 
####################################################### 
#                                                     # 
#                        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      4 
ALIGNMENT-DALI(1)      ../PARENTS/casp3.T0076_1.1cfd.rot 
ALIGNMENT-DALI(2)      ../PARENTS/casp3.T0076_1.1ncx.rot 
ALIGNMENT-DALI(3)      ../PARENTS/casp3.T0076_1.1a2x_A.rot 
ALIGNMENT-DALI(4)      ../PARENTS/casp3.T0076_1.5icb.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 1087 atoms, MODEL 1623 atoms, 674 common with TARGET 
           Number of atoms possible to evaluate: 674 
 
 
 CA-RMS TARGET<->PARENT(1cfd)	 2.655663 
 
 CA-RMS TARGET<->PARENT(1ncx)	 2.782501 
 
 CA-RMS TARGET<->PARENT(1a2x-A)	 3.224615 
 
 CA-RMS TARGET<->PARENT(5icb)	 2.843657 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    40.32           75.7   140   100.0   140     ARMSMC  
     WELL ORDERED  . . . . .    40.32           75.7   140   100.0   140     ARMSMC  
     NO INTER CONTACTS . . .    40.32           75.7   140   100.0   140     ARMSMC  
     SHIFTED CHAIN . . . . .    41.37           76.6   128   100.0   128     ARMSMC  
     ALTERNATIVE PARENT  . .    62.30           60.0    15   100.0    15     ARMSMC  
     SECONDARY STRUCTURE . .    10.52           96.9    64   100.0    64     ARMSMC  
     LARGE SHIFTS/INSERTIONS    57.83           58.3    48   100.0    48     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    42.21           71.8   110   100.0   110     ARMSMC  
     BURIED  . . . . . . . .    32.48           90.0    30   100.0    30     ARMSMC  
     CORE  . . . . . . . . .    27.00           84.8    92   100.0    92     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    90.88           35.5    62   100.0    62     ARMSSC1 
     WELL ORDERED  . . . . .    90.88           35.5    62   100.0    62     ARMSSC1 
     NO INTER CONTACTS . . .    90.88           35.5    62   100.0    62     ARMSSC1 
     RELIABLE SIDE CHAINS  .    89.69           36.7    60   100.0    60     ARMSSC1 
     CHANGED ANGLES  . . . .   106.01           15.8    38   100.0    38     ARMSSC1 
     SHIFTED CHAIN . . . . .    92.09           33.3    57   100.0    57     ARMSSC1 
     ALTERNATIVE PARENT  . .   108.19            0.0     6   100.0     6     ARMSSC1 
     SECONDARY STRUCTURE . .    90.98           35.7    28   100.0    28     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    97.13           30.0    20   100.0    20     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    87.51           34.7    49   100.0    49     ARMSSC1 
     BURIED  . . . . . . . .   102.58           38.5    13   100.0    13     ARMSSC1 
     CORE  . . . . . . . . .    87.74           38.1    42   100.0    42     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    81.14           29.2    48   100.0    48     ARMSSC2 
     WELL ORDERED  . . . . .    81.14           29.2    48   100.0    48     ARMSSC2 
     NO INTER CONTACTS . . .    81.14           29.2    48   100.0    48     ARMSSC2 
     RELIABLE SIDE CHAINS  .    70.93           37.8    37   100.0    37     ARMSSC2 
     CHANGED ANGLES  . . . .    85.06           28.9    38   100.0    38     ARMSSC2 
     SHIFTED CHAIN . . . . .    82.74           28.3    46   100.0    46     ARMSSC2 
     ALTERNATIVE PARENT  . .    36.83           50.0     4   100.0     4     ARMSSC2 
     SECONDARY STRUCTURE . .    85.86           39.1    23   100.0    23     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    88.86           14.3    14   100.0    14     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    79.05           29.7    37   100.0    37     ARMSSC2 
     BURIED  . . . . . . . .    87.80           27.3    11   100.0    11     ARMSSC2 
     CORE  . . . . . . . . .    77.73           35.3    34   100.0    34     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    86.23           23.5    17   100.0    17     ARMSSC3 
     WELL ORDERED  . . . . .    86.23           23.5    17   100.0    17     ARMSSC3 
     NO INTER CONTACTS . . .    86.23           23.5    17   100.0    17     ARMSSC3 
     RELIABLE SIDE CHAINS  .    89.03           23.1    13   100.0    13     ARMSSC3 
     CHANGED ANGLES  . . . .    86.70           25.0    16   100.0    16     ARMSSC3 
     SHIFTED CHAIN . . . . .    86.23           23.5    17   100.0    17     ARMSSC3 
     ALTERNATIVE PARENT  . .    16.60          100.0     2   100.0     2     ARMSSC3 
     SECONDARY STRUCTURE . .    67.59           36.4    11   100.0    11     ARMSSC3 
     LARGE SHIFTS/INSERTIONS   128.06            0.0     3   100.0     3     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    86.18           25.0    16   100.0    16     ARMSSC3 
     BURIED  . . . . . . . .    86.96            0.0     1   100.0     1     ARMSSC3 
     CORE  . . . . . . . . .    74.26           28.6    14   100.0    14     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    45.33           66.7     6   100.0     6     ARMSSC4 
     WELL ORDERED  . . . . .    45.33           66.7     6   100.0     6     ARMSSC4 
     NO INTER CONTACTS . . .    45.33           66.7     6   100.0     6     ARMSSC4 
     RELIABLE SIDE CHAINS  .    45.33           66.7     6   100.0     6     ARMSSC4 
     CHANGED ANGLES  . . . .    48.43           60.0     5   100.0     5     ARMSSC4 
     SHIFTED CHAIN . . . . .    45.33           66.7     6   100.0     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    49.46           66.7     3   100.0     3     ARMSSC4 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     0     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .    45.33           66.7     6   100.0     6     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .    45.33           66.7     6   100.0     6     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.94283     r(1,2) =   0.16652     r(1,3) =   0.28870 
 r(2,1) =  -0.28340     r(2,2) =  -0.85641     r(2,3) =  -0.43156 
 r(3,1) =   0.17538     r(3,2) =  -0.48870     r(3,3) =   0.85464 
THE OFFSET VECTOR: 
 v(1) =  -8.11297     v(2) =  11.81493     v(3) = -13.38118 
 
 Number of iteration  2                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.40           (Number of atoms:   49) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    3.31         71   100.0    71     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0466                            CRMSCA  
     WELL ORDERED  . . . . .    3.31         71   100.0    71     CRMSCA  
     NO INTER CONTACTS . . .    3.31         71   100.0    71     CRMSCA  
     SHIFTED CHAIN . . . . .    3.44         65   100.0    65     CRMSCA  
     ALTERNATIVE PARENT  . .    2.90          8   100.0     8     CRMSCA  
     SECONDARY STRUCTURE . .    2.09         32   100.0    32     CRMSCA  
     SHIFTED SS UNITS  . . .    2.68         16   100.0    16     CRMSCA  
     LARGE SHIFTS/INSERTIONS    5.23         25   100.0    25     CRMSCA  
     SURFACE . . . . . . . .    3.61         56   100.0    56     CRMSCA  
     BURIED  . . . . . . . .    1.80         15   100.0    15     CRMSCA  
     CORE  . . . . . . . . .    1.42         46   100.0    46     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    3.36        350   100.0   350     CRMSMC  
     WELL ORDERED  . . . . .    3.36        350   100.0   350     CRMSMC  
     NO INTER CONTACTS . . .    3.36        350   100.0   350     CRMSMC  
     SHIFTED CHAIN . . . . .    3.49        321   100.0   321     CRMSMC  
     ALTERNATIVE PARENT  . .    3.10         39   100.0    39     CRMSMC  
     SECONDARY STRUCTURE . .    2.06        159   100.0   159     CRMSMC  
     SHIFTED SS UNITS  . . .    2.62         80   100.0    80     CRMSMC  
     LARGE SHIFTS/INSERTIONS    5.28        123   100.0   123     CRMSMC  
     SURFACE . . . . . . . .    3.65        276   100.0   276     CRMSMC  
     BURIED  . . . . . . . .    1.92         74   100.0    74     CRMSMC  
     CORE  . . . . . . . . .    1.53        227   100.0   227     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    4.43        390    48.6   803     CRMSSC  
     WELL ORDERED  . . . . .    4.43        390    48.6   803     CRMSSC  
     NO INTER CONTACTS . . .    4.43        390    48.6   803     CRMSSC  
     RELIABLE SIDE CHAINS  .    4.19        354    46.2   767     CRMSSC  
     CHANGED ANGLES  . . . .    5.25        156   100.0   156     CRMSSC  
     SECONDARY STRUCTURE . .    3.14        182    46.2   394     CRMSSC  
     LARGE SHIFTS/INSERTIONS    6.73        112    47.9   234     CRMSSC  
     SURFACE . . . . . . . .    4.84        302    48.4   624     CRMSSC  
     BURIED  . . . . . . . .    2.52         88    49.2   179     CRMSSC  
     CORE  . . . . . . . . .    3.04        278    48.9   569     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    3.97        674    62.0  1087     CRMSALL 
     WELL ORDERED  . . . . .    3.97        674    62.0  1087     CRMSALL 
     NO INTER CONTACTS . . .    3.97        674    62.0  1087     CRMSALL 
     SHIFTED CHAIN . . . . .    4.10        611    60.9  1003     CRMSALL 
     ALTERNATIVE PARENT  . .    3.55         65    59.6   109     CRMSALL 
     SECONDARY STRUCTURE . .    2.72        310    59.4   522     CRMSALL 
     LARGE SHIFTS/INSERTIONS    6.00        212    63.5   334     CRMSALL 
     SURFACE . . . . . . . .    4.32        526    62.0   848     CRMSALL 
     BURIED  . . . . . . . .    2.28        148    61.9   239     CRMSALL 
     CORE  . . . . . . . . .    2.54        462    61.4   753     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     5.80      5   100.0     5       1-STDDS-5    
 CA  LOOP  2     4.05     12   100.0    12      33-ACGQNPTLAEIT-44   
 CA  LOOP  3     7.01      6   100.0     6      66-PNGFDM-71   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     5.90     25   100.0    25       1-STDDS-5    
 MC  LOOP  2     4.03     59   100.0    59      33-ACGQNPTLAEIT-44   
 MC  LOOP  3     7.07     29   100.0    29      66-PNGFDM-71   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     6.44     42    67.7    62       1-STDDS-5    
 ALL LOOP  2     4.89    100    61.0   164      33-ACGQNPTLAEIT-44   
 ALL LOOP  3     7.60     56    66.7    84      66-PNGFDM-71   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     1.16      5   100.0     5       1-STDDS-5    
 CA  LOOP  2     1.12     12   100.0    12      33-ACGQNPTLAEIT-44   
 CA  LOOP  3     2.30      6   100.0     6      66-PNGFDM-71   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     1.61     25   100.0    25       1-STDDS-5    
 MC  LOOP  2     1.14     59   100.0    59      33-ACGQNPTLAEIT-44   
 MC  LOOP  3     2.53     29   100.0    29      66-PNGFDM-71   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     2.46     42    67.7    62       1-STDDS-5    
 ALL LOOP  2     2.40    100    61.0   164      33-ACGQNPTLAEIT-44   
 ALL LOOP  3     3.52     56    66.7    84      66-PNGFDM-71   
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.208      0.458       0.452     71   100.0    71     ERRCA  
     WELL ORDERED  . . . . .    3.208      0.458       0.452     71   100.0    71     ERRCA  
     NO INTER CONTACTS . . .    3.208      0.458       0.452     71   100.0    71     ERRCA  
     SHIFTED CHAIN . . . . .    3.188      0.444       0.433     65   100.0    65     ERRCA  
     ALTERNATIVE PARENT  . .    3.338      0.487       0.509      8   100.0     8     ERRCA  
     SECONDARY STRUCTURE . .    3.496      0.511       0.528     32   100.0    32     ERRCA  
     LARGE SHIFTS/INSERTIONS    2.970      0.346       0.248     25   100.0    25     ERRCA  
     SURFACE . . . . . . . .    3.176      0.455       0.438     56   100.0    56     ERRCA  
     BURIED  . . . . . . . .    3.328      0.471       0.502     15   100.0    15     ERRCA  
     CORE  . . . . . . . . .    3.337      0.519       0.562     46   100.0    46     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.221      0.460       0.456    350   100.0   350     ERRMC  
     WELL ORDERED  . . . . .    3.221      0.460       0.456    350   100.0   350     ERRMC  
     NO INTER CONTACTS . . .    3.221      0.460       0.456    350   100.0   350     ERRMC  
     SHIFTED CHAIN . . . . .    3.198      0.445       0.436    321   100.0   321     ERRMC  
     ALTERNATIVE PARENT  . .    3.382      0.481       0.496     39   100.0    39     ERRMC  
     SECONDARY STRUCTURE . .    3.508      0.514       0.536    159   100.0   159     ERRMC  
     LARGE SHIFTS/INSERTIONS    3.007      0.353       0.264    123   100.0   123     ERRMC  
     SURFACE . . . . . . . .    3.174      0.453       0.435    276   100.0   276     ERRMC  
     BURIED  . . . . . . . .    3.398      0.486       0.531     74   100.0    74     ERRMC  
     CORE  . . . . . . . . .    3.337      0.518       0.560    227   100.0   227     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    2.951      0.364       0.341    390    48.6   803     ERRSC  
     WELL ORDERED  . . . . .    2.951      0.364       0.341    390    48.6   803     ERRSC  
     NO INTER CONTACTS . . .    2.951      0.364       0.341    390    48.6   803     ERRSC  
     RELIABLE SIDE CHAINS  .    2.925      0.370       0.349    354    46.2   767     ERRSC  
     CHANGED ANGLES  . . . .    2.898      0.318       0.280    156   100.0   156     ERRSC  
     SHIFTED CHAIN . . . . .    2.938      0.351       0.325    351    47.2   743     ERRSC  
     ALTERNATIVE PARENT  . .    3.190      0.381       0.346     33    42.9    77     ERRSC  
     SECONDARY STRUCTURE . .    3.029      0.392       0.391    182    46.2   394     ERRSC  
     LARGE SHIFTS/INSERTIONS    3.392      0.332       0.209    112    47.9   234     ERRSC  
     SURFACE . . . . . . . .    2.894      0.347       0.306    302    48.4   624     ERRSC  
     BURIED  . . . . . . . .    3.146      0.422       0.461     88    49.2   179     ERRSC  
     CORE  . . . . . . . . .    2.774      0.376       0.394    278    48.9   569     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.062      0.406       0.392    674    62.0  1087     ERRALL 
     WELL ORDERED  . . . . .    3.062      0.406       0.392    674    62.0  1087     ERRALL 
     NO INTER CONTACTS . . .    3.062      0.406       0.392    674    62.0  1087     ERRALL 
     SHIFTED CHAIN . . . . .    3.048      0.393       0.375    611    60.9  1003     ERRALL 
     ALTERNATIVE PARENT  . .    3.291      0.437       0.431     65    59.6   109     ERRALL 
     SECONDARY STRUCTURE . .    3.241      0.446       0.456    310    59.4   522     ERRALL 
     LARGE SHIFTS/INSERTIONS    3.205      0.344       0.239    212    63.5   334     ERRALL 
     SURFACE . . . . . . . .    3.009      0.393       0.364    526    62.0   848     ERRALL 
     BURIED  . . . . . . . .    3.252      0.450       0.490    148    61.9   239     ERRALL 
     CORE  . . . . . . . . .    2.997      0.434       0.462    462    61.4   753     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)        17        42        50        61        70      71      71   DISTCA 
CA  (P)     23.94     59.15     70.42     85.92     98.59              71   DISTCA 
CA  (RMS)    0.74      1.20      1.45      2.17      3.03                   DISTCA 
 
ALL (N)       116       291       386       546       658     674    1087   DISTALL 
ALL (P)     10.67     26.77     35.51     50.23     60.53            1087   DISTALL 
ALL (RMS)    0.78      1.23      1.63      2.55      3.51                   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)          46            46            25          RMSLSI 
CA  (P)       64.79         64.79         35.21          RMSLSI 
CA  (RMS)      1.65          1.42          5.23          RMSLSI 
 
 
 
END of the results output 
