Ras PLM Score Configuration

Protein := P01112
In Membrane? := no
Coupling Scoring := PLM
Compute Structures? := yes
Known Structure := 5p21
Your Job Name := ras_h_plm
Your Email := alexander.betz@googlemail.com
Domain/Family Name := 
(Generate Alignment) Tool For Generating Alignment := hhblits
(Generate Alignment) Start offset in Sequence := 1
(Generate Alignment) End offset in Sequence := 
(Generate Alignment) E-Value := -3
(Generate Alignment) Match Column Gap Pct Limit := 50
(Upload Alignment) Alignment File := 
(Lookup Alignment) PFAM Accession := PF00071
PFAM Member Selector := RASH_HUMAN
Alignment Member Gap Pct Limit := 70
Constraint Count List := 76 123 189
Structure Variant Count := 5
Contact Map EC Counts := 
Residue Contact Proximity Threshold := 5
Residue Contact Proximity Measure := nearest_atom
Overlay Computed Structure EC Count := 
Overlay Computed Structure Variant := 
False Positive Plot EC Count := 300
(Secondary Structure) Flanking Upstream Residues := 7
(Secondary Structure) Flanking Downstream Residues := 7
Membrane Helix Topology Override := 
Psipred Helix Override := 
Psipred Strand Override := 
High Conservation Filter Threshold := 100
High Conservation Filter Excludes Gaps? := no
Generate Constraints for Side Chains? := yes
Constraint Minimum Residue Offset Distance := 5
Constraint Rank Weight Function := none
N Over I Weight Numerator := 10
Tanh Weight Global := 20
Tanh Weight Count := 400
Tanh Weight Steepness := 1
Tanh Weight Epsilon := 0.3
NormCDF Weight Mean := 50
NormCDF Weight STDDEV := 25
SS Distance Weight := 5
Allowable Mismatch Offset List := 
Gap Count Limit := 3
Identical Dist := 0
Correct Ambiguous Dist := 1
Ambiguous Ambiguous Dist := 2
Other Ambiguous Dist := 4
Mismatch Dist := 34
Unaligned Residue Dist := 10
Internal Gap Open Dist := 3
Peripheral Gap Open Dist := 1
Maximum Distance Cutoff Sequence Length Denominator := 16
Maximum Distance Cutoff Absolute Minimum := 4
Substantial Coverage After Gap := 4
Suggestion Gap Count := 2
MSA Member Weighting Distance Threshold := 0.1
EC Pseudocount Adjustment := 0.5
EC Method To Resolve Ambiguous Residues := suppress_member
Maximum Domain Width := 500
Minimum Domain Width := 30
Minimum Alignment Member Count := 300
Minimum Alignment Match Col Pct := 30
PLM Field Coefficient := 0.01
PLM Coupling Coefficient := 0.01
Add Upstream Flanking Residues For Modeling := 0
Add Downstream Flanking Residues For Modeling := 0
Apply Distance Constraints := yes
Apply Angle Constraints := yes
Alpha Helix Phi Angle Degrees := -57.0
Alpha Helix Phi Angle Range := 7.0
Alpha Helix Phi Energy Constant := 0.5
Alpha Helix Phi Exponent := 2
Alpha Helix Psi Angle Degrees := -47.0
Alpha Helix Psi Angle Range := 7.0
Alpha Helix Psi Energy Constant := 0.5
Alpha Helix Psi Exponent := 2
Beta Sheet Phi Angle Degrees := -127.0
Beta Sheet Phi Angle Range := 20.0
Beta Sheet Phi Energy Constant := 0.5
Beta Sheet Phi Exponent := 2
Beta Sheet Psi Angle Degrees := 122.0
Beta Sheet Psi Angle Range := 20.0
Beta Sheet Psi Energy Constant := 0.5
Beta Sheet Psi Exponent := 2