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
HEADER ---- XX-XXX-XX xxxx COMPND --- REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT 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 3 B11 (A**2) : 0.31 REMARK 3 B22 (A**2) : 0.31 REMARK 3 B33 (A**2) : -0.47 REMARK 3 B12 (A**2) : 0.16 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (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 VALUES COUNT RMS WEIGHT 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 RMS WEIGHT 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 NCS GROUPS : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 4 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 29 A 45 1 REMARK 3 1 B 29 B 45 1 REMARK 3 2 A 56 A 81 1 REMARK 3 2 B 56 B 81 1 REMARK 3 3 A 89 A 104 1 REMARK 3 3 B 89 B 104 1 REMARK 3 4 A 111 A 114 1 REMARK 3 4 B 111 B 114 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 1 (A): 812 ; 0.04 ; 0.05 REMARK 3 TIGHT THERMAL 1 1 (A**2): 812 ; 0.10 ; 0.50 REMARK 3 REMARK 3 TWIN DETAILS REMARK 3 NUMBER OF TWIN DOMAINS : NULL REMARK 3 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 U VALUES : REFINED INDIVIDUALLY REMARK 3 CRYST1 81.965 81.965 68.289 90.00 90.00 120.00 P 32 2 1 SCALE1 0.012200 0.007044 0.000000 0.00000 SCALE2 0.000000 0.014088 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014644 0.00000
