| PDB FORMAT Version 2.3 |
| Main Index |
| REMARKS |
| REMARK 1,2,4-299 |
| REMARK 300-999 |
| REMARK 3 |
REMARK 3
OverviewREMARK 3 presents information on refinement program(s) used and the related statistics. For non- diffraction studies, REMARK 3 is used to describe any refinement done, but its format in those cases is mostly free text.
If more than one refinement package was used, they may be named in "OTHER REFINEMENT REMARKS". However, Remark 3 statistics are given for the final refinement run.
The format of this remark changes with the evolution of refinement software. Selected representative templates or examples are provided here.
Details
Refinement using X-PLOR Template
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : REMARK 3 DATA CUTOFF (SIGMA(F)) : REMARK 3 DATA CUTOFF HIGH (ABS(F)) : REMARK 3 DATA CUTOFF LOW (ABS(F)) : REMARK 3 COMPLETENESS (WORKING+TEST) (%) : REMARK 3 NUMBER OF REFLECTIONS : REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : REMARK 3 FREE R VALUE TEST SET SELECTION : REMARK 3 R VALUE (WORKING SET) : REMARK 3 FREE R VALUE : REMARK 3 FREE R VALUE TEST SET SIZE (%) : REMARK 3 FREE R VALUE TEST SET COUNT : REMARK 3 ESTIMATED ERROR OF FREE R VALUE : REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : REMARK 3 BIN RESOLUTION RANGE HIGH (A) : REMARK 3 BIN RESOLUTION RANGE LOW (A) : REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : REMARK 3 REFLECTIONS IN BIN (WORKING SET) : REMARK 3 BIN R VALUE (WORKING SET) : REMARK 3 BIN FREE R VALUE : REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : REMARK 3 BIN FREE R VALUE TEST SET COUNT : REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : REMARK 3 NUCLEIC ACID ATOMS : REMARK 3 HETEROGEN ATOMS : REMARK 3 SOLVENT ATOMS : REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : REMARK 3 MEAN B VALUE (OVERALL, A**2) : REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : REMARK 3 B22 (A**2) : REMARK 3 B33 (A**2) : REMARK 3 B12 (A**2) : REMARK 3 B13 (A**2) : REMARK 3 B23 (A**2) : REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : REMARK 3 ESD FROM SIGMAA (A) : REMARK 3 LOW RESOLUTION CUTOFF (A) : REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : REMARK 3 ESD FROM C-V SIGMAA (A) : REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : REMARK 3 BOND ANGLES (DEGREES) : REMARK 3 DIHEDRAL ANGLES (DEGREES) : REMARK 3 IMPROPER ANGLES (DEGREES) : REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : ; REMARK 3 MAIN-CHAIN ANGLE (A**2) : ; REMARK 3 SIDE-CHAIN BOND (A**2) : ; REMARK 3 SIDE-CHAIN ANGLE (A**2) : ; REMARK 3 REMARK 3 NCS MODEL : REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP POSITIONAL (A) : ; REMARK 3 GROUP B-FACTOR (A**2) : ; REMARK 3 REMARK 3 PARAMETER FILE : REMARK 3 TOPOLOGY FILE : REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS:
Refinement using CNS Template
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : REMARK 3 DATA CUTOFF (SIGMA(F)) : REMARK 3 DATA CUTOFF HIGH (ABS(F)) : REMARK 3 DATA CUTOFF LOW (ABS(F)) : REMARK 3 OUTLIER CUTOFF HIGH (RMS(ABS(F))) : REMARK 3 COMPLETENESS FOR RANGE (%) : REMARK 3 COMPLETENESS (WORKING+TEST) (%) : REMARK 3 NUMBER OF REFLECTIONS : REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : REMARK 3 FREE R VALUE TEST SET SELECTION : REMARK 3 R VALUE (WORKING SET) : REMARK 3 FREE R VALUE : REMARK 3 FREE R VALUE TEST SET SIZE (%) : REMARK 3 FREE R VALUE TEST SET COUNT : REMARK 3 ESTIMATED ERROR OF FREE R VALUE : REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : REMARK 3 BIN RESOLUTION RANGE HIGH (A) : REMARK 3 BIN RESOLUTION RANGE LOW (A) : REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : REMARK 3 REFLECTIONS IN BIN (WORKING SET) : REMARK 3 BIN R VALUE (WORKING SET) : REMARK 3 BIN FREE R VALUE : REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : REMARK 3 BIN FREE R VALUE TEST SET COUNT : REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : REMARK 3 NUCLEIC ACID ATOMS : REMARK 3 HETEROGEN ATOMS : REMARK 3 SOLVENT ATOMS : REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : REMARK 3 MEAN B VALUE (OVERALL, A**2) : REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : REMARK 3 B22 (A**2) : REMARK 3 B33 (A**2) : REMARK 3 B12 (A**2) : REMARK 3 B13 (A**2) : REMARK 3 B23 (A**2) : REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : REMARK 3 ESD FROM SIGMAA (A) : REMARK 3 LOW RESOLUTION CUTOFF (A) : REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : REMARK 3 ESD FROM C-V SIGMAA (A) : REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : REMARK 3 BOND ANGLES (DEGREES) : REMARK 3 DIHEDRAL ANGLES (DEGREES) : REMARK 3 IMPROPER ANGLES (DEGREES) : REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : ; REMARK 3 MAIN-CHAIN ANGLE (A**2) : ; REMARK 3 SIDE-CHAIN BOND (A**2) : ; REMARK 3 SIDE-CHAIN ANGLE (A**2) : ; REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : REMARK 3 KSOL : REMARK 3 BSOL : REMARK 3 REMARK 3 NCS MODEL : REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP POSITIONAL (A) : ; REMARK 3 GROUP B-FACTOR (A**2) : ; REMARK 3 REMARK 3 PARAMETER FILE : REMARK 3 TOPOLOGY FILE : REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS:
Refinement using CNX Template
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNX REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : REMARK 3 DATA CUTOFF (SIGMA(F)) : REMARK 3 DATA CUTOFF HIGH (ABS(F)) : REMARK 3 DATA CUTOFF LOW (ABS(F)) : REMARK 3 COMPLETENESS (WORKING+TEST) (%) : REMARK 3 NUMBER OF REFLECTIONS : REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : REMARK 3 FREE R VALUE TEST SET SELECTION : REMARK 3 R VALUE (WORKING + TEST SET) : REMARK 3 R VALUE (WORKING SET) : REMARK 3 FREE R VALUE : REMARK 3 FREE R VALUE TEST SET SIZE (%) : REMARK 3 FREE R VALUE TEST SET COUNT : REMARK 3 ESTIMATED ERROR OF FREE R VALUE : REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : REMARK 3 FREE R VALUE (NO CUTOFF) : REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : REMARK 3 ESTIMATED ERROR OF FREE R VALUE (NO CUTOFF) : REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : REMARK 3 BIN RESOLUTION RANGE HIGH (A) : REMARK 3 BIN RESOLUTION RANGE LOW (A) : REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : REMARK 3 REFLECTIONS IN BIN (WORKING SET) : REMARK 3 BIN R VALUE (WORKING SET) : REMARK 3 BIN FREE R VALUE : REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : REMARK 3 BIN FREE R VALUE TEST SET COUNT : REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : REMARK 3 NUCLEIC ACID ATOMS : REMARK 3 HETEROGEN ATOMS : REMARK 3 SOLVENT ATOMS : REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : REMARK 3 MEAN B VALUE (OVERALL, A**2) : REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : REMARK 3 B22 (A**2) : REMARK 3 B33 (A**2) : REMARK 3 B12 (A**2) : REMARK 3 B13 (A**2) : REMARK 3 B23 (A**2) : REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : REMARK 3 ESD FROM SIGMAA (A) : REMARK 3 LOW RESOLUTION CUTOFF (A) : REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : REMARK 3 ESD FROM C-V SIGMAA (A) : REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : REMARK 3 BOND ANGLES (DEGREES) : REMARK 3 DIHEDRAL ANGLES (DEGREES) : REMARK 3 IMPROPER ANGLES (DEGREES) : REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : ; REMARK 3 MAIN-CHAIN ANGLE (A**2) : ; REMARK 3 SIDE-CHAIN BOND (A**2) : ; REMARK 3 SIDE-CHAIN ANGLE (A**2) : ; REMARK 3 REMARK 3 NCS MODEL : REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP POSITIONAL (A) : ; REMARK 3 GROUP B-FACTOR (A**2) : ; REMARK 3 REMARK 3 PARAMETER FILE : REMARK 3 TOPOLOGY FILE : REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS:
Refinement using REFMAC Template
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.X REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : REMARK 3 DATA CUTOFF (SIGMA(F)) : REMARK 3 COMPLETENESS FOR RANGE (%) : REMARK 3 NUMBER OF REFLECTIONS : REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : REMARK 3 FREE R VALUE TEST SET SELECTION : REMARK 3 R VALUE (WORKING + TEST SET) : REMARK 3 R VALUE (WORKING SET) : REMARK 3 FREE R VALUE : REMARK 3 FREE R VALUE TEST SET SIZE (%) : REMARK 3 FREE R VALUE TEST SET COUNT : REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : REMARK 3 BIN RESOLUTION RANGE HIGH : REMARK 3 BIN RESOLUTION RANGE LOW : REMARK 3 REFLECTION IN BIN (WORKING SET) : REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : REMARK 3 BIN R VALUE (WORKING SET) : REMARK 3 BIN FREE R VALUE SET COUNT : REMARK 3 BIN FREE R VALUE : REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 ALL ATOMS : REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : REMARK 3 NUCLEIC ACID ATOMS : REMARK 3 HETEROGEN ATOMS : REMARK 3 SOLVENT ATOMS : REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : REMARK 3 MEAN B VALUE (OVERALL, A**2) : REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : REMARK 3 B22 (A**2) : REMARK 3 B33 (A**2) : REMARK 3 B12 (A**2) : REMARK 3 B13 (A**2) : REMARK 3 B23 (A**2) : REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): REMARK 3 ESU BASED ON FREE R VALUE (A): REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): ; ; REMARK 3 BOND LENGTHS OTHERS (A): ; ; REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): ; ; REMARK 3 BOND ANGLES OTHERS (DEGREES): ; ; REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): ; ; REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): ; ; REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): ; ; REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): ; ; REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): ; ; REMARK 3 GENERAL PLANES REFINED ATOMS (A): ; ; REMARK 3 GENERAL PLANES OTHERS (A): ; ; REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): ; ; REMARK 3 NON-BONDED CONTACTS OTHERS (A): ; ; REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): ; ; REMARK 3 NON-BONDED TORSION OTHERS (A): ; ; REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): ; ; REMARK 3 H-BOND (X...Y) OTHERS (A): ; ; REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): ; ; REMARK 3 POTENTIAL METAL-ION OTHERS (A): ; ; REMARK 3 SYMMETRY VDW REFINED ATOMS (A): ; ; REMARK 3 SYMMETRY VDW OTHERS (A): ; ; REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): ; ; REMARK 3 SYMMETRY H-BOND OTHERS (A): ; ; REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): ; ; REMARK 3 SYMMETRY METAL-ION OTHERS (A): ; ; REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): ; ; REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): ; ; REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): ; ; REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): ; ; REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): ; ; REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): ; ; REMARK 3 SPHERICITY; FREE ATOMS (A**2): ; ; REMARK 3 SPHERICITY; BONDED ATOMS (A**2): ; ; REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : REMARK 3 REMARK 3 CHAIN NAMES : REMARK 3 NUMBER OF COMPONENTS NCS GROUP : REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL A (A): ; ; REMARK 3 LOOSE POSITIONAL A (A): ; ; REMARK 3 MEDIUM THERMAL A (A**2): ; ; REMARK 3 LOOSE THERMAL A (A**2): ; ; REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : REMARK 3 REMARK 3 TLS GROUP : REMARK 3 NUMBER OF COMPONENTS GROUP : REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : REMARK 3 ORIGIN FOR THE GROUP (A): REMARK 3 T TENSOR REMARK 3 T11: T22: REMARK 3 T33: T12: REMARK 3 T13: T23: REMARK 3 L TENSOR REMARK 3 L11: L22: REMARK 3 L33: L12: REMARK 3 L13: L23: REMARK 3 S TENSOR REMARK 3 S11: S12: S13: REMARK 3 S21: S22: S23: REMARK 3 S31: S32: S33: REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : REMARK 3 ION PROBE RADIUS : REMARK 3 SHRINKAGE RADIUS : REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS:
Refinement using NUCLSQ Template
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NUCLSQ REMARK 3 AUTHORS : WESTHOF,DUMAS,MORAS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : REMARK 3 DATA CUTOFF (SIGMA(F)) : REMARK 3 COMPLETENESS FOR RANGE (%) : REMARK 3 NUMBER OF REFLECTIONS : REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : REMARK 3 FREE R VALUE TEST SET SELECTION : REMARK 3 R VALUE (WORKING + TEST SET) : REMARK 3 R VALUE (WORKING SET) : REMARK 3 FREE R VALUE : REMARK 3 FREE R VALUE TEST SET SIZE (%) : REMARK 3 FREE R VALUE TEST SET COUNT : REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : REMARK 3 FREE R VALUE (NO CUTOFF) : REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : REMARK 3 NUCLEIC ACID ATOMS : REMARK 3 HETEROGEN ATOMS : REMARK 3 SOLVENT ATOMS : REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : REMARK 3 MEAN B VALUE (OVERALL, A**2) : REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : REMARK 3 B22 (A**2) : REMARK 3 B33 (A**2) : REMARK 3 B12 (A**2) : REMARK 3 B13 (A**2) : REMARK 3 B23 (A**2) : REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : REMARK 3 ESD FROM SIGMAA (A) : REMARK 3 LOW RESOLUTION CUTOFF (A) : REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 SUGAR-BASE BOND DISTANCE (A) : ; REMARK 3 SUGAR-BASE BOND ANGLE DISTANCE (A) : ; REMARK 3 PHOSPHATE BONDS DISTANCE (A) : ; REMARK 3 PHOSPHATE BOND ANGLE, H-BOND (A) : ; REMARK 3 REMARK 3 PLANE RESTRAINT (A) : ; REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : ; REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION CONTACT (A) : ; REMARK 3 MULTIPLE TORSION CONTACT (A) : ; REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 SUGAR-BASE BONDS (A**2) : ; REMARK 3 SUGAR-BASE ANGLES (A**2) : ; REMARK 3 PHOSPHATE BONDS (A**2) : ; REMARK 3 PHOSPHATE BOND ANGLE, H-BOND (A**2) : ; REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS:
Refinement using PROLSQ, CCP4, PROFFT, GPRLSA, and related programs
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REMARK 3 AUTHORS : REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : REMARK 3 DATA CUTOFF (SIGMA(F)) : REMARK 3 COMPLETENESS FOR RANGE (%) : REMARK 3 NUMBER OF REFLECTIONS : REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : REMARK 3 FREE R VALUE TEST SET SELECTION : REMARK 3 R VALUE (WORKING + TEST SET) : REMARK 3 R VALUE (WORKING SET) : REMARK 3 FREE R VALUE : REMARK 3 FREE R VALUE TEST SET SIZE (%) : REMARK 3 FREE R VALUE TEST SET COUNT : REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : REMARK 3 FREE R VALUE (NO CUTOFF) : REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : REMARK 3 NUCLEIC ACID ATOMS : REMARK 3 HETEROGEN ATOMS : REMARK 3 SOLVENT ATOMS : REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : REMARK 3 MEAN B VALUE (OVERALL, A**2) : REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : REMARK 3 B22 (A**2) : REMARK 3 B33 (A**2) : REMARK 3 B12 (A**2) : REMARK 3 B13 (A**2) : REMARK 3 B23 (A**2) : REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : REMARK 3 ESD FROM SIGMAA (A) : REMARK 3 LOW RESOLUTION CUTOFF (A) : REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : ; REMARK 3 ANGLE DISTANCE (A) : ; REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : ; REMARK 3 H-BOND OR METAL COORDINATION (A) : ; REMARK 3 REMARK 3 PLANE RESTRAINT (A) : ; REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : ; REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : ; REMARK 3 MULTIPLE TORSION (A) : ; REMARK 3 H-BOND (X...Y) (A) : ; REMARK 3 H-BOND (X-H...Y) (A) : ; REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : ; REMARK 3 PLANAR (DEGREES) : ; REMARK 3 STAGGERED (DEGREES) : ; REMARK 3 TRANSVERSE (DEGREES) : ; REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : ; REMARK 3 MAIN-CHAIN ANGLE (A**2) : ; REMARK 3 SIDE-CHAIN BOND (A**2) : ; REMARK 3 SIDE-CHAIN ANGLE (A**2) : ; REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS:
Refinement using SHELXL Template
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : REMARK 3 DATA CUTOFF (SIGMA(F)) : REMARK 3 COMPLETENESS FOR RANGE (%) : REMARK 3 CROSS-VALIDATION METHOD : REMARK 3 FREE R VALUE TEST SET SELECTION : REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : REMARK 3 FREE R VALUE (NO CUTOFF) : REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : REMARK 3 FREE R VALUE (F>4SIG(F)) : REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : REMARK 3 NUCLEIC ACID ATOMS : REMARK 3 HETEROGEN ATOMS : REMARK 3 SOLVENT ATOMS : REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : REMARK 3 NUMBER OF RESTRAINTS : REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : REMARK 3 ANGLE DISTANCES (A) : REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : REMARK 3 ZERO CHIRAL VOLUMES (A**3) : REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : REMARK 3 SIMILAR ADP COMPONENTS (A**2) : REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : REMARK 3 SPECIAL CASE: REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS:
Refinement using TNT/BUSTER Template
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER/TNT REMARK 3 AUTHORS : BLANC,ROVERSI,VONRHEIN,BRICOGNE,TRONRUD, REMARK 3 : TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : REMARK 3 DATA CUTOFF (SIGMA(F)) : REMARK 3 COMPLETENESS FOR RANGE (%) : REMARK 3 NUMBER OF REFLECTIONS : REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : REMARK 3 FREE R VALUE TEST SET SELECTION : REMARK 3 R VALUE (WORKING + TEST SET) : REMARK 3 R VALUE (WORKING SET) : REMARK 3 FREE R VALUE : REMARK 3 FREE R VALUE TEST SET SIZE (%) : REMARK 3 FREE R VALUE TEST SET COUNT : REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : REMARK 3 BIN R VALUE (WORKING + TEST SET) : REMARK 3 REFLECTIONS IN BIN (WORKING SET) : REMARK 3 BIN R VALUE (WORKING SET) : REMARK 3 BIN FREE R VALUE : REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : REMARK 3 BIN FREE R VALUE TEST SET COUNT : REMARK 3 ESTIMATED ERROR OF FREE R VALUE : REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : REMARK 3 NUCLEIC ACID ATOMS : REMARK 3 HETEROGEN ATOMS : REMARK 3 SOLVENT ATOMS : REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : REMARK 3 MEAN B VALUE (OVERALL, A**2) : REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : REMARK 3 B22 (A**2) : REMARK 3 B33 (A**2) : REMARK 3 B12 (A**2) : REMARK 3 B13 (A**2) : REMARK 3 B23 (A**2) : REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : ; ; REMARK 3 BOND ANGLES (DEGREES) : ; ; REMARK 3 TORSION ANGLES (DEGREES) : ; ; REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : ; ; REMARK 3 TRIGONAL CARBON PLANES (A) : ; ; REMARK 3 GENERAL PLANES (A) : ; ; REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : ; ; REMARK 3 NON-BONDED CONTACTS (A) : ; ; REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS:
Refinement using Cryo-Electron Microscopy Template/Example
REMARK 3 REMARK 3 REFINEMENT REMARK 3 SOFTWARE PACKAGES : SIMPLEX, PYPFT, EMFIT, O, XPLOR REMARK 3 RECONSTRUCTION SCHEMA : ICOSAHEDRAL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : PDB ID 1HX6 REMARK 3 REFINEMENT SPACE : RECIPROCAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY REFINEMENT REMARK 3 REFINEMENT TARGET : R-FACTOR REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : THE CRYSTAL STRUCTURE OF THE MAJOR COAT REMARK 3 PROTEIN P3 (PDB FILE 1HX6) WAS PLACED INTO THE CRYO-EM REMARK 3 DENSITY MAP. THE CAPSID PROTEIN WAS FIRST MANUALLY REMARK 3 POSITIONED INTO THE CRYO-EM DENSITY CORRESPONDING TO REMARK 3 POSITIONS OF THE FOUR INDEPENDENT TRIMERS IN THE REMARK 3 ICOSAHEDRAL ASYMMETRIC UNIT. THESE POSITIONS WERE THEN REMARK 3 REFINED BY RIGID BODY REFINEMENT IN RECIPROCAL SPACE WITH REMARK 3 THE PROGRAM XPLOR. REMARK 3 QUALITY OF THE FIT R-FACTOR= 0.339, CROSS-CORRELATI0N REMARK 3 COEFFICIENT 0.915, ATOMS OUTSIDE DENSITY PER ICOSAHEDRAL REMARK 3 ASYMMETRIC UNIT 527 (1.5%),ATOM CLASHES PER ICOSAHEDRAL REMARK 3 ASYMMETRIC UNIT 115 (0.3%) REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : 3.68 REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : 3.44 REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 14.0 REMARK 3 NUMBER OF PARTICLES : 1800 REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 CRYO-EM RECONSTRUCTION MAGNIFICATION CALIBRATION: THE PIXEL REMARK 3 SIZE OF THE CRYO-EM MAP WAS OBTAINED USING THE X-RAY REMARK 3 STRUCTURE OF THE P3 TRIMER AS A REFERENCE. AFTER AN INITIAL REMARK 3 FITTING USING THE NOMINAL PIXEL SIZE, THE P3 TRIMERS IN THE REMARK 3 ICOSAHEDRAL ASYMMETRIC UNIT WERE GRADUALLY TRANSLATED TOWARDS REMARK 3 THE CENTER OF THE PARTICLE UNTIL THE CRYSTALLOGRAPHIC R-FACTOR REMARK 3 WAS MINIMISED. REMARK 3 REMARK 3 OTHER DETAILS: THE ORIENTATIONS WERE REFINED BY THE CROSS REMARK 3 COMMON LINES LINES METHOD (SIMPLEX) AND THE POLAR FOURIER REMARK 3 TRANSFORM METHOD. MODEL-BASED, POLAR-FOURIER-TRANSFORM REMARK 3 (FULLER ET AL. 1996, J.STRUC.BIOL. 116, 48-55; BAKER AND REMARK 3 CHENG, 1996, J.STRUC.BIOL. 116, 120-130) MODEL-BASED CROSS REMARK 3 COMMON LINES SEARCH AND REFINEMENT (CROWTHER ET AL. 1970, REMARK 3 NATURE (LONDON) 226, 421-425; FULLER ET AL. 1996, REMARK 3 J.STRUC.BIOL. 116, 48-55;FERLENGHI ET AL. 1998, J.MOL.BIOL. REMARK 3 283, 71-81). THE EFFECTIVE RESOLUTION OF THE FINAL REMARK 3 RECONSTRUCTED DENSITY WAS DETERMINED TO BE AT LEAST 25 REMARK 3 ANGSTROMS, AS MEASURED BY RANDOMLY SPLITTING THE PARTICLES REMARK 3 INTO TWO SETS AND CALCULATING THE FOURIER SHELL CORRELATION REMARK 3 OBTAINED FROM SEPARATE RECONSTRUCTIONS (HARAUZ AND VAN HEEL REMARK 3 1986, OPTIK 73, 146-156). THE EIGENVALUE SPECTRUM GAVE AN REMARK 3 INDICATION OF THE RANDOMNESS OF THE DATA THAT WAS INCLUDED REMARK 3 IN THE RECONSTRUCTION. THE COMPLETENESS OF THE DATA WAS REMARK 3 VERIFIED IN THAT ALL EIGENVALUES EXCEEDED 100. THE COORDINATES REMARK 3 ARE IN THE P, Q, R FRAME IN ANGSTROM UNITS AND CORRESPOND REMARK 3 TO ICOSAHEDRAL SYMMETRY AXES. THE ORIGIN IS CHOSEN AT THE REMARK 3 CENTER OF THE VIRUS WITH P, Q AND R ALONG MUTUALLY REMARK 3 PERPENDICULAR TWO-FOLD AXES OF THE ICOSAHEDRON. THEY SHOULD REMARK 3 REMAIN IN THAT FRAME FOR THE EASE OF THE USER IN CREATING REMARK 3 THE BIOLOGICALLY SIGNIFICANT VIRAL COMPLEX PARTICLE USING REMARK 3 THE 60 ICOSAHEDRAL SYMMETRY OPERATORS. RESIDUES NOT VISIBLE REMARK 3 IN THE ORIGINAL CRYSTAL STRUCTURES ARE NOT INCLUDED IN THE REMARK 3 CRYO-EM STRUCTURE MODEL.
Example for Solution Scatter
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : INSIGHT II 98.0 REMARK 3 AUTHORS : MSI REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1213 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DISCOVER WAS USED FOR ENERGY REMARK 3 MINIMISATION
Non-diffraction studies
Until standard refinement remarks are adopted for non-diffraction studies, their refinement details are given in REMARK 3, but its format will consist totally of free text beginning on the sixth line of the remark.
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REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM :
REMARK 3 AUTHORS :
REMARK 3
REMARK 3 FREE TEXT
Example
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REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.1
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 STRUCTURAL STATISTICS:
REMARK 3 25 SA
REMARK 3 STRUCTURES SAAVEMIN
REMARK 3 RMS DEVIATIONS FROM EXP. RESTRAINTS[A]
REMARK 3 NOE DISTANCE RESTRAINTS (1430) 0.0451 A 0.044 A
REMARK 3 DIHEDRAL ANGLE RESTRAINTS (130) 0.551 DEG 0.660 DEG
REMARK 3 DEVIATIONS FROM IDEAL GEOMETRY
REMARK 3 BONDS 0.004 A 0.004 A
REMARK 3 ANGLES 0.661 DEG 0.650 DEG
REMARK 3 IMPROPERS 0.371 DEG 0.380 DEG
REMARK 3 X-PLOR ENERGIES (IN KCAL MOL-1)[B]
REMARK 3 ENOE 167 158
REMARK 3 ECDIH 2.6 3.4
REMARK 3 ENCS 0.01 0.01
REMARK 3 EREPEL 54 50
REMARK 3 EBOND 36 33
REMARK 3 EANGLE 263 256
REMARK 3 EIMPROPER 22 23
REMARK 3 ETOTAL 545 523
REMARK 3 ATOMIC RMS DIFFERENCES[C]
REMARK 3 BACKBONE(N, CA, C') + LIGAND ATOMS 0.53+/-0.09 A
REMARK 3 ALL HEAVY ATOMS 0.91+/-0.08 A
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