CASP ROLL: the Community Wide Experiment on the
Critical Assessment of Techniques for Protein Structure Prediction on rolling basis

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Submission Rules and Format

General submission rules

  • Models from both regular groups and servers should be submitted directly by e-mail to casprol AT predictioncenter.org or using the CASP ROLL model submission facility .
  • Predictions for CASP ROLL may be submitted in 2 separate formats:
      TS    # 3D atomic coordinates (Tertiary Structure) prediction
      RR    # Residue-Residue separation distance prediction
    

  • One team may make a prediction of a target by submitting up to five models in TS or RR formats.
  • Each submission must begin with the PFRMAT, TARGET and AUTHOR records, contain the METHOD field and at least one block starting with the MODEL and ending with the END record.
  • Each submission file should contain prediction for only one target.
  • Each submission file should contain only one of the allowed format categories.
  • Each submission file may contain either one or several models in the same prediction category. Most of the evaluation and assessment will focus on the model labeled '1' (model index 1, see MODEL record). Each model should begin with the MODEL record, end with the END record, and contain no target residue repetitions. You may specify only one set of required header fields (PFRMAT, TARGET, AUTHOR, METHOD) above the first MODEL record in the prediction file. A multiple-model file will be split into separate files (one model per file) and each model will be sent separately to the verification server.
  • Submission of a duplicate model (same target, format category, group, model index) will replace previously accepted model, provided it is received before the target has expired.
  • Each submitted model is automatically verified by the format verification server. In case of successful submission no confirmation email will be sent. A unique ACCESSION CODE is composed from the number of the target, prediction format category, prediction group number, and model index.
       Example:
    
       Accession code  R0001TS005_2  has the following components:
         R0001   target number
         TS      Tertiary Structure (PFRMAT TS)
         005     prediction group 5
         2       model index 2 
    
    The accepted predictions could be viewed using Model Viewer link from the CASP ROLL web page.
    If the submission contains an error, regular group leader or server contact person will be immediately notified through email. If your prediction is rejected for format inconsistency, you will have the possibility to correct problems and re-send prediction(s) within the target prediction time window.

Submission rules specific to regular group predictions (3+ week deadline)

  • Predictions can be submitted by a group leader or a group member with submission privileges. The group leader can set the privileges (regular member or submitter) for every member of his group using the 'Review member status' option from 'My CASP ROLL profile' link. Members of prediction groups who intend to submit predictions should receive submission permission from the group leader first and then use the 12-digit Registration Code of the group to submit predictions for that group.
  • When sending predictions by email, please remember to use as an origination point only the email address registered with the Prediction Center (make sure we have the updated email address for you on file - check for this your "My Personal Data" link from our menu). If you cannot use the registered email address for submission, please use the submission form instead .
  • Time for returning regular predictions is set separately for each target through the Target List form. Usually regular predictors have around 3 weeks from the date of target release to return a prediction. For the most difficult targets this period may be prolonged.

Submission rules specific to server group predictions

  • CASP ROLL queries will be sent to the registered servers from the CASP distribution server casprol-meta AT predictioncenter.org. Email servers are requested to reply to this address immediately upon receiving the query with an acceptance email with subject: "R0xxx - query received by MY_SERVER". This will help us to track whether your server received a request from us so that we can timely address any connectivity issues. Please do not send your predictions to this address as they will be ignored.
  • We will be sending 3 variables to your server's submission URL (or email): the SEQUENCE, the TARGET-NAME and the REPLY-E-MAIL (where to return the results). Names for these server-specific parameters will be taken from your server registration form.
  • Server models should be returned automatically to the address specified in the REPLY-E-MAIL field of the query. Please note that the return address should be always taken from our query and not hard-coded as we may change it during the season.
  • Servers are requested to return predictions in 72 hours from the target release time. No additional time for corrections will be allotted, but corrections will be accepted within the original 72 hour window. Please, send your corrections manually to the address specified in the REPLY-E-MAIL field of the original query. Remember, that corrections can be submitted only by a group leader or a group member with submission privileges. The group leader can set the privileges (regular member or submitter) for every member of his group using the 'Review member status' option from 'My CASP ROLL profile' link. Members of prediction groups who intend to submit predictions should receive submission permission from the group leader first.
  • Server models must be submitted in the body of the email as a plain text. Predictions in attachments to the emails will be rejected. Subject of the email preferrably should contain the target number and the group name.
  • Each submission may contain several models. If server returns more than 5 models, the models numbered 6 and higher will be ignored.
  • The submission engine will resend the query if it encounters obvious connecting problems (network timeouts, 'no response' etc.). Failures that go beyond that require special attention, but we'll make every effort to notify server curators ASAP if we suspect something is not working.


Format description

All submissions contain records described below. Each of these records must begin with a standard keyword. In all submissions standard keywords must begin in the first column of a record. The keyword set is as follows:
PFRMAT     Format specification code:  TS , RR  
TARGET     Target identifier from the CASP ROLL target table
AUTHOR     XXXX-XXXX-XXXX   (registration code of the Group Leader) or Server Group Name 
SCORE      Reliability of the model (optional) 
REMARK     Comment record (may appear anywhere after the first 3 required lines, optional)
METHOD     Records describing the methods used
MODEL      Beginning of the data section for the submitted model
PARENT     Specifies structure template used to generate the TS model 
TER        Terminates independent segments of structure in the TS model
END        End of the submitted model

Models should be submitted in Plain Text format.


Record PFRMAT should appear on the first line of the prediction and is used for all submissions.

   PFRMAT TS
     TS  indicates that submission contains 3D atomic coordinates
         in standard PDB format

   PFRMAT RR
     RR  indicates that submission contains a residue-residue 
         separation distance prediction


Record TARGET should appear on the second line of the prediction and is used for all submissions.

   TARGET Rxxxx
     Rxxxx indicates id of the target predicted.


Record AUTHOR should appear on the third line of the prediction and is used for all submissions.

 For all groups:
   AUTHOR XXXX-XXXX-XXXX
          XXXX-XXXX-XXXX indicates the Group Registration code.
          This is the code obtained by the group leader upon registration.

	  Note: Members of prediction groups who intend to submit predictions
          should receive submission permissions from the group leader and 
	  use the registration code of the Group for all predictions submitted by 
	  that group. If sending predictions by email, please send them from the 
	  registered emails of the group leader or group submitter. 
	  If you can not use these emails for submission, please login to our 
	  website and then use our web-based submission facility. 

 Servers alternatively can be identified using their registered group names: 
   AUTHOR MY_SERVER_NAME     
      or 
   REMARK AUTHOR MY_SERVER_NAME
          where MY_SERVER_NAME is a name selected for the server group at registration
 


SCORE Optional. This record may be used to report a model reliability score. It will not influence the evaluation.


REMARK Optional. PDB style 'REMARK' records may be used anywhere in the submission. These records may contain any text and will in general not influence evaluation.


Records METHOD are used for all submissions.
These records describe the methods used. Predictors are urged to provide as full a description of the methods as possible, including references, data libraries used, and values of default and non-default parameters. These descriptions will be made available via the Prediction Center WEB pages as well as printed along with the other materials distributed at the meeting. Length of 100 - 500 words is suggested.


Record MODEL is used for all submissions.
Signifies the beginning of model data.

   MODEL  n  
     n          Model index n is used to indicate predictor's ranking
                according to her/his belief which model is closest to the 
                target structure (1 <= n <= 5). Model index is included
                automatically in the ACCESSION CODE. All models with index
                higher than 5 will be discarded.


Record PARENT is required only for the submissions in the TS format.
PARENT record indicates structure templates used to generate any independent segment of MODEL (see description of the TS format below). The PARENT record should be placed as the first record of any such independent segment. Only one PARENT record per structure segment is allowed. For multimeric predictions only one PARENT record per whole structure is allowed.

   PARENT N/A
     Indicates that a prediction is not directly based on any known
     structure. Note that this is the only indication in the file that the
     prediction is ab initio, so is a critical piece of information.

   PARENT 1abc_A
     Indicates that the model or the independent segment of structure is
     based on a single PDB entry 1abc chain A (use _A to indicate chain A).
     All template-based predictions should be submitted with this form 
     of the PARENT record. Note that, in order to be accepted, the code 
     must correspond to a current PDB entry.

   PARENT 1cdc 2def_g [3hij_k ...]
     Indicates that the model is based on more than one structural template. 
     Up to five PDB chains may be listed here with additional detailed information 
     included in the METHOD records. Subdomains of the target structure found 
     to correspond to different known folds may be submitted as independent 
     segments of structure with reference to only one PDB chain per segment.  


Record TER is used to terminate an independent segment of structure (PFRMAT TS). Every TER record should correspond to the preceding PARENT record in the model.

   TER


3D atomic coordinates (PFRMAT TS).
Standard PDB atom records are used for the atomic coordinates. Format of the submission requires that 80 column long records are used. These may be spaces when needed (see target template PDB files as provided in specific target descriptions available through the CASP ROLL target table).

Coordinates for each model or an independent structure segment should begin with a single PARENT record and terminate with a TER record (see above).

It is requested that coordinate data be supplied for at least all non-hydrogen main chain atoms, i.e. the N, CA, C and O atoms of every residue. Specifically, if only CA atoms are predicted by the method, predictors are encouraged to build the main chain atoms for every residue before submission to CASP. One program that can make such a conversion is Maxsprout server of Liisa Holm and co-workers. (If only CA atoms were submitted it would not be possible to run most of the analysis software, which would severely limit the evaluation of that prediction.)

When multiple independent segments of structure are used in a prediction, they will be evaluated separately with no assumption of a common frame of reference between the segments. For any given MODEL, no target residue may be repeated among all such independent structure segments. Even though all of the independent PARENT-TER frames will be evaluated, only the best scoring frame will contribute to the group score on any given evaluation domain. Potential multi-domain nature of targets will be addressed in the evaluation even if the prediction is made in a single frame of reference (i.e. without separation into multiple segments of structure).

For quaternary structure predictions, coordinates for all chains should be submitted in the same frame of reference and therefore only one PARENT - TER section is allowed per prediction. This means that no TER record should separate different chains (this is different from the PDB!). First chain should be labeled as A and all the subsequent chains should follow the latin alphabet, e.g., tetramer's chains should be labeled as A, B, C, D.
There will be no announcements or assignments of targets to oligomeric prediction category. Instead, for every target you can submit either tertiary structure prediction or quaternary structure prediction. There is no need to submit monomer in addition to a multimer: we will automatically extract coordinates of the first chain from the quaternary prediction and save it as a monomer for future mainstream evaluation alongside with monomers submitted by other groups. Multimeric predictions will be evaluated separately. Tentative oligomeric state of the protein (if provided by the experimentalists) will be announced through our Target List page, but it is up to predictor to decide what oligomerization state the protein is in.

Atoms for which a prediction has been made must contain a value between 0.01 and 1.00 (usually "1.00") in the occupancy field; those for which no prediction has been made must either contain "0.00" in that field or be skipped altogether.

In place of temperature factor field, the error estimates, in Angstroms, should be provided. If your method can not produce these estimates - please put some high number (e.g., "99.9") in that field. We strongly encourage predictors to submit their error estimates for own predictions as these results will be separately evaluated in the quality assessment category.


Residue-Residue separation prediction (PFRMAT RR).
Data in this format are inserted between MODEL and END records of the submission file.
Format for the predicted separation distance between pairs of residues. The distance is defined as the separation between C-beta atoms (C-alpha for glycine residues).

The (five column) RR format:

   i  j  d1  d2  p

   Notes (see Example 2):
     - entire target sequence should be split over multiple lines with a
       maximum of 50 residues per line
     - for intrachain residue-residue contacts residue number indices 
       i and j should be used for distance specification (i < j), i.e. 
       only one diagonal of the separation matrix should be supplied
     - the distances d1 and d2 (real numbers) should indicate the range of 
       Cb-Cb distance predicted for the residue pair (C-alpha for glycines)
     - the real number p should range from 0.0 - 1.0 to indicate
       probability of the distance falling between the predicted range
     - residue 'contacts' (defined here - as in CASP2 - as Cb-Cb<8A) can be 
       predicted with this format as:
         i  j  0  8  p
     - any pair NOT listed is assumed to be NOT considered by predictor
     - for multichain predictions residue indices should be composed of 
       chain ID and residue number, e.g. A2, B44 (see Example 4B).


END record is used for all predictions and indicates the end of a single model submission.


Example 1. Atomic coordinates (Tertiary Structure)

The primary CASP ROLL format used for tertiary structure prediction

(A) An example of TS prediction.

PFRMAT TS
TARGET R9999
AUTHOR 1234-5678-9000
REMARK Predictor remarks
METHOD Description of methods used
METHOD Description of methods used
MODEL  1 
PARENT 1abc 1def_A
ATOM      1  N   GLU     1      10.982  -9.774   1.377  1.00  0.50
ATOM      2  CA  GLU     1       9.623  -9.833   1.984  1.00  0.50
ATOM      3  C   GLU     1       8.913 -11.104   1.521  1.00  0.50
ATOM      4  O   GLU     1       9.187 -11.630   0.461  1.00  0.50
ATOM      5  CB  GLU     1       8.814  -8.614   1.546  1.00  0.50
ATOM      6  CG  GLU     1       7.372  -8.754   2.039  1.00  0.50
ATOM      7  CD  GLU     1       7.339  -8.625   3.562  1.00  0.50
ATOM      8  OE1 GLU     1       8.370  -8.307   4.131  1.00  0.50
ATOM      9  OE2 GLU     1       6.284  -8.846   4.132  1.00  0.50
ATOM     10  N   THR     2       7.998 -11.599   2.304  1.00  1.60
ATOM     11  CA  THR     2       7.266 -12.832   1.907  1.00  1.60
ATOM     12  C   THR     2       6.096 -12.456   1.005  1.00  1.60
ATOM     13  O   THR     2       5.008 -12.217   1.466  1.00  1.60
ATOM     14  CB  THR     2       6.731 -13.533   3.157  1.00  1.60
ATOM     15  OG1 THR     2       7.662 -13.379   4.220  1.00  1.60
ATOM     16  CG2 THR     2       6.526 -15.019   2.864  1.00  1.60
ATOM     17  N   VAL     3       6.308 -12.396  -0.278  1.00  1.70
ATOM     18  CA  VAL     3       5.190 -12.030  -1.187  1.00  1.70
ATOM     19  C   VAL     3       3.954 -12.870  -0.844  1.00  1.70
ATOM     20  O   VAL     3       2.834 -12.471  -1.090  1.00  1.70
ATOM     21  CB  VAL     3       5.608 -12.274  -2.641  1.00  1.70
ATOM     22  CG1 VAL     3       5.542 -13.771  -2.959  1.00  1.70
ATOM     23  CG2 VAL     3       4.664 -11.514  -3.573  1.00  1.70
ATOM     24  N   GLU     4       4.146 -14.029  -0.272  1.00  1.70
ATOM     25  CA  GLU     4       2.976 -14.882   0.086  1.00  1.60
ATOM     26  C   GLU     4       2.153 -14.190   1.175  1.00  1.50
ATOM     27  O   GLU     4       0.942 -14.141   1.109  1.00  1.40
ATOM     28  CB  GLU     4       3.465 -16.238   0.597  1.00  1.30
ATOM     29  CG  GLU     4       2.336 -17.264   0.479  1.00  1.20
ATOM     30  CD  GLU     4       2.929 -18.671   0.391  1.00  1.10
ATOM     31  OE1 GLU     4       4.056 -18.846   0.823  1.00  1.00
ATOM     32  OE2 GLU     4       2.246 -19.551  -0.108  1.00  0.90
TER
END
(B) A model consisting of 2 independent structure segments (could be a target modeled from two PDB domains, where relative orientation is unknown; could be 2 fragments predicted by ab initio methods - ab initio example shown). In a single MODEL no residue should appear twice among all such segments.
PFRMAT TS
TARGET R9999
AUTHOR 1234-5678-9000
REMARK Predictor remarks
METHOD Description of methods used
METHOD Description of methods used
MODEL  1
PARENT N/A
ATOM      1  N   GLU     1      10.982  -9.774   1.377  1.00  0.50
ATOM      2  CA  GLU     1       9.623  -9.833   1.984  1.00  0.50
ATOM      3  C   GLU     1       8.913 -11.104   1.521  1.00  0.50
ATOM      4  O   GLU     1       9.187 -11.630   0.461  1.00  0.50
ATOM      5  CB  GLU     1       8.814  -8.614   1.546  1.00  0.50
ATOM      6  CG  GLU     1       7.372  -8.754   2.039  1.00  0.50
ATOM      7  CD  GLU     1       7.339  -8.625   3.562  1.00  0.50
ATOM      8  OE1 GLU     1       8.370  -8.307   4.131  1.00  0.50
ATOM      9  OE2 GLU     1       6.284  -8.846   4.132  1.00  0.50
ATOM     10  N   THR     2       7.998 -11.599   2.304  1.00  1.60
ATOM     11  CA  THR     2       7.266 -12.832   1.907  1.00  1.60
ATOM     12  C   THR     2       6.096 -12.456   1.005  1.00  1.60
ATOM     13  O   THR     2       5.008 -12.217   1.466  1.00  1.60
ATOM     14  CB  THR     2       6.731 -13.533   3.157  1.00  1.60
ATOM     15  OG1 THR     2       7.662 -13.379   4.220  1.00  1.60
ATOM     16  CG2 THR     2       6.526 -15.019   2.864  1.00  1.60
ATOM     24  N   GLU     4       4.146 -14.029  -0.272  1.00  1.70
ATOM     25  CA  GLU     4       2.976 -14.882   0.086  1.00  1.60
ATOM     26  C   GLU     4       2.153 -14.190   1.175  1.00  1.50
ATOM     27  O   GLU     4       0.942 -14.141   1.109  1.00  1.40
ATOM     28  CB  GLU     4       3.465 -16.238   0.597  1.00  1.30
ATOM     29  CG  GLU     4       2.336 -17.264   0.479  1.00  1.20
ATOM     30  CD  GLU     4       2.929 -18.671   0.391  1.00  1.10
ATOM     31  OE1 GLU     4       4.056 -18.846   0.823  1.00  1.00
ATOM     32  OE2 GLU     4       2.246 -19.551  -0.108  1.00  0.90
TER
PARENT N/A
ATOM     17  N   VAL     3       6.308 -12.396  -0.278  1.00  1.70
ATOM     18  CA  VAL     3       5.190 -12.030  -1.187  1.00  1.70
ATOM     19  C   VAL     3       3.954 -12.870  -0.844  1.00  1.70
ATOM     20  O   VAL     3       2.834 -12.471  -1.090  1.00  1.70
ATOM     21  CB  VAL     3       5.608 -12.274  -2.641  1.00  1.70
ATOM     22  CG1 VAL     3       5.542 -13.771  -2.959  1.00  1.70
ATOM     23  CG2 VAL     3       4.664 -11.514  -3.573  1.00  1.70
TER
END


Example 2. Residue-Residue contact prediction

The flexibility offered by the new format allows algorithms parameterized to predict any distance range to be used. Below is an example of how to use the new residue-residue separation distance format to submit a prediction of residue contacts defined as Cb-Cb distances < 8 A.
PFRMAT RR
TARGET R9999
AUTHOR 1234-5678-9000
REMARK Predictor remarks
METHOD Description of methods used
METHOD Description of methods used
MODEL  1
HLEGSIGILLKKHEIVFDGC       # <- entire target sequence (up to 50 
HDFGRTYIWQMSD              #    residues per line)
1  9  0  8  0.70        
1 10  0  8  0.70           # <- indices of residues: i and j (integers), 
1 12  0  8  0.60           # <- the range of Cb-Cb distance predicted
1 14  0  8  0.20           #    for the residue pair: d1 and d2 (real),
1 15  0  8  0.10           # <- probability of the distance between 
1 17  0  8  0.30           #    Cb atoms being within the specified
1 19  0  8  0.50           #    range: p (real)
2  8  0  8  0.90
3  7  0  8  0.70
3 12  0  8  0.40
3 14  0  8  0.70
3 15  0  8  0.30
4  6  0  8  0.90
7 14  0  8  0.30
9 14  0  8  0.50
END


Example 4. Multichain predictions

(A) An example of 3D atomic coordinates model prediction.
PFRMAT TS
TARGET R9999
AUTHOR 1234-5678-9000
REMARK Predictor remarks
METHOD Description of methods used
METHOD Description of methods used
MODEL  1 
PARENT N/A
ATOM      1  N   GLU A   1      22.576  19.032  -5.026  1.00  0.00
ATOM      2  CA  GLU A   1      22.879  20.313  -4.321  1.00  0.00
ATOM      3  CB  GLU A   1      22.285  21.478  -5.449  1.00  0.00
ATOM      4  CG  GLU A   1      23.018  21.946  -6.707  1.00  0.00
ATOM      5  CD  GLU A   1      24.351  22.625  -6.434  1.00  0.00
ATOM      6  OE1 GLU A   1      25.379  21.908  -6.380  1.00  0.00
ATOM      7  OE2 GLU A   1      24.381  23.879  -6.291  1.00  0.00
ATOM      8  O   GLU A   1      22.237  20.962  -2.117  1.00  0.00
ATOM      9  C   GLU A   1      21.857  20.684  -3.261  1.00  0.00
ATOM     10  N   VAL A   2      20.585  20.675  -3.601  1.00  0.00
ATOM     11  CA  VAL A   2      19.530  21.006  -2.624  1.00  0.00
ATOM     12  CB  VAL A   2      18.277  21.590  -3.319  1.00  0.00
ATOM     13  CG1 VAL A   2      17.182  21.859  -2.270  1.00  0.00
ATOM     14  CG2 VAL A   2      18.656  22.833  -4.079  1.00  0.00
ATOM     15  O   VAL A   2      18.770  18.750  -2.603  1.00  0.00
ATOM     16  C   VAL A   2      19.096  19.721  -1.933  1.00  0.00
ATOM     17  N   HIS A   3      19.115  19.700  -0.603  1.00  0.00
ATOM     18  CA  HIS A   3      18.780  18.489   0.122  1.00  0.00
ATOM     19  CB  HIS A   3      19.559  18.445   1.410  1.00  0.00
ATOM     20  CG  HIS A   3      21.015  18.684   1.224  1.00  0.00
ATOM     21  CD2 HIS A   3      21.767  19.803   1.367  1.00  0.00
ATOM     22  ND1 HIS A   3      21.851  17.721   0.702  1.00  0.00
ATOM     23  CE1 HIS A   3      23.072  18.220   0.589  1.00  0.00
ATOM     24  NE2 HIS A   3      23.048  19.478   0.985  1.00  0.00
ATOM     25  O   HIS A   3      16.777  19.181   1.220  1.00  0.00
ATOM     26  C   HIS A   3      17.296  18.417   0.409  1.00  0.00
REMARK 
REMARK Predictors should NOT use TER separator between chains 
REMARK
ATOM   1321  N   GLU B   1     -22.603 -17.981  -4.847  1.00  0.00
ATOM   1322  CA  GLU B   1     -22.889 -19.285  -4.180  1.00  0.00
ATOM   1323  CB  GLU B   1     -22.342 -20.410  -5.372  1.00  0.00
ATOM   1324  CG  GLU B   1     -23.122 -20.828  -6.619  1.00  0.00
ATOM   1325  CD  GLU B   1     -24.447 -21.511  -6.324  1.00  0.00
ATOM   1326  OE1 GLU B   1     -25.468 -20.792  -6.207  1.00  0.00
ATOM   1327  OE2 GLU B   1     -24.479 -22.769  -6.227  1.00  0.00
ATOM   1328  O   GLU B   1     -22.172 -20.020  -2.026  1.00  0.00
ATOM   1329  C   GLU B   1     -21.830 -19.701  -3.172  1.00  0.00
ATOM   1330  N   VAL B   2     -20.572 -19.685  -3.557  1.00  0.00
ATOM   1331  CA  VAL B   2     -19.485 -20.056  -2.630  1.00  0.00
ATOM   1332  CB  VAL B   2     -18.260 -20.619  -3.392  1.00  0.00
ATOM   1333  CG1 VAL B   2     -17.131 -20.932  -2.393  1.00  0.00
ATOM   1334  CG2 VAL B   2     -18.674 -21.832  -4.184  1.00  0.00
ATOM   1335  O   VAL B   2     -18.711 -17.807  -2.553  1.00  0.00
ATOM   1336  C   VAL B   2     -19.020 -18.800  -1.909  1.00  0.00
ATOM   1337  N   HIS B   3     -18.990 -18.829  -0.580  1.00  0.00
ATOM   1338  CA  HIS B   3     -18.623 -17.648   0.178  1.00  0.00
ATOM   1339  CB  HIS B   3     -19.356 -17.649   1.494  1.00  0.00
ATOM   1340  CG  HIS B   3     -20.819 -17.875   1.353  1.00  0.00
ATOM   1341  CD2 HIS B   3     -21.571 -18.995   1.480  1.00  0.00
ATOM   1342  ND1 HIS B   3     -21.667 -16.890   0.896  1.00  0.00
ATOM   1343  CE1 HIS B   3     -22.894 -17.378   0.809  1.00  0.00
ATOM   1344  NE2 HIS B   3     -22.864 -18.650   1.156  1.00  0.00
ATOM   1345  O   HIS B   3     -16.586 -18.389   1.177  1.00  0.00
ATOM   1346  C   HIS B   3     -17.129 -17.592   0.414  1.00  0.00
TER
END
(B) An example of how to use the RR format to submit a prediction of interchain (chains A and B) residue-residue contacts defined as Cb-Cb distances < 8 A.
PFRMAT RR
TARGET R9999
AUTHOR 1234-5678-9000
REMARK Predictor remarks
METHOD Description of methods used
METHOD Description of methods used
MODEL  1
HLEGSIGILLKKHEIVFDGC         # <- entire target sequence (up to 50 
HDFGRTYIWQMSD                #    residues per line)
A1 B9   0  8  0.70        
A1 B10  0  8  0.70           # <- indices of residues: Ai and Bj, 
A1 B12  0  8  0.60           # <- the range of Cb-Cb distance predicted
A1 B14  0  8  0.20           #    for the residue pair: d1 and d2 (real),
A1 B15  0  8  0.10           # <- probability of the distance between 
A1 B17  0  8  0.30           #    Cb atoms being within the specified
A1 B19  0  8  0.50           #    range: p (real)
A2 B8   0  8  0.90
A3 B7   0  8  0.70
A3 B12  0  8  0.40
A3 B14  0  8  0.70
A3 B15  0  8  0.30
A4 B6   0  8  0.90
A7 B14  0  8  0.30
A9 B14  0  8  0.50
END

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