTERNATIVE PARENT  . .   10.92         25    55.6    45     CRMSALL 
     SECONDARY STRUCTURE . .    9.97        123    59.4   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS   10.34        129    53.8   240     CRMSALL 
     SURFACE . . . . . . . .    9.56        236    53.9   438     CRMSALL 
     BURIED  . . . . . . . .    8.58         98    65.3   150     CRMSALL 
     CORE  . . . . . . . . .    8.55        205    58.9   348     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1    14.25      5    71.4     7       1-AEIEVGR-7    
 CA  LOOP  2    10.21      3   100.0     3      26-GGG-28   
 CA  LOOP  3     2.94      7    70.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     5.05      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1    14.14     24    70.6    34       1-AEIEVGR-7    
 MC  LOOP  2     9.27     12   100.0    12      26-GGG-28   
 MC  LOOP  3     3.23     35    70.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     5.18     19   100.0    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1    14.14     24    45.3    53       1-AEIEVGR-7    
 ALL LOOP  2     9.27     12   100.0    12      26-GGG-28   
 ALL LOOP  3     3.23     35    40.2    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     5.18     19    54.3    35      65-RQGR-68   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     1.86      5    71.4     7       1-AEIEVGR-7    
 CA  LOOP  2     0.08      3   100.0     3      26-GGG-28   
 CA  LOOP  3     2.72      7    70.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     2.14      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.45     24    70.6    34       1-AEIEVGR-7    
 MC  LOOP  2     1.75     12   100.0    12      26-GGG-28   
 MC  LOOP  3     3.08     35    70.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     2.37     19   100.0    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     2.45     24    45.3    53       1-AEIEVGR-7    
 ALL LOOP  2     1.75     12   100.0    12      26-GGG-28   
 ALL LOOP  3     3.08     35    40.2    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     2.37     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 . . . . . . . . . .    8.157      1.000       0.500     70    92.1    76     ERRCA  
     WELL ORDERED  . . . . .    8.157      1.000       0.500     70    92.1    76     ERRCA  
     NO INTER CONTACTS . . .    8.157      1.000       0.500     70    92.1    76     ERRCA  
     SHIFTED CHAIN . . . . .    8.238      1.000       0.500     65    92.9    70     ERRCA  
     ALTERNATIVE PARENT  . .    9.779      1.000       0.500      5   100.0     5     ERRCA  
     SECONDARY STRUCTURE . .    9.346      1.000       0.500     26    96.3    27     ERRCA  
     LARGE SHIFTS/INSERTIONS    8.821      1.000       0.500     27    84.4    32     ERRCA  
     SURFACE . . . . . . . .    8.489      1.000       0.500     49    90.7    54     ERRCA  
     BURIED  . . . . . . . .    7.383      1.000       0.500     21    95.5    22     ERRCA  
     CORE  . . . . . . . . .    7.741      1.000       0.500     43    97.7    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    8.242      1.000       0.500    334    90.0   371     ERRMC  
     WELL ORDERED  . . . . .    8.242      1.000       0.500    334    90.0   371     ERRMC  
     NO INTER CONTACTS . . .    8.242      1.000       0.500    334    90.0   371     ERRMC  
     SHIFTED CHAIN . . . . .    8.288      1.000       0.500    309    90.6   341     ERRMC  
     ALTERNATIVE PARENT  . .    9.849      1.000       0.500     25   100.0    25     ERRMC  
     SECONDARY STRUCTURE . .    9.477      1.000       0.500    123    92.5   133     ERRMC  
     LARGE SHIFTS/INSERTIONS    8.777      1.000       0.500    129    83.8   154     ERRMC  
     SURFACE . . . . . . . .    8.465      1.000       0.500    236    89.4   264     ERRMC  
     BURIED  . . . . . . . .    7.703      1.000       0.500     98    91.6   107     ERRMC  
     CORE  . . . . . . . . .    7.904      1.000       0.500    205    94.5   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    8.648      1.000       0.500     54    19.0   284     ERRSC  
     WELL ORDERED  . . . . .    8.648      1.000       0.500     54    19.0   284     ERRSC  
     NO INTER CONTACTS . . .    8.648      1.000       0.500     54    19.0   284     ERRSC  
     RELIABLE SIDE CHAINS  .    8.648      1.000       0.500     54    22.5   240     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   192     ERRSC  
     SHIFTED CHAIN . . . . .    8.712      1.000       0.500     49    18.7   262     ERRSC  
     ALTERNATIVE PARENT  . .   10.292      1.000       0.500      5    20.0    25     ERRSC  
     SECONDARY STRUCTURE . .    9.911      1.000       0.500     19    19.2    99     ERRSC  
     LARGE SHIFTS/INSERTIONS    9.650      1.000       0.500     21    18.8   112     ERRSC  
     SURFACE . . . . . . . .    8.948      1.000       0.500     40    18.0   222     ERRSC  
     BURIED  . . . . . . . .    7.792      1.000       0.500     14    22.6    62     ERRSC  
     CORE  . . . . . . . . .    8.010      1.000       0.500     33    19.2   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    8.242      1.000       0.500    334    56.8   588     ERRALL 
     WELL ORDERED  . . . . .    8.242      1.000       0.500    334    56.8   588     ERRALL 
     NO INTER CONTACTS . . .    8.242      1.000       0.500    334    56.8   588     ERRALL 
     SHIFTED CHAIN . . . . .    8.288      1.000       0.500    309    57.0   542     ERRALL 
     ALTERNATIVE PARENT  . .    9.849      1.000       0.500     25    55.6    45     ERRALL 
     SECONDARY STRUCTURE . .    9.477      1.000       0.500    123    59.4   207     ERRALL 
     LARGE SHIFTS/INSERTIONS    8.777      1.000       0.500    129    53.8   240     ERRALL 
     SURFACE . . . . . . . .    8.465      1.000       0.500    236    53.9   438     ERRALL 
     BURIED  . . . . . . . .    7.703      1.000       0.500     98    65.3   150     ERRALL 
     CORE  . . . . . . . . .    7.904      1.000       0.500    205    58.9   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         7         9        22        47      70      76   DISTCA 
CA  (P)      0.00      9.21     11.84     28.95     61.84              76   DISTCA 
CA  (RMS)    0.00      1.50      1.79      3.57      6.40                   DISTCA 
 
ALL (N)         2        21        38        88       225     334     588   DISTALL 
ALL (P)      0.34      3.57      6.46     14.97     38.27             588   DISTALL 
ALL (RMS)    0.64      1.48      2.01      3.32      6.44                   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            43            27          RMSLSI 
CA  (P)       57.89         56.58         35.53          RMSLSI 
CA  (RMS)      1.67          8.42         10.33          RMSLSI 
 
 
 
END of the results output 
