From mailer@bialko.llnl.gov  Sat Jun 15 15:42:29 2002
Date: Sat, 15 Jun 2002 15:42:23 -0700 (PDT)
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# 
# Protein Structure Prediction Center, LLNL, Livermore, CA
# Verification system Sat Jun 15 15:15:52 PDT 2002 by Adam Zemla
# 
# The PIN number of your submission is: PIN_269905_10815
# (PIN number is not an ACCESSION CODE)
# 

Thank you for your submission.
Your prediction has been accepted with an ACCESSION CODE:

T0135SS007_1 
 
Current information on models submitted in prediction  T0135SS007
 MODEL_INDEX      PIN               CODE             DATE           E-mail
T0135SS007_1  PIN_269905_10815 6269-7633-6117  06/15/02 15:15:52 casp5@bialko.llnl.gov
 
PLEASE NOTE: Submission of a duplicate prediction (same target, format, 
       model index) will REPLACE an existing submission (ACCESSION CODE), 
       provided it is received before the target has expired. 
 
The current status of models accepted for target  T0135
 MODEL_INDEX      PIN               CODE             DATE           E-mail
T0135SS007_1  PIN_269905_10815 6269-7633-6117  06/15/02 15:15:52 casp5@bialko.llnl.gov 


For more information on accepted models submitted to CASP5 see: 
http://PredictionCenter.llnl.gov/casp5/models/casp5-models.html

Please check below if the verified data 
of your submission is correct.

# Reading prediction format SS

PFRMAT SS
TARGET T0135
AUTHOR 6269-7633-6117

# Reading MODEL  1

# Reading prediction format SS             (DONE)

# Checking the SS prediction MODEL  1
# Checking the SS prediction MODEL  1      (DONE)

# MODEL index: 1 

# Total number of residues in model:           108 
# Number of residues with nonzero confidence:  108 
# Number of METHOD records:                     42 

# No errors.


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PFRMAT SS
TARGET T0135
AUTHOR 6269-7633-6117
METHOD CAFASP
METHOD samt99
METHOD  This prediction was derived from the following methods
METHOD  by averaging the corresponding probabilities: 
METHOD  Method 0:
METHOD  TARGET seed-seqs-5115.a2m(1)
METHOD  Using neural net overrep-2500-IDaa13-5-9-7-10-5-9-11-ehl2-seeded2-stride-trained.net
METHOD  This is a 4-layer network, with 
METHOD  window units
METHOD      5     9
METHOD      7    10
METHOD      5     9
METHOD     11     3 (1 EHL2 )
METHOD  The input amino acid frequencies were determined from
METHOD  alignment /var/tmp/hmm-target99-work-14313//target-align-14313.a2m
METHOD  with weighted counts, using EntropyWeight(1.4 bits/column, 10)
METHOD  The weighting was determined by the posterior distribution
METHOD  after regularizing with /projects/compbio/lib/recode3.20comp.
METHOD  Counts were regularized to probabilities using
METHOD  /projects/compbio/lib/recode3.20comp
METHOD  Total sequence weight for alignment was 11.4415
METHOD 
METHOD  CHAIN 1
METHOD  Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: seed-seqs-5115.a2m(1)
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.cc76.20712/model.mod
METHOD  database_files: /projects/compbio/programs/hmm-server-2.0/src/pcc/data/overrep-2260.verify.mixed.seq /projects/compbio/programs/hmm-server-2.0/src/pcc/data/overrep-2260.verify.mixed.2d
METHOD  scoring_mode: local
METHOD  null_model: reverse
METHOD  scoring_algorithm: EM
METHOD  adjust_score: 2
METHOD  date: Wed Jun 12 13:04:53 2002
METHOD  Method 2:
METHOD  ###begin 0
METHOD 
METHOD  Protein secondary structure prediction by universal HMM
METHOD  HMM file: /projects/compbio/programs/hmm-server-2.0/src/pcc/scripts/gdac.test.initreest.38state.abb.isites.gd.updated.ghmm-128reest-1-128-105-0.07gd
METHOD  Alignment file: /var/tmp/hmm-target99-work-14313//target-align-14313.a2m
METHOD 
METHOD  guide seq name: seed-seqs-5115.a2m(1), 108 bases, 51F9FA0D checksum.
METHOD  ###end 0
MODEL 1
M C    0.692
A C    0.607
T C    0.572
R C    0.525
T C    0.483
P C    0.432
K H    0.401
L H    0.374
V E    0.376
K E    0.398
H E    0.523
T E    0.625
L E    0.639
L E    0.626
T E    0.572
R E    0.491
F E    0.376
K C    0.515
D C    0.562
E C    0.601
I C    0.627
T C    0.653
R H    0.682
E H    0.696
Q H    0.708
I H    0.774
D H    0.793
N H    0.791
Y H    0.779
I H    0.781
N H    0.775
D H    0.753
Y H    0.781
T H    0.756
N H    0.737
L H    0.708
L H    0.693
D H    0.673
L H    0.608
I H    0.487
P C    0.462
S C    0.436
M C     0.43
K C    0.392
S E    0.396
F E    0.458
N E    0.444
W E    0.407
G C    0.545
T C    0.555
D C    0.569
L C    0.583
G C    0.623
M C    0.611
E C    0.695
S H    0.466
A H      0.5
E H    0.531
L H    0.473
N C    0.498
R C    0.538
G C    0.591
Y C    0.502
T C    0.417
H E    0.503
A E    0.594
F E    0.622
E E    0.612
S E    0.567
T E    0.479
F E    0.398
E C    0.532
S C    0.642
K H    0.602
S H    0.625
G H    0.618
L H    0.669
Q H    0.666
E H    0.654
Y H     0.57
L H    0.425
D C    0.545
S C    0.703
A H    0.597
A H    0.649
L H    0.665
A H    0.664
A H    0.675
F H    0.669
A H    0.664
E H    0.654
G H    0.622
F H    0.574
L H     0.52
P H    0.537
T H    0.495
L H    0.433
S C     0.55
Q C    0.544
R C    0.379
L E    0.566
V E    0.608
I E    0.585
D E    0.468
Y C    0.404
F C    0.525
L C     0.56
Y C    0.625
END




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