Overview
REMARK 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.
Refinement packages are being enhanced to output PDB REMARK 3. A token: value template style facilitates parsing. Spacer REMARK 3 lines are interspersed for visually organizing the information.
The templates below have been adopted in consultation with program authors. PDB is continuing this dialogue with program authors, and expects the library of PDB records output by the programs to greatly increase in the near future.
Instead of providing aRecord Formattable, each template is given as it appears in PDB entries.
Details
* The value "NULL" is given when there is no data available for a particular token.
This remark will be output by X-PLOR(online) for direct submission to PDB. Structures done using earlier versions of X-PLOR will contain the same template, but with many of the data items containing "NULL".
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 1 POSITIONAL (A) : ; REMARK 3 GROUP 1 B-FACTOR (A**2) : ; REMARK 3 GROUP 2 POSITIONAL (A) : ; REMARK 3 GROUP 2 B-FACTOR (A**2) : ; REMARK 3 GROUP 3 POSITIONAL (A) : ; REMARK 3 GROUP 3 B-FACTOR (A**2) : ; REMARK 3 GROUP 4 POSITIONAL (A) : ; REMARK 3 GROUP 4 B-FACTOR (A**2) : ; REMARK 3 REMARK 3 PARAMETER FILE 1 : REMARK 3 PARAMETER FILE 2 : REMARK 3 PARAMETER FILE 3 : REMARK 3 PARAMETER FILE 4 : REMARK 3 PARAMETER FILE 5 : REMARK 3 PARAMETER FILE 6 : REMARK 3 TOPOLOGY FILE 1 : REMARK 3 TOPOLOGY FILE 2 : REMARK 3 TOPOLOGY FILE 3 : REMARK 3 TOPOLOGY FILE 4 : REMARK 3 TOPOLOGY FILE 5 : REMARK 3 TOPOLOGY FILE 6 : REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS:
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:
Template
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:
This remark will be output by SHELXL-96 for direct submission to PDB. Structures done using earlier versions of SHELX will use the same template, but with many of the data items containing "NULL".
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:
Template
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,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 USING ALL DATA, NO SIGMA 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 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : REMARK 3 NUCLEIC ACID ATOMS : REMARK 3 OTHER ATOMS : REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : REMARK 3 KSOL : REMARK 3 BSOL : REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS:
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.
Template
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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