Starting phenix.real_space_refine on Wed Sep 17 05:17:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9czn_46422/09_2025/9czn_46422_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9czn_46422/09_2025/9czn_46422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9czn_46422/09_2025/9czn_46422.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9czn_46422/09_2025/9czn_46422.map" model { file = "/net/cci-nas-00/data/ceres_data/9czn_46422/09_2025/9czn_46422_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9czn_46422/09_2025/9czn_46422_neut.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 3260 2.51 5 N 840 2.21 5 O 900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5020 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "B" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "C" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "D" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "E" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "F" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "G" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "H" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "I" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "J" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "K" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "L" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "M" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "N" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "O" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "P" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "Q" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "R" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "S" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "T" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Time building chain proxies: 1.52, per 1000 atoms: 0.30 Number of scatterers: 5020 At special positions: 0 Unit cell: (111.724, 112.778, 44.268, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 900 8.00 N 840 7.00 C 3260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 198.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1120 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 54.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 13 removed outlier: 6.515A pdb=" N TYR A 10 " --> pdb=" O GLU C 11 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N HIS C 13 " --> pdb=" O TYR A 10 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL A 12 " --> pdb=" O HIS C 13 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N TYR C 10 " --> pdb=" O GLU E 11 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N HIS E 13 " --> pdb=" O TYR C 10 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL C 12 " --> pdb=" O HIS E 13 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TYR E 10 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N HIS G 13 " --> pdb=" O TYR E 10 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL E 12 " --> pdb=" O HIS G 13 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TYR G 10 " --> pdb=" O GLU I 11 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N HIS I 13 " --> pdb=" O TYR G 10 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL G 12 " --> pdb=" O HIS I 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 18 removed outlier: 6.427A pdb=" N LEU A 17 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU C 17 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU E 17 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU G 17 " --> pdb=" O VAL I 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 23 through 24 Processing sheet with id=AA4, first strand: chain 'A' and resid 30 through 41 removed outlier: 6.871A pdb=" N LEU C 34 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N MET A 35 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL C 36 " --> pdb=" O MET A 35 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU E 34 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N MET C 35 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL E 36 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU G 34 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N MET E 35 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL G 36 " --> pdb=" O MET E 35 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU I 34 " --> pdb=" O GLY G 33 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N MET G 35 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL I 36 " --> pdb=" O MET G 35 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 18 removed outlier: 9.019A pdb=" N GLU B 11 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 10.113A pdb=" N HIS D 14 " --> pdb=" O GLU B 11 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N HIS B 13 " --> pdb=" O HIS D 14 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N LYS D 16 " --> pdb=" O HIS B 13 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLN B 15 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N VAL D 18 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU B 17 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N GLU D 11 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 10.113A pdb=" N HIS F 14 " --> pdb=" O GLU D 11 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N HIS D 13 " --> pdb=" O HIS F 14 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N LYS F 16 " --> pdb=" O HIS D 13 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLN D 15 " --> pdb=" O LYS F 16 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N VAL F 18 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU D 17 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N GLU F 11 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 10.113A pdb=" N HIS H 14 " --> pdb=" O GLU F 11 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N HIS F 13 " --> pdb=" O HIS H 14 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N LYS H 16 " --> pdb=" O HIS F 13 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLN F 15 " --> pdb=" O LYS H 16 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N VAL H 18 " --> pdb=" O GLN F 15 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU F 17 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N GLU H 11 " --> pdb=" O VAL J 12 " (cutoff:3.500A) removed outlier: 10.113A pdb=" N HIS J 14 " --> pdb=" O GLU H 11 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N HIS H 13 " --> pdb=" O HIS J 14 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N LYS J 16 " --> pdb=" O HIS H 13 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLN H 15 " --> pdb=" O LYS J 16 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N VAL J 18 " --> pdb=" O GLN H 15 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU H 17 " --> pdb=" O VAL J 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 23 through 24 Processing sheet with id=AA7, first strand: chain 'B' and resid 30 through 41 removed outlier: 6.408A pdb=" N ILE B 31 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LEU D 34 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLY B 33 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 10.225A pdb=" N VAL D 36 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N MET B 35 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N GLY D 38 " --> pdb=" O MET B 35 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLY B 37 " --> pdb=" O GLY D 38 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL D 40 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL B 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE D 31 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LEU F 34 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLY D 33 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 10.225A pdb=" N VAL F 36 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N MET D 35 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N GLY F 38 " --> pdb=" O MET D 35 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLY D 37 " --> pdb=" O GLY F 38 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL F 40 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL D 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU H 34 " --> pdb=" O GLY F 33 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET F 35 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL H 36 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU J 34 " --> pdb=" O GLY H 33 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N MET H 35 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL J 36 " --> pdb=" O MET H 35 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.515A pdb=" N TYR K 10 " --> pdb=" O GLU M 11 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N HIS M 13 " --> pdb=" O TYR K 10 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL K 12 " --> pdb=" O HIS M 13 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TYR M 10 " --> pdb=" O GLU O 11 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N HIS O 13 " --> pdb=" O TYR M 10 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL M 12 " --> pdb=" O HIS O 13 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TYR O 10 " --> pdb=" O GLU Q 11 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N HIS Q 13 " --> pdb=" O TYR O 10 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL O 12 " --> pdb=" O HIS Q 13 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N TYR Q 10 " --> pdb=" O GLU S 11 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N HIS S 13 " --> pdb=" O TYR Q 10 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL Q 12 " --> pdb=" O HIS S 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'K' and resid 16 through 18 removed outlier: 6.428A pdb=" N LEU K 17 " --> pdb=" O VAL M 18 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU M 17 " --> pdb=" O VAL O 18 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU O 17 " --> pdb=" O VAL Q 18 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU Q 17 " --> pdb=" O VAL S 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 23 through 24 Processing sheet with id=AB2, first strand: chain 'K' and resid 30 through 41 removed outlier: 6.871A pdb=" N LEU M 34 " --> pdb=" O GLY K 33 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N MET K 35 " --> pdb=" O LEU M 34 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL M 36 " --> pdb=" O MET K 35 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU O 34 " --> pdb=" O GLY M 33 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N MET M 35 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL O 36 " --> pdb=" O MET M 35 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU Q 34 " --> pdb=" O GLY O 33 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N MET O 35 " --> pdb=" O LEU Q 34 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL Q 36 " --> pdb=" O MET O 35 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU S 34 " --> pdb=" O GLY Q 33 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N MET Q 35 " --> pdb=" O LEU S 34 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL S 36 " --> pdb=" O MET Q 35 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 18 removed outlier: 9.020A pdb=" N GLU L 11 " --> pdb=" O VAL N 12 " (cutoff:3.500A) removed outlier: 10.113A pdb=" N HIS N 14 " --> pdb=" O GLU L 11 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N HIS L 13 " --> pdb=" O HIS N 14 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N LYS N 16 " --> pdb=" O HIS L 13 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLN L 15 " --> pdb=" O LYS N 16 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N VAL N 18 " --> pdb=" O GLN L 15 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU L 17 " --> pdb=" O VAL N 18 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N GLU N 11 " --> pdb=" O VAL P 12 " (cutoff:3.500A) removed outlier: 10.112A pdb=" N HIS P 14 " --> pdb=" O GLU N 11 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N HIS N 13 " --> pdb=" O HIS P 14 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N LYS P 16 " --> pdb=" O HIS N 13 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLN N 15 " --> pdb=" O LYS P 16 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N VAL P 18 " --> pdb=" O GLN N 15 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU N 17 " --> pdb=" O VAL P 18 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N GLU P 11 " --> pdb=" O VAL R 12 " (cutoff:3.500A) removed outlier: 10.113A pdb=" N HIS R 14 " --> pdb=" O GLU P 11 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N HIS P 13 " --> pdb=" O HIS R 14 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N LYS R 16 " --> pdb=" O HIS P 13 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLN P 15 " --> pdb=" O LYS R 16 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N VAL R 18 " --> pdb=" O GLN P 15 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU P 17 " --> pdb=" O VAL R 18 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N GLU R 11 " --> pdb=" O VAL T 12 " (cutoff:3.500A) removed outlier: 10.112A pdb=" N HIS T 14 " --> pdb=" O GLU R 11 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N HIS R 13 " --> pdb=" O HIS T 14 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N LYS T 16 " --> pdb=" O HIS R 13 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLN R 15 " --> pdb=" O LYS T 16 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N VAL T 18 " --> pdb=" O GLN R 15 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU R 17 " --> pdb=" O VAL T 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'L' and resid 23 through 24 Processing sheet with id=AB5, first strand: chain 'L' and resid 30 through 41 removed outlier: 6.408A pdb=" N ILE L 31 " --> pdb=" O ILE N 32 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LEU N 34 " --> pdb=" O ILE L 31 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLY L 33 " --> pdb=" O LEU N 34 " (cutoff:3.500A) removed outlier: 10.225A pdb=" N VAL N 36 " --> pdb=" O GLY L 33 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N MET L 35 " --> pdb=" O VAL N 36 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N GLY N 38 " --> pdb=" O MET L 35 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLY L 37 " --> pdb=" O GLY N 38 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL N 40 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL L 39 " --> pdb=" O VAL N 40 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE N 31 " --> pdb=" O ILE P 32 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N LEU P 34 " --> pdb=" O ILE N 31 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N GLY N 33 " --> pdb=" O LEU P 34 " (cutoff:3.500A) removed outlier: 10.225A pdb=" N VAL P 36 " --> pdb=" O GLY N 33 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N MET N 35 " --> pdb=" O VAL P 36 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N GLY P 38 " --> pdb=" O MET N 35 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLY N 37 " --> pdb=" O GLY P 38 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL P 40 " --> pdb=" O GLY N 37 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL N 39 " --> pdb=" O VAL P 40 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE P 31 " --> pdb=" O ILE R 32 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N LEU R 34 " --> pdb=" O ILE P 31 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N GLY P 33 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 10.225A pdb=" N VAL R 36 " --> pdb=" O GLY P 33 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N MET P 35 " --> pdb=" O VAL R 36 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N GLY R 38 " --> pdb=" O MET P 35 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLY P 37 " --> pdb=" O GLY R 38 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL R 40 " --> pdb=" O GLY P 37 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL P 39 " --> pdb=" O VAL R 40 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE R 31 " --> pdb=" O ILE T 32 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LEU T 34 " --> pdb=" O ILE R 31 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLY R 33 " --> pdb=" O LEU T 34 " (cutoff:3.500A) removed outlier: 10.225A pdb=" N VAL T 36 " --> pdb=" O GLY R 33 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N MET R 35 " --> pdb=" O VAL T 36 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N GLY T 38 " --> pdb=" O MET R 35 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLY R 37 " --> pdb=" O GLY T 38 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL T 40 " --> pdb=" O GLY R 37 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL R 39 " --> pdb=" O VAL T 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 96 hydrogen bonds defined for protein. 288 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.71 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1001 1.31 - 1.43: 1189 1.43 - 1.55: 2790 1.55 - 1.67: 90 1.67 - 1.79: 30 Bond restraints: 5100 Sorted by residual: bond pdb=" SD MET I 35 " pdb=" CE MET I 35 " ideal model delta sigma weight residual 1.791 1.667 0.124 2.50e-02 1.60e+03 2.48e+01 bond pdb=" SD MET M 35 " pdb=" CE MET M 35 " ideal model delta sigma weight residual 1.791 1.667 0.124 2.50e-02 1.60e+03 2.47e+01 bond pdb=" SD MET Q 35 " pdb=" CE MET Q 35 " ideal model delta sigma weight residual 1.791 1.667 0.124 2.50e-02 1.60e+03 2.47e+01 bond pdb=" SD MET G 35 " pdb=" CE MET G 35 " ideal model delta sigma weight residual 1.791 1.667 0.124 2.50e-02 1.60e+03 2.47e+01 bond pdb=" SD MET S 35 " pdb=" CE MET S 35 " ideal model delta sigma weight residual 1.791 1.667 0.124 2.50e-02 1.60e+03 2.47e+01 ... (remaining 5095 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 5562 2.02 - 4.05: 953 4.05 - 6.07: 263 6.07 - 8.09: 42 8.09 - 10.12: 40 Bond angle restraints: 6860 Sorted by residual: angle pdb=" N HIS O 13 " pdb=" CA HIS O 13 " pdb=" C HIS O 13 " ideal model delta sigma weight residual 109.07 119.19 -10.12 1.52e+00 4.33e-01 4.43e+01 angle pdb=" N HIS S 13 " pdb=" CA HIS S 13 " pdb=" C HIS S 13 " ideal model delta sigma weight residual 109.07 119.18 -10.11 1.52e+00 4.33e-01 4.43e+01 angle pdb=" N HIS A 13 " pdb=" CA HIS A 13 " pdb=" C HIS A 13 " ideal model delta sigma weight residual 109.07 119.18 -10.11 1.52e+00 4.33e-01 4.42e+01 angle pdb=" N HIS G 13 " pdb=" CA HIS G 13 " pdb=" C HIS G 13 " ideal model delta sigma weight residual 109.07 119.17 -10.10 1.52e+00 4.33e-01 4.42e+01 angle pdb=" N HIS I 13 " pdb=" CA HIS I 13 " pdb=" C HIS I 13 " ideal model delta sigma weight residual 109.07 119.17 -10.10 1.52e+00 4.33e-01 4.41e+01 ... (remaining 6855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.72: 2680 16.72 - 33.43: 110 33.43 - 50.15: 30 50.15 - 66.86: 0 66.86 - 83.58: 20 Dihedral angle restraints: 2840 sinusoidal: 1040 harmonic: 1800 Sorted by residual: dihedral pdb=" C HIS I 13 " pdb=" N HIS I 13 " pdb=" CA HIS I 13 " pdb=" CB HIS I 13 " ideal model delta harmonic sigma weight residual -122.60 -129.59 6.99 0 2.50e+00 1.60e-01 7.82e+00 dihedral pdb=" C HIS A 13 " pdb=" N HIS A 13 " pdb=" CA HIS A 13 " pdb=" CB HIS A 13 " ideal model delta harmonic sigma weight residual -122.60 -129.58 6.98 0 2.50e+00 1.60e-01 7.79e+00 dihedral pdb=" C HIS Q 13 " pdb=" N HIS Q 13 " pdb=" CA HIS Q 13 " pdb=" CB HIS Q 13 " ideal model delta harmonic sigma weight residual -122.60 -129.55 6.95 0 2.50e+00 1.60e-01 7.73e+00 ... (remaining 2837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 322 0.069 - 0.137: 238 0.137 - 0.205: 170 0.205 - 0.274: 34 0.274 - 0.342: 16 Chirality restraints: 780 Sorted by residual: chirality pdb=" CA HIS A 13 " pdb=" N HIS A 13 " pdb=" C HIS A 13 " pdb=" CB HIS A 13 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CA HIS I 13 " pdb=" N HIS I 13 " pdb=" C HIS I 13 " pdb=" CB HIS I 13 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CA HIS S 13 " pdb=" N HIS S 13 " pdb=" C HIS S 13 " pdb=" CB HIS S 13 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 ... (remaining 777 not shown) Planarity restraints: 880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA R 42 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.24e+00 pdb=" C ALA R 42 " 0.053 2.00e-02 2.50e+03 pdb=" O ALA R 42 " -0.019 2.00e-02 2.50e+03 pdb=" OXT ALA R 42 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 42 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.21e+00 pdb=" C ALA D 42 " 0.053 2.00e-02 2.50e+03 pdb=" O ALA D 42 " -0.019 2.00e-02 2.50e+03 pdb=" OXT ALA D 42 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA P 42 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.21e+00 pdb=" C ALA P 42 " 0.053 2.00e-02 2.50e+03 pdb=" O ALA P 42 " -0.019 2.00e-02 2.50e+03 pdb=" OXT ALA P 42 " -0.019 2.00e-02 2.50e+03 ... (remaining 877 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.03: 2958 3.03 - 3.50: 4897 3.50 - 3.96: 8493 3.96 - 4.43: 10384 4.43 - 4.90: 18460 Nonbonded interactions: 45192 Sorted by model distance: nonbonded pdb=" O VAL T 36 " pdb=" CA GLY T 37 " model vdw 2.563 2.752 nonbonded pdb=" O VAL H 36 " pdb=" CA GLY H 37 " model vdw 2.563 2.752 nonbonded pdb=" O VAL J 36 " pdb=" CA GLY J 37 " model vdw 2.563 2.752 nonbonded pdb=" O VAL L 36 " pdb=" CA GLY L 37 " model vdw 2.563 2.752 nonbonded pdb=" O VAL B 36 " pdb=" CA GLY B 37 " model vdw 2.563 2.752 ... (remaining 45187 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 6.880 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.124 5100 Z= 1.014 Angle : 1.900 10.118 6860 Z= 1.272 Chirality : 0.120 0.342 780 Planarity : 0.010 0.030 880 Dihedral : 13.570 83.578 1720 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.33), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.26 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.004 TYR H 10 PHE 0.020 0.007 PHE P 19 HIS 0.007 0.003 HIS J 13 Details of bonding type rmsd covalent geometry : bond 0.02014 ( 5100) covalent geometry : angle 1.89957 ( 6860) hydrogen bonds : bond 0.11449 ( 96) hydrogen bonds : angle 9.64256 ( 288) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.241 Fit side-chains REVERT: A 26 SER cc_start: 0.8455 (p) cc_final: 0.8126 (m) REVERT: A 28 LYS cc_start: 0.7807 (mttt) cc_final: 0.7248 (mppt) REVERT: C 35 MET cc_start: 0.8178 (ttp) cc_final: 0.7747 (ttm) REVERT: D 10 TYR cc_start: 0.7809 (m-80) cc_final: 0.7532 (m-80) REVERT: D 22 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7988 (mt-10) REVERT: F 22 GLU cc_start: 0.8237 (mt-10) cc_final: 0.8022 (mt-10) REVERT: G 10 TYR cc_start: 0.8398 (m-80) cc_final: 0.7974 (m-80) REVERT: G 35 MET cc_start: 0.8032 (ttp) cc_final: 0.7774 (ttm) REVERT: H 10 TYR cc_start: 0.7887 (m-80) cc_final: 0.7485 (m-80) REVERT: I 11 GLU cc_start: 0.7654 (tt0) cc_final: 0.7384 (tt0) REVERT: I 26 SER cc_start: 0.8441 (p) cc_final: 0.8025 (m) REVERT: K 26 SER cc_start: 0.8253 (p) cc_final: 0.8020 (m) REVERT: M 11 GLU cc_start: 0.7806 (tt0) cc_final: 0.7598 (tt0) REVERT: Q 23 ASP cc_start: 0.7235 (t0) cc_final: 0.6997 (m-30) REVERT: Q 28 LYS cc_start: 0.7578 (mttt) cc_final: 0.7345 (mptt) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.6099 time to fit residues: 85.2249 Evaluate side-chains 117 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS B 14 HIS C 14 HIS D 14 HIS E 14 HIS F 14 HIS F 15 GLN G 14 HIS H 14 HIS I 14 HIS J 14 HIS K 14 HIS L 14 HIS M 14 HIS N 14 HIS O 14 HIS P 14 HIS Q 14 HIS R 14 HIS S 14 HIS T 14 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.148133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.136210 restraints weight = 4658.851| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 0.82 r_work: 0.3657 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3565 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5100 Z= 0.142 Angle : 0.531 3.702 6860 Z= 0.315 Chirality : 0.056 0.128 780 Planarity : 0.002 0.007 880 Dihedral : 15.253 89.988 700 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.80 % Allowed : 8.20 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.34), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.35 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR D 10 PHE 0.010 0.003 PHE Q 20 HIS 0.007 0.002 HIS B 14 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 5100) covalent geometry : angle 0.53114 ( 6860) hydrogen bonds : bond 0.04431 ( 96) hydrogen bonds : angle 7.87028 ( 288) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 0.221 Fit side-chains REVERT: A 28 LYS cc_start: 0.8780 (mttt) cc_final: 0.8409 (mppt) REVERT: B 10 TYR cc_start: 0.7928 (m-80) cc_final: 0.7718 (m-80) REVERT: C 23 ASP cc_start: 0.8360 (m-30) cc_final: 0.8123 (m-30) REVERT: I 26 SER cc_start: 0.8767 (p) cc_final: 0.8381 (m) REVERT: K 11 GLU cc_start: 0.8321 (tt0) cc_final: 0.8069 (tt0) REVERT: K 28 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8069 (mtmm) REVERT: L 10 TYR cc_start: 0.8170 (m-80) cc_final: 0.7967 (m-80) REVERT: M 28 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8334 (mtmm) REVERT: O 28 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8156 (mtmm) REVERT: O 34 LEU cc_start: 0.9286 (tt) cc_final: 0.9065 (tt) outliers start: 9 outliers final: 1 residues processed: 147 average time/residue: 0.5539 time to fit residues: 84.5809 Evaluate side-chains 128 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 124 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain K residue 28 LYS Chi-restraints excluded: chain M residue 28 LYS Chi-restraints excluded: chain O residue 28 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 21 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 20.0000 chunk 28 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.140970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.129643 restraints weight = 4771.439| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 0.80 r_work: 0.3611 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 5100 Z= 0.336 Angle : 0.713 6.473 6860 Z= 0.411 Chirality : 0.061 0.136 780 Planarity : 0.004 0.010 880 Dihedral : 14.406 89.534 700 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.60 % Allowed : 11.80 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.34), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.64 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.003 TYR T 10 PHE 0.020 0.006 PHE B 19 HIS 0.006 0.002 HIS H 13 Details of bonding type rmsd covalent geometry : bond 0.00807 ( 5100) covalent geometry : angle 0.71271 ( 6860) hydrogen bonds : bond 0.05457 ( 96) hydrogen bonds : angle 7.47155 ( 288) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.202 Fit side-chains REVERT: G 10 TYR cc_start: 0.8776 (m-80) cc_final: 0.8564 (m-80) REVERT: H 10 TYR cc_start: 0.8193 (m-80) cc_final: 0.7922 (m-80) REVERT: I 26 SER cc_start: 0.8808 (p) cc_final: 0.8483 (m) REVERT: K 28 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.7879 (mtmm) REVERT: O 28 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8178 (mtmm) REVERT: Q 23 ASP cc_start: 0.8113 (m-30) cc_final: 0.7894 (m-30) outliers start: 18 outliers final: 5 residues processed: 133 average time/residue: 0.5973 time to fit residues: 82.3675 Evaluate side-chains 130 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain J residue 35 MET Chi-restraints excluded: chain K residue 28 LYS Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain M residue 28 LYS Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 28 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 3 optimal weight: 0.0020 chunk 38 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.143870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.132432 restraints weight = 4784.826| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 0.77 r_work: 0.3669 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 2.01 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5100 Z= 0.188 Angle : 0.568 5.209 6860 Z= 0.335 Chirality : 0.057 0.130 780 Planarity : 0.002 0.008 880 Dihedral : 13.903 88.611 700 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.40 % Allowed : 13.20 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.35), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.65 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYR L 10 PHE 0.014 0.004 PHE B 19 HIS 0.005 0.002 HIS K 13 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 5100) covalent geometry : angle 0.56790 ( 6860) hydrogen bonds : bond 0.04262 ( 96) hydrogen bonds : angle 7.33457 ( 288) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.187 Fit side-chains REVERT: H 10 TYR cc_start: 0.8006 (m-80) cc_final: 0.7767 (m-80) REVERT: I 26 SER cc_start: 0.8839 (p) cc_final: 0.8480 (m) REVERT: K 28 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.7925 (mtmm) REVERT: M 28 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8253 (mtmm) REVERT: O 28 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8143 (mtmm) REVERT: O 34 LEU cc_start: 0.9275 (tt) cc_final: 0.9039 (tt) outliers start: 22 outliers final: 6 residues processed: 136 average time/residue: 0.5842 time to fit residues: 82.3596 Evaluate side-chains 134 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain K residue 28 LYS Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain M residue 28 LYS Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 28 LYS Chi-restraints excluded: chain Q residue 28 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 58 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.140936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.129438 restraints weight = 4848.514| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 0.79 r_work: 0.3607 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 5100 Z= 0.313 Angle : 0.687 6.329 6860 Z= 0.401 Chirality : 0.060 0.133 780 Planarity : 0.003 0.010 880 Dihedral : 13.936 88.156 700 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.00 % Allowed : 14.40 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.34), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.81 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.003 TYR N 10 PHE 0.020 0.006 PHE K 19 HIS 0.006 0.002 HIS K 13 Details of bonding type rmsd covalent geometry : bond 0.00745 ( 5100) covalent geometry : angle 0.68662 ( 6860) hydrogen bonds : bond 0.05174 ( 96) hydrogen bonds : angle 7.25179 ( 288) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.139 Fit side-chains REVERT: G 10 TYR cc_start: 0.8792 (m-80) cc_final: 0.8538 (m-80) REVERT: H 10 TYR cc_start: 0.8110 (m-80) cc_final: 0.7886 (m-80) REVERT: I 26 SER cc_start: 0.8869 (p) cc_final: 0.8489 (m) REVERT: K 28 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.7852 (mtmm) REVERT: M 28 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8188 (mtmm) REVERT: O 28 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8209 (mtmm) REVERT: O 34 LEU cc_start: 0.9311 (tt) cc_final: 0.9062 (tt) outliers start: 15 outliers final: 6 residues processed: 129 average time/residue: 0.6157 time to fit residues: 82.3137 Evaluate side-chains 133 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain K residue 28 LYS Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain M residue 28 LYS Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 28 LYS Chi-restraints excluded: chain Q residue 28 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.144809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.133300 restraints weight = 4863.479| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 0.79 r_work: 0.3678 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 2.07 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5100 Z= 0.147 Angle : 0.525 4.562 6860 Z= 0.312 Chirality : 0.057 0.128 780 Planarity : 0.002 0.008 880 Dihedral : 13.335 86.762 700 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.80 % Allowed : 17.20 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.34), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.75 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYR N 10 PHE 0.012 0.003 PHE A 19 HIS 0.004 0.002 HIS O 13 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 5100) covalent geometry : angle 0.52482 ( 6860) hydrogen bonds : bond 0.03894 ( 96) hydrogen bonds : angle 7.21023 ( 288) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.191 Fit side-chains REVERT: H 10 TYR cc_start: 0.8017 (m-80) cc_final: 0.7785 (m-80) REVERT: I 26 SER cc_start: 0.8843 (p) cc_final: 0.8475 (m) REVERT: K 28 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.7893 (mtmm) REVERT: M 28 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8355 (mtmm) REVERT: O 28 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8120 (mtmm) REVERT: R 10 TYR cc_start: 0.7953 (m-80) cc_final: 0.7738 (m-80) outliers start: 9 outliers final: 2 residues processed: 131 average time/residue: 0.5727 time to fit residues: 77.7751 Evaluate side-chains 131 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 126 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 28 LYS Chi-restraints excluded: chain M residue 28 LYS Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 28 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.140354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.129211 restraints weight = 4820.390| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 0.76 r_work: 0.3637 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 5100 Z= 0.349 Angle : 0.719 6.719 6860 Z= 0.418 Chirality : 0.060 0.138 780 Planarity : 0.004 0.011 880 Dihedral : 13.777 88.204 700 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.40 % Allowed : 17.00 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.34), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.91 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.003 TYR C 10 PHE 0.022 0.007 PHE D 19 HIS 0.006 0.002 HIS O 14 Details of bonding type rmsd covalent geometry : bond 0.00834 ( 5100) covalent geometry : angle 0.71899 ( 6860) hydrogen bonds : bond 0.05307 ( 96) hydrogen bonds : angle 7.16999 ( 288) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.191 Fit side-chains REVERT: H 10 TYR cc_start: 0.8139 (m-80) cc_final: 0.7920 (m-80) REVERT: I 26 SER cc_start: 0.8888 (p) cc_final: 0.8503 (m) REVERT: K 28 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.7877 (mtmm) REVERT: M 28 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8238 (mtmm) REVERT: O 28 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8190 (mtmm) outliers start: 17 outliers final: 6 residues processed: 133 average time/residue: 0.5861 time to fit residues: 80.7243 Evaluate side-chains 134 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain K residue 28 LYS Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain M residue 28 LYS Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 28 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 19 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.142574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.131376 restraints weight = 4857.328| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 0.77 r_work: 0.3669 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 1.98 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5100 Z= 0.220 Angle : 0.609 6.053 6860 Z= 0.356 Chirality : 0.058 0.129 780 Planarity : 0.003 0.008 880 Dihedral : 13.486 87.277 700 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.60 % Allowed : 18.00 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.34), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.87 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.003 TYR C 10 PHE 0.017 0.005 PHE B 19 HIS 0.005 0.002 HIS R 13 Details of bonding type rmsd covalent geometry : bond 0.00522 ( 5100) covalent geometry : angle 0.60942 ( 6860) hydrogen bonds : bond 0.04515 ( 96) hydrogen bonds : angle 7.21513 ( 288) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.242 Fit side-chains REVERT: G 10 TYR cc_start: 0.8658 (m-80) cc_final: 0.8385 (m-80) REVERT: H 10 TYR cc_start: 0.8093 (m-80) cc_final: 0.7831 (m-80) REVERT: I 26 SER cc_start: 0.8884 (p) cc_final: 0.8530 (m) REVERT: K 28 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.7883 (mtmm) REVERT: M 28 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8250 (mtmm) REVERT: O 28 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8172 (mtmm) outliers start: 13 outliers final: 5 residues processed: 132 average time/residue: 0.6233 time to fit residues: 85.2126 Evaluate side-chains 132 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain K residue 28 LYS Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain M residue 28 LYS Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 28 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 39 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.143259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.131787 restraints weight = 4780.210| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 0.77 r_work: 0.3650 rms_B_bonded: 1.12 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 2.02 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5100 Z= 0.210 Angle : 0.608 7.057 6860 Z= 0.353 Chirality : 0.058 0.131 780 Planarity : 0.003 0.008 880 Dihedral : 13.407 86.896 700 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.80 % Allowed : 18.00 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.34), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.87 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.003 TYR C 10 PHE 0.016 0.004 PHE B 19 HIS 0.005 0.002 HIS O 13 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 5100) covalent geometry : angle 0.60805 ( 6860) hydrogen bonds : bond 0.04460 ( 96) hydrogen bonds : angle 7.17685 ( 288) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.170 Fit side-chains REVERT: H 10 TYR cc_start: 0.8079 (m-80) cc_final: 0.7822 (m-80) REVERT: I 26 SER cc_start: 0.8901 (p) cc_final: 0.8526 (m) REVERT: K 28 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.7858 (mtmm) REVERT: M 28 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8280 (mtmm) REVERT: O 28 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8185 (mtmm) outliers start: 9 outliers final: 4 residues processed: 133 average time/residue: 0.6018 time to fit residues: 82.8853 Evaluate side-chains 132 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain K residue 28 LYS Chi-restraints excluded: chain M residue 28 LYS Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 28 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 15 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.142518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.131047 restraints weight = 4784.706| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 0.78 r_work: 0.3655 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 5100 Z= 0.250 Angle : 0.652 7.294 6860 Z= 0.377 Chirality : 0.059 0.132 780 Planarity : 0.003 0.009 880 Dihedral : 13.467 86.839 700 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.00 % Allowed : 19.40 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.34), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.90 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.003 TYR C 10 PHE 0.018 0.005 PHE B 19 HIS 0.005 0.002 HIS O 13 Details of bonding type rmsd covalent geometry : bond 0.00596 ( 5100) covalent geometry : angle 0.65161 ( 6860) hydrogen bonds : bond 0.04753 ( 96) hydrogen bonds : angle 7.16792 ( 288) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.184 Fit side-chains REVERT: G 10 TYR cc_start: 0.8593 (m-80) cc_final: 0.8334 (m-80) REVERT: H 10 TYR cc_start: 0.8102 (m-80) cc_final: 0.7838 (m-80) REVERT: I 26 SER cc_start: 0.8892 (p) cc_final: 0.8531 (m) REVERT: K 28 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.7861 (mtmm) REVERT: M 28 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8254 (mtmm) REVERT: O 28 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8175 (mtmm) outliers start: 10 outliers final: 4 residues processed: 128 average time/residue: 0.6054 time to fit residues: 81.9820 Evaluate side-chains 131 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain K residue 28 LYS Chi-restraints excluded: chain M residue 28 LYS Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 28 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 36 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.143490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.131902 restraints weight = 4848.035| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 0.79 r_work: 0.3670 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 2.02 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 5100 Z= 0.211 Angle : 0.611 7.369 6860 Z= 0.354 Chirality : 0.058 0.131 780 Planarity : 0.003 0.008 880 Dihedral : 13.352 86.858 700 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.80 % Allowed : 19.20 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.34), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.88 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.003 TYR C 10 PHE 0.016 0.004 PHE T 19 HIS 0.005 0.002 HIS R 13 Details of bonding type rmsd covalent geometry : bond 0.00501 ( 5100) covalent geometry : angle 0.61123 ( 6860) hydrogen bonds : bond 0.04406 ( 96) hydrogen bonds : angle 7.18892 ( 288) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2227.53 seconds wall clock time: 38 minutes 43.69 seconds (2323.69 seconds total)