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resonance-engine/docs/protein-fold-analysis.txt
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Tiger c268172acc chore: reorganize repo structure 
- Move Navigator foreword from README.md to docs/foreword.md
- Move protein_fold_analysis.txt from results/ to docs/
- Move experimental-verification.md from experimentation/ to docs/
- Move navigator_prime_analysis.py from root to scripts/
- Move navigator_prime_analysis_v2.py from root to scripts/
- Rewrite README.md as clean project documentation
- Update project structure to reflect actual repo layout
2026-03-30 17:48:33 +07:00

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======================================================================
PROTEIN FOLDING FRACTAL ECHO ANALYZER
======================================================================
Source: D:\Resonance_Engine\sweep_results\em_direct_sweep_20260327_080716.csv
Points: 375
Coherence: 0.737800 to 0.852700
Mean=0.750005 Std=0.026647
======================================================================
TEST 1: BASIN COUNTING (Ramachandran has 4-5 basins)
======================================================================
om=0.5: 9 distinct, 1 basins
om=0.6: 10 distinct, 1 basins
om=0.7: 5 distinct, 1 basins
om=0.8: 7 distinct, 2 basins
om=0.9: 5 distinct, 1 basins
om=1.0: 6 distinct, 2 basins
om=1.1: 6 distinct, 1 basins
om=1.2: 6 distinct, 1 basins
om=1.3: 7 distinct, 1 basins
om=1.4: 7 distinct, 2 basins
om=1.5: 8 distinct, 2 basins
om=1.6: 7 distinct, 2 basins
om=1.7: 8 distinct, 2 basins
om=1.8: 7 distinct, 2 basins
om=1.9: 3 distinct, 1 basins
Slices with 3-6 basins: 0/15
======================================================================
TEST 2: FORBIDDEN FRACTION (Ramachandran ~35% allowed)
======================================================================
Top 35% threshold: 0.739500
Allowed fraction: 44.3%
Ramachandran target: 35%
Difference: 9.3%
PASS
======================================================================
TEST 3: FUNNEL TOPOLOGY (proteins have positive skewness)
======================================================================
0.7378-0.7493: 318 ########################################
0.7493-0.7608: 0
0.7608-0.7723: 0
0.7723-0.7838: 0
0.7838-0.7953: 24 ###
0.7953-0.8067: 3
0.8067-0.8182: 1
0.8182-0.8297: 26 ###
0.8297-0.8412: 0
0.8412-0.8527: 3
Skewness: +2.1874
>>> FUNNEL DETECTED
======================================================================
TEST 4: AMINO ACID CLASS MAPPING (5 classes expected)
======================================================================
om=0.5: range=0.002100 -> beta_branched
om=0.6: range=0.001800 -> pre_proline
om=0.7: range=0.001300 -> pre_proline
om=0.8: range=0.001500 -> pre_proline
om=0.9: range=0.002200 -> beta_branched
om=1.0: range=0.001700 -> pre_proline
om=1.1: range=0.001400 -> pre_proline
om=1.2: range=0.001100 -> pre_proline
om=1.3: range=0.001700 -> pre_proline
om=1.4: range=0.001800 -> pre_proline
om=1.5: range=0.002000 -> beta_branched
om=1.6: range=0.001700 -> pre_proline
om=1.7: range=0.114900 -> glycine
om=1.8: range=0.018900 -> general
om=1.9: range=0.011800 -> general
Classes found: 4/5 = ['beta_branched', 'general', 'glycine', 'pre_proline']
======================================================================
TEST 5: LEVINTHAL COMPRESSION
======================================================================
Combinations: 375
Distinct modes: 39
Compression: 9.6:1
======================================================================
TEST 6: HIERARCHICAL STRUCTURE
======================================================================
CATH: 4 classes -> 41 arch -> 1393 topo
Lattice: 15 classes -> 39 topo
======================================================================
VERDICT
======================================================================
Basin count (3-6) FAIL
Forbidden fraction (25-45%) PASS
Funnel topology PASS
Amino acid classes (3+/5) PASS
Levinthal compression (>2:1) PASS
Hierarchical structure PASS
PASSED: 5/6
STRONG EVIDENCE: Fractal echo extends to protein folding
======================================================================
PROTEIN FOLDING FRACTAL ECHO ANALYZER
======================================================================
Source: D:\Resonance_Engine\sweep_results\em_direct_sweep_20260327_145447.csv
Points: 375
Coherence: 0.737000 to 0.739300
Mean=0.738280 Std=0.000571
======================================================================
TEST 1: BASIN COUNTING (Ramachandran has 4-5 basins)
======================================================================
om=0.5: 6 distinct, 2 basins
om=0.6: 3 distinct, 1 basins
om=0.7: 8 distinct, 2 basins
om=0.8: 8 distinct, 2 basins
om=0.9: 8 distinct, 1 basins
om=1.0: 3 distinct, 1 basins
om=1.1: 10 distinct, 2 basins
om=1.2: 5 distinct, 2 basins
om=1.3: 10 distinct, 1 basins
om=1.4: 4 distinct, 1 basins
om=1.5: 11 distinct, 3 basins <<<
om=1.6: 8 distinct, 1 basins
om=1.7: 11 distinct, 1 basins
om=1.8: 8 distinct, 2 basins
om=1.9: 2 distinct, 1 basins
Slices with 3-6 basins: 1/15
======================================================================
TEST 2: FORBIDDEN FRACTION (Ramachandran ~35% allowed)
======================================================================
Top 35% threshold: 0.738500
Allowed fraction: 40.0%
Ramachandran target: 35%
Difference: 5.0%
PASS
======================================================================
TEST 3: FUNNEL TOPOLOGY (proteins have positive skewness)
======================================================================
0.7370-0.7372: 15 #########
0.7372-0.7375: 8 ####
0.7375-0.7377: 33 ####################
0.7377-0.7379: 53 ################################
0.7379-0.7381: 66 ########################################
0.7381-0.7384: 37 ######################
0.7384-0.7386: 50 ##############################
0.7386-0.7388: 33 ####################
0.7388-0.7391: 31 ##################
0.7391-0.7393: 49 #############################
Skewness: -0.0718
>>> FLAT LANDSCAPE
======================================================================
TEST 4: AMINO ACID CLASS MAPPING (5 classes expected)
======================================================================
om=0.5: range=0.000700 -> pre_proline
om=0.6: range=0.001500 -> pre_proline
om=0.7: range=0.001800 -> pre_proline
om=0.8: range=0.000900 -> pre_proline
om=0.9: range=0.001100 -> pre_proline
om=1.0: range=0.000500 -> pre_proline
om=1.1: range=0.001800 -> pre_proline
om=1.2: range=0.000900 -> pre_proline
om=1.3: range=0.001400 -> pre_proline
om=1.4: range=0.001400 -> pre_proline
om=1.5: range=0.002300 -> beta_branched
om=1.6: range=0.001900 -> pre_proline
om=1.7: range=0.002000 -> beta_branched
om=1.8: range=0.001800 -> pre_proline
om=1.9: range=0.000200 -> proline
Classes found: 3/5 = ['beta_branched', 'pre_proline', 'proline']
======================================================================
TEST 5: LEVINTHAL COMPRESSION
======================================================================
Combinations: 375
Distinct modes: 23
Compression: 16.3:1
======================================================================
TEST 6: HIERARCHICAL STRUCTURE
======================================================================
CATH: 4 classes -> 41 arch -> 1393 topo
Lattice: 15 classes -> 23 topo
======================================================================
VERDICT
======================================================================
Basin count (3-6) FAIL
Forbidden fraction (25-45%) PASS
Funnel topology FAIL
Amino acid classes (3+/5) PASS
Levinthal compression (>2:1) PASS
Hierarchical structure PASS
PASSED: 4/6
STRONG EVIDENCE: Fractal echo extends to protein folding
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