AlignMaster output ============================================================ Length of target sequence: 137 residues Searching sequences of known 3D structures Found 12UCE.pdb with P(N)=5.0e-12 Found 11AYZ.pdb with P(N)=1.2e-08 Found 11AAK.pdb with P(N)=5.3e-08 Found 12AAK.pdb with P(N)=5.3e-08 Found 11UCZ.pdb with P(N)=1.1e-07 Found 12UCZ.pdb with P(N)=1.1e-07 Found 11A3S.pdb with P(N)=1.0e-05 Extracting template sequences Running pair-wise alignments with target sequence Sequence identity of templates with target: 12UCE.pdb: 22.85 % identity 11AYZ.pdb: 27.8 % identity 11AAK.pdb: 17.15 % identity 12AAK.pdb: 17.15 % identity 11UCZ.pdb: 29.6 % identity 12UCZ.pdb: 29.6 % identity 11A3S.pdb: 22.5 % identity Looking for template groups Global alignment overview: Taget Sequence: |====================================================================| 12UCE.pdb | ------------------------------------------------- 11AYZ.pdb | ------------------------------------------------ 11AAK.pdb | ----------------------------------------------------- 12AAK.pdb | ----------------------------------------------------- 11UCZ.pdb | -------------------------- 12UCZ.pdb | -------------------------- 11A3S.pdb | -------------------------------------------------- AlignMaster found 1 regions to model separately: 1: Using template(s) 11A3S.pdb 11AAK.pdb 11AYZ.pdb 11UCZ.pdb 12AAK.pdb 12UCE.pdb 12UCZ.pdb 12UCE.pdb has been rejected, too low similarity with Target sequence (22.85 % identity.) 11AAK.pdb has been rejected, too low similarity with Target sequence (17.15 % identity.) 12AAK.pdb has been rejected, too low similarity with Target sequence (17.15 % identity.) 11A3S.pdb has been rejected, too low similarity with Target sequence (22.5 % identity.) Creating Batch files for ProMod (if any): Batch.1: residues 30 - 137 of submitted sequence. Exiting AlignMaster ProModII trace log for Batch.1 ============================================================ ProModII: Loading Template: 11AYZ.pdb ProModII: Loading Template: 11UCZ.pdb ProModII: Loading Template: 12UCZ.pdb ProModII: Loading Raw Sequence ProModII: Iterative Template Fitting ProModII: Iterative Template Fitting ProModII: Generating Structural Alignment ProModII: Aligning Raw Sequence ProModII: Refining Raw Sequence Alignment ProModII: Weighting Backbones ProModII: Averaging Sidechains ProModII: Adding Missing Sidechains ProModII: Small Ligation (C-N < 3.0A) ignored; ProModII: GROMOS will repair it at residue ASP 73 ProModII: Building CSP loop with anchor residues THR 60 and GLU 63 ProModII: Number of Ligations found: (1) ProModII: all loops are bad; continuing CSP with larger segment ProModII: Building CSP loop with anchor residues PRO 59 and GLU 63 ProModII: Number of Ligations found: (10) ProModII: ACCEPTING loop 5: clash= 1 FF= 53.8 PP=-18.41 ProModII: Dumping Preliminary Model ProModII: Dumping Sequence Alignment ProModII: Done. Gromos96 trace log for Batch.1 ============================================================ Now running PROCS1 on file batch-procs0.dat ... Done. Now running PROCS2 on file batch-procs1.dat ... Done. Now running PROGMT on file batch-procs2.dat ... Done. Now running PROGCH on file batch-procs2.dat ... Done. Now running PROMD on file batch-progch.dat ... Done. Now running PROMD on file batch-promd0.dat ... Done. Detection of SS-Bonds within batch ...