New Records in 3.

2 Page 1

Protein Data Bank Changes Guide

New Changes in Version 3.20

September 15, 2008

Version 3.20 of the PDB file format introduces a small number of changes and extensions supporting
the annotation practices adopted by the wwPDB. These annotation practices are described in detail
in the documentation section of the wwPDB website. The complete details of the PDB file format can
be found at http://www.wwpdb.org/docs.html.
New Records in 3.2 Page 2

1. SPLIT
When a structure has too many atoms to be represented in a single PDB formatted file, it
will be split into smaller entries that will all be identified with a new record named
SPLIT. Appears after TITLE.

1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
SPLIT 1VOQ 1VOR 1VOS 1VOU 1VOV 1VOW 1VOX 1VOY
SPLIT 2 1VP0 1VOZ

Example:
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
HEADER RIBOSOME 06-OCT-04 1VOV
TITLE CRYSTAL STRUCTURE OF FIVE 70S RIBOSOMES FROM ESCHERICHIA
TITLE 2 COLI IN COMPLEX WITH PROTEIN Y. THIS FILE CONTAINS THE 30S
TITLE 3 SUBUNIT OF ONE 70S RIBOSOME.
SPLIT 1VOQ 1VOR 1VOS 1VOU 1VOV 1VOW 1VOX 1VOY 1VOZ
SPLIT 2 1VP0 1VOZ

2. COMPND
An additional column will be added to extend the continuation lines up to 999.

Example:
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
COMPND 97 MOL_ID: 25;
COMPND 98 MOLECULE: 50S RIBOSOMAL PROTEIN L32E;
COMPND 99 CHAIN: Y;
COMPND 100 SYNONYM: HL5;
COMPND 101 MOL_ID: 26;
COMPND 102 MOLECULE: 50S RIBOSOMAL PROTEIN L37AE;
COMPND 103 CHAIN: Z;
COMPND 104 MOL_ID: 27;
COMPND 105 MOLECULE: 50S RIBOSOMAL PROTEIN L37E;
COMPND 106 CHAIN: 1;
COMPND 107 SYNONYM: L35E;

3. SOURCE
The NCBI Taxonomy IDs for the organism (ORGANISM_TAXID) and expression system
(EXPRESSION_SYSTEM_TAXID) are now included in the SOURCE record if they are available.

Example:
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: LACTOBACILLUS CASEI;
SOURCE 4 ORGANISM_TAXID: 1582;
SOURCE 5 GENE: THYA;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562
SOURCE 9 EXPRESSION_SYSTEM_STRAIN: CHI2913RECA;
SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PSCTS9
New Records in 3.2 Page 3

An additional column will be added to extend the continuation lines up to 999.

Example:
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
SOURCE 99 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE 100 MOL_ID: 29;
SOURCE 101 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE 102 MOL_ID: 30;
SOURCE 103 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE 104 MOL_ID: 31;
SOURCE 105 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;

4. EXPDTA
The experimental methods have been standardized and follow an enumeration list. Multiple
exp methods will be listed here for joint refinement or hybrid methods. NMR entries will
be identified by solution and solid state. EM entries will be identified by electron
crystallography and electron microscopy.

X-RAY DIFFRACTION
NEUTRON DIFFRACTION
FIBER DIFFRACTION
ELECTRON CRYSTALLOGRAPHY
ELECTRON MICROSCOPY
SOLUTION NMR
SOLID-STATE NMR
SOLUTION SCATTERING

Example 1:
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
EXPDTA SOLID-STATE NMR

Example 2, joint refinement:

1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
EXPDTA X-RAY DIFFRACTION; NEUTRON DIFFRACTION

5. NUMMDL
The new record NUMMDL specifies the number of models. Appears after EXPDTA.

Example, ensemble without minimized average:

1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
EXPDTA SOLUTION NMR
NUMMDL 20

6. MDLTYP
The new record MDLTYP specifies the minimized average or Ca/P atoms chains. Appears after
EXPDTA with continuous lines.

Example 1, only one minimized average:

1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
New Records in 3.2 Page 4

Example 2, chains contain Ca or P atoms only:

1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
MDLTYP CA ATOMS ONLY, CHAIN A, B, C, D, E, F, G, H, I, J, K; P ATOMS ONLY,
MDLTYP 2 CHAIN X, Y, Z

Example 3, minimized average AND chains contain Ca or P atoms only:

1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
MDLTYP MINIMIZED AVERAGE; CA ATOMS ONLY, CHAIN A, B

7. JRNL
Country code, ASTM and ISBN have been removed.

The PubMed ID and corresponding Digital Object Identifier (DOI) for the primary citation
have been added. Each DOI consists of a publisher prefix, a slash ("/"), and a suffix of
numbers and letters of any length. The PubMed ID and DOI start at column 20.

Example:
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
JRNL REF PROC.NATL.ACAD.SCI.USA V. 105 4621 2008
JRNL REFN ISSN 0027-8424
JRNL PMID 18344321
JRNL DOI 10.1073/pnas.0712393105

8. REMARK 2
Format has been changed to allow display of low resolution.
Resolution becomes f7.2 to allow for space and 100.00 ANGSTROM.

Example:
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
REMARK 2 RESOLUTION. 1.74 ANGSTROMS.

9. REMARK 4
The versioning now has format x.xx with uniform date format dd-mmm-yy.

Example:
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
REMARK 4 2G86 COMPLIES WITH FORMAT V. 3.20, 01-AUG-07

10. REMARK 100

For entries processed at RCSB, PDBE, or PDBJ, this remark indicates the data processing
site, processing date with uniform format dd-mmm-yy, and site ID code. For entries
processed at BNL, this record will only include the data processing site.

Examples:
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB on 10-MAR-06.
REMARK 100 THE RCSB ID CODE IS RCSB036809.

REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE on 13-FEB-07.

REMARK 100 THE PDBE ID CODE IS EBI-28843.

REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ on 21-MAR-05.

New Records in 3.2 Page 5

REMARK 100 THE RCSB ID CODE IS RCSB026278.

REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.

11. REMARK 200

This remark will have the uniform date format dd-mmm-yy.

Example:
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
REMARK 200 DATE OF DATA COLLECTION : 01-JAN-96

12. REMARK 240

This remark is mandatory for ELECTRON CRYSTALLOGRAPHY. Three new records have been added:
RECONSTRUCTION METHOD, SAMPLE TYPE, and SPECIMEN TYPE. The DATE OF DATA COLLECTION will
have the uniform date format dd-mmm-yy.

Example:
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
REMARK 240
REMARK 240 EXPERIMENTAL DETAILS
REMARK 240 RECONSTRUCTION METHOD : CRYSTALLOGRAPHY
REMARK 240 SAMPLE TYPE : 2D CRYSTAL
REMARK 240 SPECIMEN TYPE : VITREOUS ICE (CRYO EM)
REMARK 240 DATA AQUISITION
REMARK 240 DATE OF DATA COLLECTION : 01-DEC-03
REMARK 240 TEMPERATURE (KELVIN) : 300.0
REMARK 240 PH : 6.00
REMARK 240 NUMBER OF CRYSTALS USED : 286
REMARK 240 MICROSCOPE MODEL : JEM3000SFF
REMARK 240 DETECTOR TYPE : CCD
REMARK 240 ACCELERATION VOLTAGE (KV) : 300
REMARK 240 NUMBER OF UNIQUE REFLECTIONS : 22293
REMARK 240 RESOLUTION RANGE HIGH (A) : 1.9
REMARK 240 RESOLUTION RANGE LOW (A) : 20.000
REMARK 240 DATA SCALING SOFTWARE : SOFTWARE
REMARK 240 COMPLETENESS FOR RANGE (%) : 80.0
REMARK 240 DATA REDUNDANCY : 5.700
REMARK 240 IN THE HIGHEST RESOLUTION SHELL.
REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90
REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.0
REMARK 240 COMPLETENESS FOR SHELL (%) : 82.0
REMARK 240 DATA REDUNDANCY IN SHELL : 5.70
REMARK 240 R MERGE FOR SHELL (I) : 0.166
REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR
REMARK 240 REPLACEMENT
REMARK 240 SOFTWARE USED : CNS
REMARK 240 STARTING MODEL : PDB ENTRY 1SOR
New Records in 3.2 Page 6

13. REMARK 245

This remark is mandatory for ELECTRON MICROSCOPY. Four new PDB records have been added:
RECONSTRUCTION METHOD, SAMPLE TYPE, SPECIMEN TYPE, and PARTICLE TYPE if SAMPLE TYPE is
PARTICLE. The DATE OF EXPERIMENT will have the uniform date format dd-mmm-yy.

Example:
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
REMARK 245
REMARK 245 EXPERIMENTAL DETAILS
REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE
REMARK 245 SPECIMEN TYPE : VITREOUS ICE (CRYO EM)
REMARK 245
REMARK 245 ELECTRON MICROSCOPE SAMPLE
REMARK 245 SAMPLE TYPE : PARTICLE
REMARK 245 PARTICLE TYPE : MIXED SYMMETRY
REMARK 245 NAME OF SAMPLE : BACTERIOPHAGE T4
REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 20.00
REMARK 245 SAMPLE SUPPORT DETAILS : NULL
REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL
REMARK 245 SAMPLE BUFFER : H2O
REMARK 245 PH : 7.50
REMARK 245 SAMPLE DETAILS : PHAGE
REMARK 245
REMARK 245 DATA ACQUISITION
REMARK 245 DATE OF EXPERIMENT : 06-JAN-02
REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL
REMARK 245 TEMPERATURE (KELVIN) : 100.00
REMARK 245 MICROSCOPE MODEL : FEI/PHILIPS CM300FEG/T
REMARK 245 DETECTOR TYPE : NULL
REMARK 245 MINIMUM DEFOCUS (NM) : 500.00
REMARK 245 MAXIMUM DEFOCUS (NM) : 3400.00
REMARK 245 MINIMUM TILT ANGLE (DEGREES) : 0.00
REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : 0.00
REMARK 245 NOMINAL CS : 1.40
REMARK 245 IMAGING MODE : BRIGHT FIELD
REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 20.00
REMARK 245 ILLUMINATION MODE : SPOT SCAN
REMARK 245 NOMINAL MAGNIFICATION : 45000
REMARK 245 CALIBRATED MAGNIFICATION : 47000
REMARK 245 SOURCE : FIELD EMISSION GUN
REMARK 245 ACCELERATION VOLTAGE (KV) : 300
REMARK 245 IMAGING DETAILS : NULL

14. REMARK 300

The point symmetry will be in the last line of REMARK 300.

Example:
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
REMARK 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR
REMARK 300 CYCLIC POINT SYMMETRY (SCHOENFLIES SYMBOL = C38).
New Records in 3.2 Page 7

15. REMARK 350

In SPLIT entries, REMARK 350 reports the quaternary structure for the partial structure.
Surface area is not reported.

Example, SPLIT entries:

1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 QUATERNARY STRUCTURE FOR THIS ENTRY: 21MERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I,
REMARK 350 AND CHAINS: J, K, L, M, N, O, P, Q, R,
REMARK 350 AND CHAINS: S, T, a
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000

In non-SPLIT entries, REMARK 350 reports the full quaternary structure and software-
calculated outputs, if available.

Example, non-SPLIT entries:

1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DODECAMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DODECAMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 2990 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 9330 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.1 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I,
REMARK 350 AND CHAINS: J, K, L
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000

16. REMARK 465

For NMR ensembles, the missing residues will be listed in model range.

Example:
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465 MODELS 1-20
REMARK 465 RES C SSSEQI
REMARK 465 MET A 1
REMARK 465 GLY A 2
New Records in 3.2 Page 8

17. REMARK 470

For NMR ensembles, the missing atoms will be listed in model range.

Example:
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(RES=RESIDUE NAME;
REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 470 MODELS 1-25
REMARK 470 RES CSSEQI ATOMS
REMARK 470 ILE A 20 CD1
REMARK 470 THR A 59 CG2

18. REMARK 800

REMARK 800 will distinguish between author-provided and software-generated SITE records
with an “EVIDENCE CODE” where the value can be AUTHOR/SOFTWARE/UNKNOWN. This appears
after SITE_IDENTIFIER.

Example:
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890

REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BIL A 19
REMARK 800
REMARK 800 SITE_IDENTIFIER: CAT
REMARK 800 EVIDENCE_CODE: AUTHOR
REMARK 800 SITE_DESCRIPTION: DESIGNATED RECOGNITION REGION IN PRIMARY
REMARK 800 REFERENCE. PROPOSED TO AFFECT SUBSTRATE SPECIFICITY.
New Records in 3.2 Page 9

19. DBREF, DBREF1, and DBREF2

The DBREF record provides cross-reference links between PDB sequences and the
corresponding database entry or entries in a given, fixed character space. This record
will continue to be used as long as an accession code fits in the space provided (e.g.,
UNP code). Two new DBREF records (DBREF1 and DBREF2) will only be used when the
accession code or sequence numbering does not fit to DBREF format such as (e.g., UNIMES
or GB).

Example, DBREF:
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
DBREF 2J83 A 61 322 UNP Q8TL28 Q8TL28_METAC 61 322

In the new format, 20 characters are reserved for accession code and 10 characters are
reserved for DB numbering.

Example, DBREF1 and DBREF2:

1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
DBREF1 2J83 A 61 322 UNIMES UPI000148A153
DBREF2 2J83 A MES00005880000 61 322

DBREF1 2J83 A 61 322 GB AE017221

DBREF2 2J83 A 46197919 1534489 1537377

All entries will self-reference if a database sequence is not available.

Example, No Database Sequence:

1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
DBREF 2JSK A 1 23 PDB 2JSK 2JSK 1 23

20. REMARK 630, Peptide inhibitors

New record REMARK 630 describes the chemistry, function, or structure features for any
antibiotics, inhibitors or peptide inhibitors that are treated as single molecules.

Template:
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
REMARK 630 MOLECULE TYPE:
REMARK 630 MOLECULE NAME:
REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 630
REMARK 630 M RES C SSSEQI
REMARK 630 SOURCE:
REMARK 630 SUBCOMP:
REMARK 630 STRUCTURE DETAILS:
REMARK 630 OTHER DETAILS:

21. REMARK 3 for Phenix template/example and joint refinement for X-ray/Neutron

Phenix templates have been added to REMARK 3.

Example, PHENIX:
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
REMARK 3
New Records in 3.2 Page 10

REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE)
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-
REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO,
REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL
REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE
REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM
REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH,
REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER
REMARK 3 : ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.99
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.07
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7
REMARK 3 NUMBER OF REFLECTIONS : 242645
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.293
REMARK 3 R VALUE (WORKING SET) : 0.291
REMARK 3 FREE R VALUE : 0.335
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980
REMARK 3 FREE R VALUE TEST SET COUNT : 12081
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 40.0700 - 9.2600 0.98 8197 419 0.1970 0.2050
REMARK 3 2 9.2600 - 7.3700 0.98 7994 409 0.1560 0.1990
REMARK 3 3 7.3700 - 6.4400 0.99 7965 413 0.2060 0.2470
REMARK 3 4 6.4400 - 5.8500 0.99 7924 426 0.2330 0.2740
REMARK 3 5 5.8500 - 5.4300 0.98 7833 444 0.2550 0.3160
REMARK 3 6 5.4300 - 5.1200 0.98 7811 408 0.2530 0.3110
REMARK 3 7 5.1200 - 4.8600 0.97 7819 387 0.2550 0.3210
REMARK 3 8 4.8600 - 4.6500 0.97 7693 423 0.2690 0.3260
REMARK 3 9 4.6500 - 4.4700 0.97 7737 394 0.2790 0.2920
REMARK 3 10 4.4700 - 4.3200 0.97 7691 403 0.2690 0.3280
REMARK 3 11 4.3200 - 4.1800 0.97 7731 402 0.2560 0.3040
REMARK 3 12 4.1800 - 4.0600 0.98 7760 407 0.2610 0.3170
REMARK 3 13 4.0600 - 3.9500 0.97 7685 398 0.2710 0.3070
REMARK 3 14 3.9500 - 3.8600 0.98 7758 403 0.2970 0.3650
REMARK 3 15 3.8600 - 3.7700 0.98 7713 431 0.2890 0.3260
REMARK 3 16 3.7700 - 3.6900 0.98 7737 386 0.2870 0.3520
REMARK 3 17 3.6900 - 3.6200 0.98 7719 410 0.2910 0.3230
REMARK 3 18 3.6200 - 3.5500 0.98 7683 426 0.2770 0.3200
REMARK 3 19 3.5500 - 3.4800 0.98 7756 375 0.2950 0.3480
REMARK 3 20 3.4800 - 3.4300 0.98 7720 414 0.3110 0.3780
REMARK 3 21 3.4300 - 3.3700 0.98 7742 372 0.3200 0.3760
REMARK 3 22 3.3700 - 3.3200 0.98 7667 411 0.3440 0.4360
REMARK 3 23 3.3200 - 3.2700 0.98 7700 414 0.3410 0.3840
REMARK 3 24 3.2700 - 3.2200 0.97 7667 411 0.3350 0.3870
REMARK 3 25 3.2200 - 3.1800 0.97 7541 419 0.3400 0.3790
REMARK 3 26 3.1800 - 3.1400 0.96 7637 402 0.3460 0.4220
REMARK 3 27 3.1400 - 3.1000 0.96 7613 381 0.3580 0.3940
REMARK 3 28 3.1000 - 3.0600 0.96 7538 427 0.3790 0.4290
REMARK 3 29 3.0600 - 3.0300 0.95 7440 376 0.3760 0.4350
REMARK 3 30 3.0300 - 2.9900 0.77 6093 290 0.3950 0.4490
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
New Records in 3.2 Page 11

REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL

REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : 0.30
REMARK 3 B_SOL : 56.99
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.510
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.180
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 50.24
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.67
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -12.34000
REMARK 3 B22 (A**2) : -11.49000
REMARK 3 B33 (A**2) : 23.84000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.059 59703
REMARK 3 ANGLE : 3.995 80640
REMARK 3 CHIRALITY : 0.243 9800
REMARK 3 PLANARITY : 0.013 10535
REMARK 3 DIHEDRAL : 24.960 22449
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 2
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: CHAIN A
REMARK 3 ORIGIN FOR THE GROUP (A): 34.3280 -44.3362 -33.2464
REMARK 3 T TENSOR
REMARK 3 T11: -0.3752 T22: -0.2836
REMARK 3 T33: -0.1972 T12: -0.0686
REMARK 3 T13: 0.0888 T23: -0.1454
REMARK 3 L TENSOR
REMARK 3 L11: -0.0328 L22: -0.0264
REMARK 3 L33: -0.0458 L12: -0.0047
REMARK 3 L13: 0.0289 L23: -0.0435
REMARK 3 S TENSOR
REMARK 3 S11: -0.0220 S12: 0.7030 S13: 0.0888
REMARK 3 S21: -0.7542 S22: -0.0140 S23: -0.0265
REMARK 3 S31: -0.2584 S32: 0.0315 S33: 0.0000
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: CHAIN B
REMARK 3 ORIGIN FOR THE GROUP (A): 45.1940 -82.3594 -33.3841
REMARK 3 T TENSOR
REMARK 3 T11: -0.0302 T22: -0.0378
REMARK 3 T33: -0.0668 T12: -0.0642
REMARK 3 T13: 0.1450 T23: -0.0811
REMARK 3 L TENSOR
REMARK 3 L11: 0.0154 L22: 0.0032
REMARK 3 L33: -0.0145 L12: 0.0014
REMARK 3 L13: 0.0441 L23: 0.0209
REMARK 3 S TENSOR
New Records in 3.2 Page 12

REMARK 3 S11: -0.0023 S12: 0.6259 S13: 0.1176

REMARK 3 S21: -0.6677 S22: -0.0510 S23: 0.0868
REMARK 3 S31: -0.1498 S32: -0.2360 S33: 0.0000
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : 3
REMARK 3 NCS GROUP : 1
REMARK 3 NCS OPERATOR : 1
REMARK 3 REFERENCE SELECTION: CHAIN A AND (RESSEQ 2:525 )
REMARK 3 SELECTION : CHAIN B AND (RESSEQ 2:525 )
REMARK 3 ATOM PAIRS NUMBER : 3856
REMARK 3 RMSD : 0.214
REMARK 3 NCS OPERATOR : 2
REMARK 3 REFERENCE SELECTION: CHAIN A AND (RESSEQ 2:525 )
REMARK 3 SELECTION : CHAIN C AND (RESSEQ 2:525 )
REMARK 3 ATOM PAIRS NUMBER : 3856
REMARK 3 RMSD : 0.214
REMARK 3 NCS GROUP : 2
REMARK 3 NCS OPERATOR : 1
REMARK 3 REFERENCE SELECTION: CHAIN H AND (RESSEQ 2:525 )
REMARK 3 SELECTION : CHAIN I AND (RESSEQ 2:525 )
REMARK 3 ATOM PAIRS NUMBER : 3856
REMARK 3 RMSD : 0.224
REMARK 3 NCS OPERATOR : 2
REMARK 3 REFERENCE SELECTION: CHAIN H AND (RESSEQ 2:525 )
REMARK 3 SELECTION : CHAIN J AND (RESSEQ 2:525 )
REMARK 3 ATOM PAIRS NUMBER : 3856
REMARK 3 RMSD : 0.231
REMARK 3 NCS GROUP : 3
REMARK 3 NCS OPERATOR : 1
REMARK 3 REFERENCE SELECTION: CHAIN O AND (RESSEQ 1:97 )
REMARK 3 SELECTION : CHAIN P AND (RESSEQ 1:97 )
REMARK 3 ATOM PAIRS NUMBER : 728
REMARK 3 RMSD : 0.207
REMARK 3 NCS OPERATOR : 2
REMARK 3 REFERENCE SELECTION: CHAIN O AND (RESSEQ 1:97 )
REMARK 3 SELECTION : CHAIN Q AND (RESSEQ 1:97 )
REMARK 3 ATOM PAIRS NUMBER : 728
REMARK 3 RMSD : 0.211
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL

Example, PHENIX X-ray/neutron joint refinement:

1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE)
REMARK 3 AUTHORS : PAUL ADAMS, PAVEL AFONINE, VICENT CHEN, IAN
REMARK 3 : DAVIS, KRESHNA GOPAL, RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG, ROBERT IMMORMINO, TOM IOERGER,
REMARK 3 : AIRLIE MCCOY, ERIK MCKEE, NIGEL MORIARTY,
REMARK 3 : REETAL PAI, RANDY READ, JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON, TOD ROMO, JIM
REMARK 3 : SACCHETTINI, NICHOLAS SAUTER, JACOB SMITH,
REMARK 3 : LAURENT STORONI, TOM TERWILLIGER, PETER
REMARK 3 : ZWART
REMARK 3
REMARK 3 X-RAY DATA.
REMARK 3
REMARK 3 REFINEMENT TARGET : ML
REMARK 3
New Records in 3.2 Page 13

REMARK 3 DATA USED IN REFINEMENT.

REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.752
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.563
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.33
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.78
REMARK 3 NUMBER OF REFLECTIONS : 31524
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.1320
REMARK 3 R VALUE (WORKING SET) : 0.1286
REMARK 3 FREE R VALUE : 0.1660
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.36
REMARK 3 FREE R VALUE TEST SET COUNT : 2952
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 33.5691 - 4.8295 99.36 1424 130 14.09 17.98
REMARK 3 2 4.8295 - 3.8351 99.68 1420 125 10.35 11.36
REMARK 3 3 3.8351 - 3.3508 99.87 1378 129 10.50 12.46
REMARK 3 4 3.3508 - 3.0447 100.00 1413 122 11.75 13.73
REMARK 3 5 3.0447 - 2.8265 100.00 1385 138 11.98 16.91
REMARK 3 6 2.8265 - 2.6600 100.00 1384 131 12.78 16.50
REMARK 3 7 2.6600 - 2.5268 100.00 1351 162 12.18 17.96
REMARK 3 8 2.5268 - 2.4168 100.00 1394 137 12.38 15.72
REMARK 3 9 2.4168 - 2.3238 99.80 1381 130 12.31 15.43
REMARK 3 10 2.3238 - 2.2437 99.87 1385 142 12.59 17.55
REMARK 3 11 2.2437 - 2.1735 100.00 1368 123 12.06 18.73
REMARK 3 12 2.1735 - 2.1114 99.80 1377 143 11.86 15.53
REMARK 3 13 2.1114 - 2.0558 99.74 1337 171 11.30 16.96
REMARK 3 14 2.0558 - 2.0057 99.80 1353 143 11.92 15.94
REMARK 3 15 2.0057 - 1.9601 99.48 1386 144 12.20 16.05
REMARK 3 16 1.9601 - 1.9184 99.80 1340 136 12.98 19.21
REMARK 3 17 1.9184 - 1.8800 99.54 1380 142 13.77 21.17
REMARK 3 18 1.8800 - 1.8445 99.60 1371 141 14.14 18.20
REMARK 3 19 1.8445 - 1.8116 99.61 1344 172 15.59 22.03
REMARK 3 20 1.8116 - 1.7809 99.46 1321 158 16.78 22.15
REMARK 3 21 1.7809 - 1.7522 79.23 1080 133 20.53 25.69
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 GRID STEP FACTOR : 4.00
REMARK 3 K_SOL : 0.347
REMARK 3 B_SOL : 29.392
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.19
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.39
REMARK 3
REMARK 3 OVERALL SCALE FACTORS.
REMARK 3 SCALE = SUM(|F_OBS|*|F_MODEL|)/SUM(|F_MODEL|**2) : 0.8070
REMARK 3 ANISOTROPIC SCALE MATRIX ELEMENTS (IN CARTESIAN BASIS).
REMARK 3 B11 : 5.3378
REMARK 3 B22 : 5.4560
REMARK 3 B33 : 4.2407
REMARK 3 B12 : 0.0000
REMARK 3 B13 : 0.4309
REMARK 3 B23 : 0.0000
REMARK 3
REMARK 3 NEUTRON DATA.
REMARK 3
New Records in 3.2 Page 14

REMARK 3 REFINEMENT TARGET : ML

REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.194
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.110
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.53
REMARK 3 COMPLETENESS FOR RANGE (%) : 72.79
REMARK 3 NUMBER OF REFLECTIONS : 11884
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.2596
REMARK 3 R VALUE (WORKING SET) : 0.2566
REMARK 3 FREE R VALUE : 0.2912
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.35
REMARK 3 FREE R VALUE TEST SET COUNT : 992
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 40.1164 - 4.1959 92.61 2018 176 19.78 20.59
REMARK 3 2 4.1959 - 3.3309 88.97 1915 175 21.10 25.35
REMARK 3 3 3.3309 - 2.9100 77.65 1669 152 25.71 30.82
REMARK 3 4 2.9100 - 2.6440 69.69 1475 141 26.71 30.75
REMARK 3 5 2.6440 - 2.4545 63.92 1350 133 28.77 33.51
REMARK 3 6 2.4545 - 2.3098 59.97 1269 117 30.95 33.64
REMARK 3 7 2.3098 - 2.1942 56.09 1196 98 32.32 36.32
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 GRID STEP FACTOR : 4.00
REMARK 3 K_SOL : 0.530
REMARK 3 B_SOL : 82.904
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.45
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.92
REMARK 3
REMARK 3 OVERALL SCALE FACTORS.
REMARK 3 SCALE = SUM(|F_OBS|*|F_MODEL|)/SUM(|F_MODEL|**2) : 0.7477
REMARK 3 ANISOTROPIC SCALE MATRIX ELEMENTS (IN CARTESIAN BASIS).
REMARK 3 B11 : -0.7034
REMARK 3 B22 : -6.6254
REMARK 3 B33 : -7.0719
REMARK 3 B12 : -0.0000
REMARK 3 B13 : -1.2513
REMARK 3 B23 : -0.0000
REMARK 3
REMARK 3 MODEL CONTENT.
REMARK 3 ELEMENT ATOM RECORD COUNT OCCUPANCY SUM
REMARK 3 C 1659 1659.00
REMARK 3 D 2552 2552.00
REMARK 3 F 2 2.00
REMARK 3 O 769 769.00
REMARK 3 N 434 434.00
REMARK 3 P 3 3.00
REMARK 3 S 14 14.00
REMARK 3 Br 1 1.00
REMARK 3 TOTAL 5434 5434.00
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD MAX COUNT
New Records in 3.2 Page 15

REMARK 3 BOND : 0.018 0.153 5216

REMARK 3 ANGLE : 1.759 18.550 9458
REMARK 3 CHIRALITY : 0.160 1.197 392
REMARK 3 PLANARITY : 0.011 0.144 779
REMARK 3 DIHEDRAL : 25.100 176.474 1363
REMARK 3 MIN NONBONDED DISTANCE : 1.736
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES (HISTOGRAM).
REMARK 3 BONDS ANGLES NONBONDED
REMARK 3 0.00-0.02 4077 0.00 -1.85 7402 1.74-2.03 98
REMARK 3 0.02-0.03 733 1.85 -3.71 1672 2.03-2.33 1573
REMARK 3 0.03-0.05 247 3.71 -5.56 282 2.33-2.63 5095
REMARK 3 0.05-0.06 92 5.56 -7.42 67 2.63-2.92 7736
REMARK 3 0.06-0.08 33 7.42 -9.27 21 2.92-3.22 7666
REMARK 3 0.08-0.09 17 9.27 -11.13 5 3.22-3.51 9214
REMARK 3 0.09-0.11 8 11.13 -12.98 5 3.51-3.81 11450
REMARK 3 0.11-0.12 4 12.98 -14.84 2 3.81-4.11 14012
REMARK 3 0.12-0.14 3 14.84 -16.69 1 4.11-4.40 16177
REMARK 3 0.14-0.15 2 16.69 -18.55 1 4.40-4.70 20263
REMARK 3
REMARK 3 ATOMIC DISPLACEMENT PARAMETERS.
REMARK 3 WILSON B : 17.52
REMARK 3 ATOMS NUMBER OF ATOMS ISOTROPIC OR EQUIVALENT
REMARK 3 ISO. ANISO. MIN MAX MEAN
REMARK 3 ALL : 5434 0 0.63 96.73 17.02
REMARK 3 ALL (NO H) : 2882 0 1.76 96.73 17.15
REMARK 3 SOLVENT : 285 0 4.56 74.96 33.18
REMARK 3 NON-SOLVENT : 2597 0 1.76 96.73 15.39
REMARK 3 HYDROGENS : 2552 0 0.63 91.23 16.87
REMARK 3
REMARK 3 ATOMIC DISPLACEMENT PARAMETERS (HISTOGRAM, NON-H).
REMARK 3 ISOTROPIC OR EQUIVALENT
REMARK 3 1.76-11.26 1375
REMARK 3 11.26-20.75 764
REMARK 3 20.75-30.25 309
REMARK 3 30.25-39.75 172
REMARK 3 39.75-49.24 114
REMARK 3 49.24-58.74 65
REMARK 3 58.74-68.24 43
REMARK 3 68.24-77.74 26
REMARK 3 77.74-87.23 9
REMARK 3 87.23-96.73 5
REMARK 3