Dear all,
a solved 2.6 Ang. structure shows the following estimated coordinate errors
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE(A): 0.468
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.279
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.217
Similar values are calculated by REFMAC independent of its version. The reverse
order
(at least for Rvalue and Rfree) makes more sense to me. Using the formula for
the ESDs given in the REFMAC documentation also a reverse order seems to be
correct (Parameters are given in the full pdb-header attached).
Unclear to me is whether the restraints are included in the item Nparam or not.
I choose Nparam=4 x Natom. Or what could be the reason for discrepancy?
Any comments are welcome
Jürgen
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COMPND---
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.5.0102
REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON
REMARK 3
REMARK 3REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00
REMARK 3 DATA CUTOFF(SIGMA(F)) : NONE
REMARK 3 COMPLETENESS FOR RANGE(%) : 99.47
REMARK 3 NUMBER OF REFLECTIONS :8006
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.18574
REMARK 3 R VALUE(WORKING SET) : 0.18343
REMARK 3 FREE R VALUE : 0.23766
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.6
REMARK 3 FREE R VALUE TEST SET COUNT : 390
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 15
REMARK 3 BIN RESOLUTION RANGE HIGH :2.600
REMARK 3 BIN RESOLUTION RANGE LOW:2.690
REMARK 3 REFLECTION IN BIN (WORKING SET) : 745
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) :99.00
REMARK 3 BIN R VALUE (WORKING SET) :0.328
REMARK 3 BIN FREE R VALUE SET COUNT : 47
REMARK 3 BIN FREE R VALUE:0.344
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 ALL ATOMS: 1577
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.998
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3B11 (A**2) : 0.31
REMARK 3B22 (A**2) : 0.31
REMARK 3B33 (A**2) :-0.47
REMARK 3B12 (A**2) : 0.16
REMARK 3B13 (A**2) : 0.00
REMARK 3B23 (A**2) : 0.00
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE(A): 0.468
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.279
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.217
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.904
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUESCOUNTRMSWEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS(A): 1597 ; 0.012 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): 1056 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2161 ; 1.478 ; 2.002
REMARK 3 BOND ANGLES OTHERS (DEGREES): 2597 ; 0.914 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1(DEGREES): 202 ; 5.627 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2(DEGREES):80 ;41.672 ;25.750
REMARK 3 TORSION ANGLES, PERIOD 3(DEGREES): 275 ;18.636 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4(DEGREES):10 ;14.102 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 246 ; 0.079 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1800 ; 0.004 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 282 ; 0.001 ; 0.020
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMSWEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1011 ; 2.421 ; 2.000
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS(A**2): 415 ; 0.613 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1630 ; 4.453 ; 3.000
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 586 ; 6.769 ; 4.500
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 527 ;10.362 ; 6.000
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT
