 
####################################################### 
#                                                     # 
#                        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:     # 
#                        # 
########################## 
# 
CONANA-INTER           ../CONANA/T0073.inter 
CONANA-PAIR            ../CONANA/T0073.pair 
# 
NUMBER-OF-PARENTS      1 
ALIGNMENT-DALI(1)      ../PARENTS/casp3.T0073.1cos.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 358 atoms, MODEL 93 atoms, 93 common with TARGET 
           Number of atoms possible to evaluate: 93 
 
 
 CA-RMS TARGET<->PARENT(1cos)	 1.128383 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    94     ARMSMC  
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    94     ARMSMC  
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    19     ARMSMC  
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    46     ARMSMC  
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSMC  
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    82     ARMSMC  
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    17     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    87     ARMSMC  
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     7     ARMSMC  
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    77     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    37     ARMSSC1 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    37     ARMSSC1 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0     6     ARMSSC1 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    37     ARMSSC1 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    27     ARMSSC1 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    17     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    32     ARMSSC1 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     7     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    34     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     3     ARMSSC1 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    30     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    32     ARMSSC2 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    29     ARMSSC2 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0     5     ARMSSC2 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    20     ARMSSC2 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    19     ARMSSC2 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    13     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    29     ARMSSC2 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     6     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    29     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     3     ARMSSC2 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    26     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    18     ARMSSC3 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    15     ARMSSC3 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0     3     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    15     ARMSSC3 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    17     ARMSSC3 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0     8     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    16     ARMSSC3 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     3     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    18     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    15     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0     8     ARMSSC4 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0     5     ARMSSC4 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0     1     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0     8     ARMSSC4 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0     7     ARMSSC4 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0     5     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0     7     ARMSSC4 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     2     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0     8     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) =   0.39667     r(1,2) =  -0.53089     r(1,3) =   0.74887 
 r(2,1) =  -0.80098     r(2,2) =  -0.59869     r(2,3) =  -0.00016 
 r(3,1) =   0.44843     r(3,2) =  -0.59977     r(3,3) =  -0.66271 
THE OFFSET VECTOR: 
 v(1) =   9.58093     v(2) =  33.52651     v(3) =  12.00373 
 
 Number of iteration 43                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.20           (Number of atoms:   24) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    7.31         48   100.0    48     CRMSCA  
     CRN = ALL/NP  . . . . .    0.1522                            CRMSCA  
     WELL ORDERED  . . . . .    7.31         48   100.0    48     CRMSCA  
     NO INTER CONTACTS . . .    8.14         10   100.0    10     CRMSCA  
     SHIFTED CHAIN . . . . .    9.45         24   100.0    24     CRMSCA  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSCA  
     SECONDARY STRUCTURE . .    6.05         41   100.0    41     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS   13.43          9   100.0     9     CRMSCA  
     SURFACE . . . . . . . .    6.97         44   100.0    44     CRMSCA  
     BURIED  . . . . . . . .   10.32          4   100.0     4     CRMSCA  
     CORE  . . . . . . . . .    4.91         39   100.0    39     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    6.97         93    39.2   237     CRMSMC  
     WELL ORDERED  . . . . .    6.97         93    39.2   237     CRMSMC  
     NO INTER CONTACTS . . .    6.87         18    38.3    47     CRMSMC  
     SHIFTED CHAIN . . . . .    9.02         45    38.5   117     CRMSMC  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSMC  
     SECONDARY STRUCTURE . .    6.07         82    40.0   205     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS   12.67         17    39.5    43     CRMSMC  
     SURFACE . . . . . . . .    6.88         86    39.3   219     CRMSMC  
     BURIED  . . . . . . . .    7.98          7    38.9    18     CRMSMC  
     CORE  . . . . . . . . .    4.86         76    39.2   194     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    6.60         45    26.9   167     CRMSSC  
     WELL ORDERED  . . . . .    6.60         45    28.8   156     CRMSSC  
     NO INTER CONTACTS . . .    4.83          8    30.8    26     CRMSSC  
     RELIABLE SIDE CHAINS  .    6.60         45    32.8   137     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   100     CRMSSC  
     SECONDARY STRUCTURE . .    6.08         41    28.1   146     CRMSSC  
     LARGE SHIFTS/INSERTIONS   11.75          8    24.2    33     CRMSSC  
     SURFACE . . . . . . . .    6.79         42    27.1   155     CRMSSC  
     BURIED  . . . . . . . .    2.58          3    25.0    12     CRMSSC  
     CORE  . . . . . . . . .    4.81         37    27.6   134     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    6.97         93    26.0   358     CRMSALL 
     WELL ORDERED  . . . . .    6.97         93    26.8   347     CRMSALL 
     NO INTER CONTACTS . . .    6.87         18    27.7    65     CRMSALL 
     SHIFTED CHAIN . . . . .    9.02         45    26.3   171     CRMSALL 
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSALL 
     SECONDARY STRUCTURE . .    6.07         82    26.5   310     CRMSALL 
     LARGE SHIFTS/INSERTIONS   12.67         17    25.0    68     CRMSALL 
     SURFACE . . . . . . . .    6.88         86    26.0   331     CRMSALL 
     BURIED  . . . . . . . .    7.98          7    25.9    27     CRMSALL 
     CORE  . . . . . . . . .    4.86         76    26.2   290     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1    14.16      8   100.0     8      41-SKLQALKG-48   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1    13.42     15    39.5    38      41-SKLQALKG-48   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1    13.42     15    26.3    57      41-SKLQALKG-48   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     0.41      8   100.0     8      41-SKLQALKG-48   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     0.51     15    39.5    38      41-SKLQALKG-48   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     0.51     15    26.3    57      41-SKLQALKG-48   
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.294      0.481       0.270     48   100.0    48     ERRCA  
     WELL ORDERED  . . . . .    4.294      0.481       0.270     48   100.0    48     ERRCA  
     NO INTER CONTACTS . . .    4.506      0.418       0.220     10   100.0    10     ERRCA  
     SHIFTED CHAIN . . . . .    6.450      0.611       0.326     24   100.0    24     ERRCA  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRCA  
     SECONDARY STRUCTURE . .    3.396      0.436       0.253     41   100.0    41     ERRCA  
     LARGE SHIFTS/INSERTIONS   11.285      0.816       0.408      9   100.0     9     ERRCA  
     SURFACE . . . . . . . .    4.151      0.485       0.275     44   100.0    44     ERRCA  
     BURIED  . . . . . . . .    5.866      0.437       0.219      4   100.0     4     ERRCA  
     CORE  . . . . . . . . .    2.681      0.403       0.239     39   100.0    39     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.097      0.478       0.270     93    39.2   237     ERRMC  
     WELL ORDERED  . . . . .    4.097      0.478       0.270     93    39.2   237     ERRMC  
     NO INTER CONTACTS . . .    3.707      0.421       0.225     18    38.3    47     ERRMC  
     SHIFTED CHAIN . . . . .    6.131      0.605       0.327     45    38.5   117     ERRMC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRMC  
     SECONDARY STRUCTURE . .    3.454      0.445       0.258     82    40.0   205     ERRMC  
     LARGE SHIFTS/INSERTIONS   10.529      0.801       0.400     17    39.5    43     ERRMC  
     SURFACE . . . . . . . .    4.117      0.488       0.278     86    39.3   219     ERRMC  
     BURIED  . . . . . . . .    3.853      0.359       0.180      7    38.9    18     ERRMC  
     CORE  . . . . . . . . .    2.658      0.406       0.241     76    39.2   194     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.886      0.476       0.270     45    26.9   167     ERRSC  
     WELL ORDERED  . . . . .    3.886      0.476       0.270     45    28.8   156     ERRSC  
     NO INTER CONTACTS . . .    2.709      0.423       0.231      8    30.8    26     ERRSC  
     RELIABLE SIDE CHAINS  .    3.886      0.476       0.270     45    32.8   137     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   100     ERRSC  
     SHIFTED CHAIN . . . . .    5.766      0.600       0.328     21    27.6    76     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRSC  
     SECONDARY STRUCTURE . .    3.512      0.455       0.263     41    28.1   146     ERRSC  
     LARGE SHIFTS/INSERTIONS    9.679      0.783       0.392      8    24.2    33     ERRSC  
     SURFACE . . . . . . . .    4.080      0.491       0.280     42    27.1   155     ERRSC  
     BURIED  . . . . . . . .    1.169      0.255       0.128      3    25.0    12     ERRSC  
     CORE  . . . . . . . . .    2.634      0.409       0.244     37    27.6   134     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.097      0.478       0.270     93    26.0   358     ERRALL 
     WELL ORDERED  . . . . .    4.097      0.478       0.270     93    26.8   347     ERRALL 
     NO INTER CONTACTS . . .    3.707      0.421       0.225     18    27.7    65     ERRALL 
     SHIFTED CHAIN . . . . .    6.131      0.605       0.327     45    26.3   171     ERRALL 
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRALL 
     SECONDARY STRUCTURE . .    3.454      0.445       0.258     82    26.5   310     ERRALL 
     LARGE SHIFTS/INSERTIONS   10.529      0.801       0.400     17    25.0    68     ERRALL 
     SURFACE . . . . . . . .    4.117      0.488       0.278     86    26.0   331     ERRALL 
     BURIED  . . . . . . . .    3.853      0.359       0.180      7    25.9    27     ERRALL 
     CORE  . . . . . . . . .    2.658      0.406       0.241     76    26.2   290     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)        12        22        24        28        40      48      48   DISTCA 
CA  (P)     25.00     45.83     50.00     58.33     83.33              48   DISTCA 
CA  (RMS)    0.70      1.02      1.20      1.86      4.45                   DISTCA 
 
ALL (N)        23        41        47        57        79      93     358   DISTALL 
ALL (P)      6.42     11.45     13.13     15.92     22.07             358   DISTALL 
ALL (RMS)    0.69      1.00      1.30      2.02      4.43                   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)          39            39             9          RMSLSI 
CA  (P)       81.25         81.25         18.75          RMSLSI 
CA  (RMS)      1.02          4.91         13.43          RMSLSI 
 
 
 
END of the results output 
