 
####################################################### 
#                                                     # 
#                        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 456 atoms, 399 common with TARGET 
           Number of atoms possible to evaluate: 307 
 
 
 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 . . . . . . . . . .    75.19           38.5   122    81.3   150     ARMSMC  
     WELL ORDERED  . . . . .    75.19           38.5   122    81.3   150     ARMSMC  
     NO INTER CONTACTS . . .    75.19           38.5   122    81.3   150     ARMSMC  
     SHIFTED CHAIN . . . . .    77.71           36.4   110    79.7   138     ARMSMC  
     ALTERNATIVE PARENT  . .    75.89            0.0     8    80.0    10     ARMSMC  
     SECONDARY STRUCTURE . .    60.51           51.0    49    90.7    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS    97.11           13.2    38    61.3    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    77.89           39.3    84    79.2   106     ARMSMC  
     BURIED  . . . . . . . .    68.82           36.8    38    86.4    44     ARMSMC  
     CORE  . . . . . . . . .    62.81           50.0    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) =  -0.78990     r(1,2) =  -0.06136     r(1,3) =  -0.61016 
 r(2,1) =  -0.24712     r(2,2) =  -0.87877     r(2,3) =   0.40829 
 r(3,1) =  -0.56124     r(3,2) =   0.47329     r(3,3) =   0.67897 
THE OFFSET VECTOR: 
 v(1) =  21.04653     v(2) =  17.23485     v(3) =  -5.66982 
 
 Number of iteration  4                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.43           (Number of atoms:   36) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    3.79         64    84.2    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0592                            CRMSCA  
     WELL ORDERED  . . . . .    3.79         64    84.2    76     CRMSCA  
     NO INTER CONTACTS . . .    3.79         64    84.2    76     CRMSCA  
     SHIFTED CHAIN . . . . .    3.85         58    82.9    70     CRMSCA  
     ALTERNATIVE PARENT  . .    4.71          4    80.0     5     CRMSCA  
     SECONDARY STRUCTURE . .    3.15         26    96.3    27     CRMSCA  
     SHIFTED SS UNITS  . . .    1.21          6   100.0     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS    4.74         20    62.5    32     CRMSCA  
     SURFACE . . . . . . . .    3.96         44    81.5    54     CRMSCA  
     BURIED  . . . . . . . .    3.38         20    90.9    22     CRMSCA  
     CORE  . . . . . . . . .    3.27         44   100.0    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    3.87        307    82.7   371     CRMSMC  
     WELL ORDERED  . . . . .    3.87        307    82.7   371     CRMSMC  
     NO INTER CONTACTS . . .    3.87        307    82.7   371     CRMSMC  
     SHIFTED CHAIN . . . . .    3.94        278    81.5   341     CRMSMC  
     ALTERNATIVE PARENT  . .    4.75         20    80.0    25     CRMSMC  
     SECONDARY STRUCTURE . .    3.29        128    96.2   133     CRMSMC  
     SHIFTED SS UNITS  . . .    1.33         30   100.0    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS    4.82         92    59.7   154     CRMSMC  
     SURFACE . . . . . . . .    4.02        210    79.5   264     CRMSMC  
     BURIED  . . . . . . . .    3.51         97    90.7   107     CRMSMC  
     CORE  . . . . . . . . .    3.38        215    99.1   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    4.07         51    18.0   284     CRMSSC  
     WELL ORDERED  . . . . .    4.07         51    18.0   284     CRMSSC  
     NO INTER CONTACTS . . .    4.07         51    18.0   284     CRMSSC  
     RELIABLE SIDE CHAINS  .    4.07         51    21.2   240     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   192     CRMSSC  
     SECONDARY STRUCTURE . .    3.37         24    24.2    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS    5.48         12    10.7   112     CRMSSC  
     SURFACE . . . . . . . .    4.21         34    15.3   222     CRMSSC  
     BURIED  . . . . . . . .    3.77         17    27.4    62     CRMSSC  
     CORE  . . . . . . . . .    3.52         39    22.7   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    3.87        307    52.2   588     CRMSALL 
     WELL ORDERED  . . . . .    3.87        307    52.2   588     CRMSALL 
     NO INTER CONTACTS . . .    3.87        307    52.2   588     CRMSALL 
     SHIFTED CHAIN . . . . .    3.94        278    51.3   542     CRMSALL 
     ALTERNATIVE PARENT  . .    4.75         20    44.4    45     CRMSALL 
     SECONDARY STRUCTURE . .    3.29        128    61.8   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS    4.82         92    38.3   240     CRMSALL 
     SURFACE . . . . . . . .    4.02        210    47.9   438     CRMSALL 
     BURIED  . . . . . . . .    3.51         97    64.7   150     CRMSALL 
     CORE  . . . . . . . . .    3.38        215    61.8   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     3.81      3   100.0     3      26-GGG-28   
 CA  LOOP  3     4.57      6    60.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     5.88      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     3.68     12   100.0    12      26-GGG-28   
 MC  LOOP  3     4.34     28    56.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     6.02     18    94.7    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     3.68     12   100.0    12      26-GGG-28   
 ALL LOOP  3     4.34     28    32.2    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     6.02     18    51.4    35      65-RQGR-68   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 CA  LOOP  2     0.05      3   100.0     3      26-GGG-28   
 CA  LOOP  3     2.34      6    60.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     1.23      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     1.53     12   100.0    12      26-GGG-28   
 MC  LOOP  3     2.40     28    56.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     1.90     18    94.7    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 ALL LOOP  2     1.53     12   100.0    12      26-GGG-28   
 ALL LOOP  3     2.40     28    32.2    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     1.90     18    51.4    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 . . . . . . . . . .    3.060      1.000       0.500     64    84.2    76     ERRCA  
     WELL ORDERED  . . . . .    3.060      1.000       0.500     64    84.2    76     ERRCA  
     NO INTER CONTACTS . . .    3.060      1.000       0.500     64    84.2    76     ERRCA  
     SHIFTED CHAIN . . . . .    3.147      1.000       0.500     58    82.9    70     ERRCA  
     ALTERNATIVE PARENT  . .    4.090      1.000       0.500      4    80.0     5     ERRCA  
     SECONDARY STRUCTURE . .    2.421      1.000       0.500     26    96.3    27     ERRCA  
     LARGE SHIFTS/INSERTIONS    4.365      1.000       0.500     20    62.5    32     ERRCA  
     SURFACE . . . . . . . .    3.253      1.000       0.500     44    81.5    54     ERRCA  
     BURIED  . . . . . . . .    2.638      1.000       0.500     20    90.9    22     ERRCA  
     CORE  . . . . . . . . .    2.467      1.000       0.500     44   100.0    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.139      1.000       0.500    307    82.7   371     ERRMC  
     WELL ORDERED  . . . . .    3.139      1.000       0.500    307    82.7   371     ERRMC  
     NO INTER CONTACTS . . .    3.139      1.000       0.500    307    82.7   371     ERRMC  
     SHIFTED CHAIN . . . . .    3.226      1.000       0.500    278    81.5   341     ERRMC  
     ALTERNATIVE PARENT  . .    4.171      1.000       0.500     20    80.0    25     ERRMC  
     SECONDARY STRUCTURE . .    2.565      1.000       0.500    128    96.2   133     ERRMC  
     LARGE SHIFTS/INSERTIONS    4.356      1.000       0.500     92    59.7   154     ERRMC  
     SURFACE . . . . . . . .    3.315      1.000       0.500    210    79.5   264     ERRMC  
     BURIED  . . . . . . . .    2.760      1.000       0.500     97    90.7   107     ERRMC  
     CORE  . . . . . . . . .    2.619      1.000       0.500    215    99.1   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.230      1.000       0.500     51    18.0   284     ERRSC  
     WELL ORDERED  . . . . .    3.230      1.000       0.500     51    18.0   284     ERRSC  
     NO INTER CONTACTS . . .    3.230      1.000       0.500     51    18.0   284     ERRSC  
     RELIABLE SIDE CHAINS  .    3.230      1.000       0.500     51    21.2   240     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   192     ERRSC  
     SHIFTED CHAIN . . . . .    3.360      1.000       0.500     46    17.6   262     ERRSC  
     ALTERNATIVE PARENT  . .    4.281      1.000       0.500      4    16.0    25     ERRSC  
     SECONDARY STRUCTURE . .    2.677      1.000       0.500     24    24.2    99     ERRSC  
     LARGE SHIFTS/INSERTIONS    4.838      1.000       0.500     12    10.7   112     ERRSC  
     SURFACE . . . . . . . .    3.369      1.000       0.500     34    15.3   222     ERRSC  
     BURIED  . . . . . . . .    2.951      1.000       0.500     17    27.4    62     ERRSC  
     CORE  . . . . . . . . .    2.735      1.000       0.500     39    22.7   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.139      1.000       0.500    307    52.2   588     ERRALL 
     WELL ORDERED  . . . . .    3.139      1.000       0.500    307    52.2   588     ERRALL 
     NO INTER CONTACTS . . .    3.139      1.000       0.500    307    52.2   588     ERRALL 
     SHIFTED CHAIN . . . . .    3.226      1.000       0.500    278    51.3   542     ERRALL 
     ALTERNATIVE PARENT  . .    4.171      1.000       0.500     20    44.4    45     ERRALL 
     SECONDARY STRUCTURE . .    2.565      1.000       0.500    128    61.8   207     ERRALL 
     LARGE SHIFTS/INSERTIONS    4.356      1.000       0.500     92    38.3   240     ERRALL 
     SURFACE . . . . . . . .    3.315      1.000       0.500    210    47.9   438     ERRALL 
     BURIED  . . . . . . . .    2.760      1.000       0.500     97    64.7   150     ERRALL 
     CORE  . . . . . . . . .    2.619      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)        13        29        37        49        64      64      76   DISTCA 
CA  (P)     17.11     38.16     48.68     64.47     84.21              76   DISTCA 
CA  (RMS)    0.77      1.15      1.49      2.43      3.79                   DISTCA 
 
ALL (N)        49       141       175       234       306     307     588   DISTALL 
ALL (P)      8.33     23.98     29.76     39.80     52.04             588   DISTALL 
ALL (RMS)    0.74      1.29      1.57      2.45      3.83                   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            20          RMSLSI 
CA  (P)       57.89         57.89         26.32          RMSLSI 
CA  (RMS)      1.67          3.27          4.74          RMSLSI 
 
 
 
END of the results output 
