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phenix.real_space_refine - Real-Space Refinement
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Input files:
  Model: predict_and_build.pdb
  Map: map.mrc
  Resolution: 3.2 A

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Refinement Strategy
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Strategy: Individual sites + Individual B-factors + Morphing
Number of cycles: 5
Weight optimization: automatic

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Refinement Progress
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Starting map-model CC: 0.650

Cycle 1: CC = 0.668
Cycle 2: CC = 0.685
Cycle 3: CC = 0.698
Cycle 4: CC = 0.710
Cycle 5: CC = 0.720

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Final Statistics
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Final map-model CC: 0.720

Resolution used: 3.2 A
Number of atoms: 625

Geometry:
  Bond RMSD: 0.010 A
  Angle RMSD: 1.35 degrees

Ramachandran:
  Favored: 94.2%
  Allowed: 5.5%
  Outliers: 0.3%

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Output Files
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Refined model: model_rsr_001.pdb

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phenix.real_space_refine completed successfully
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