Starting phenix.real_space_refine on Thu Mar 6 05:03:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9czn_46422/03_2025/9czn_46422_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9czn_46422/03_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_46422/03_2025/9czn_46422.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9czn_46422/03_2025/9czn_46422.map" model { file = "/net/cci-nas-00/data/ceres_data/9czn_46422/03_2025/9czn_46422_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9czn_46422/03_2025/9czn_46422_neut.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 3.75, per 1000 atoms: 0.75 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: 1.24 Conformation dependent library (CDL) restraints added in 625.8 milliseconds 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: 0.61 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: 1.29 Time building geometry restraints manager: 1.48 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: 0.01 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: 1.470 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.590 Find NCS groups from input model: 0.230 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:13.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.270 ------------------------------------------------------------------------------- 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= 1.395 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.007 0.003 HIS J 13 PHE 0.020 0.007 PHE P 19 TYR 0.016 0.004 TYR H 10 *********************** 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 : 0.564 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: 0.7247 (mppt) REVERT: C 35 MET cc_start: 0.8178 (ttp) cc_final: 0.7749 (ttm) REVERT: D 10 TYR cc_start: 0.7809 (m-80) cc_final: 0.7531 (m-80) REVERT: D 22 GLU cc_start: 0.8261 (mt-10) cc_final: 0.8061 (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: 0.7779 (ttm) REVERT: H 10 TYR cc_start: 0.7887 (m-80) cc_final: 0.7488 (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: 0.7597 (tt0) REVERT: Q 23 ASP cc_start: 0.7235 (t0) cc_final: 0.6992 (m-30) REVERT: Q 28 LYS cc_start: 0.7578 (mttt) cc_final: 0.7344 (mptt) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 1.2516 time to fit residues: 175.3161 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 : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.148183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.136284 restraints weight = 4611.336| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 0.82 r_work: 0.3668 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5100 Z= 0.232 Angle : 0.531 3.682 6860 Z= 0.315 Chirality : 0.056 0.130 780 Planarity : 0.002 0.007 880 Dihedral : 15.245 89.927 700 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.40 % Allowed : 8.40 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.006 0.002 HIS B 14 PHE 0.009 0.003 PHE Q 20 TYR 0.011 0.002 TYR D 10 *********************** 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 153 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 146 time to evaluate : 0.514 Fit side-chains REVERT: A 28 LYS cc_start: 0.8751 (mttt) cc_final: 0.8380 (mppt) REVERT: B 10 TYR cc_start: 0.7884 (m-80) cc_final: 0.7675 (m-80) REVERT: C 23 ASP cc_start: 0.8313 (m-30) cc_final: 0.8071 (m-30) REVERT: I 26 SER cc_start: 0.8760 (p) cc_final: 0.8378 (m) REVERT: K 11 GLU cc_start: 0.8276 (tt0) cc_final: 0.8023 (tt0) REVERT: K 28 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8040 (mtmm) REVERT: L 10 TYR cc_start: 0.8144 (m-80) cc_final: 0.7941 (m-80) REVERT: M 28 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8309 (mtmm) REVERT: O 28 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8122 (mtmm) REVERT: O 34 LEU cc_start: 0.9284 (tt) cc_final: 0.9064 (tt) outliers start: 7 outliers final: 0 residues processed: 146 average time/residue: 1.1502 time to fit residues: 174.4670 Evaluate side-chains 124 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 121 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 32 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 = 0.3885 r_free = 0.3885 target = 0.140175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.129003 restraints weight = 4833.079| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 0.77 r_work: 0.3623 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.061 5100 Z= 0.629 Angle : 0.752 6.933 6860 Z= 0.433 Chirality : 0.062 0.141 780 Planarity : 0.004 0.011 880 Dihedral : 14.427 89.190 700 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.60 % Allowed : 11.00 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.34), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.68 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS K 13 PHE 0.022 0.007 PHE B 19 TYR 0.018 0.003 TYR T 10 *********************** 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 152 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.711 Fit side-chains REVERT: I 26 SER cc_start: 0.8812 (p) cc_final: 0.8489 (m) REVERT: K 28 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.7853 (mtmm) REVERT: O 28 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8172 (mtmm) outliers start: 23 outliers final: 7 residues processed: 134 average time/residue: 2.0845 time to fit residues: 286.4813 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 : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 ILE 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 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 = 0.3922 r_free = 0.3922 target = 0.143174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.131690 restraints weight = 4834.628| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 0.78 r_work: 0.3655 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5100 Z= 0.335 Angle : 0.590 5.233 6860 Z= 0.347 Chirality : 0.058 0.129 780 Planarity : 0.003 0.008 880 Dihedral : 13.919 87.908 700 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.80 % Allowed : 13.00 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.35), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.67 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS K 13 PHE 0.015 0.004 PHE K 19 TYR 0.012 0.002 TYR N 10 *********************** 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 147 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.573 Fit side-chains REVERT: H 10 TYR cc_start: 0.8042 (m-80) cc_final: 0.7832 (m-80) REVERT: I 26 SER cc_start: 0.8853 (p) cc_final: 0.8487 (m) REVERT: K 28 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.7867 (mtmm) REVERT: M 28 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8266 (mtmm) REVERT: O 28 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8158 (mtmm) REVERT: O 34 LEU cc_start: 0.9285 (tt) cc_final: 0.9037 (tt) outliers start: 19 outliers final: 4 residues processed: 133 average time/residue: 1.2306 time to fit residues: 170.3552 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 : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 53 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 55 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 = 0.142619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.131158 restraints weight = 4801.640| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 0.78 r_work: 0.3657 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 2.02 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5100 Z= 0.352 Angle : 0.595 5.222 6860 Z= 0.352 Chirality : 0.058 0.128 780 Planarity : 0.003 0.008 880 Dihedral : 13.727 88.042 700 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.40 % Allowed : 14.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (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 HIS 0.005 0.002 HIS K 13 PHE 0.016 0.005 PHE K 19 TYR 0.015 0.002 TYR N 10 *********************** 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 143 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.751 Fit side-chains REVERT: H 10 TYR cc_start: 0.8094 (m-80) cc_final: 0.7880 (m-80) REVERT: I 26 SER cc_start: 0.8868 (p) cc_final: 0.8501 (m) REVERT: K 28 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.7871 (mtmm) REVERT: M 28 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8247 (mtmm) REVERT: O 28 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8176 (mtmm) REVERT: O 34 LEU cc_start: 0.9275 (tt) cc_final: 0.9039 (tt) outliers start: 17 outliers final: 5 residues processed: 129 average time/residue: 2.2689 time to fit residues: 300.7280 Evaluate side-chains 133 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 24 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.3894 r_free = 0.3894 target = 0.141028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.129607 restraints weight = 4813.242| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 0.78 r_work: 0.3625 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 2.18 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 5100 Z= 0.478 Angle : 0.669 6.285 6860 Z= 0.393 Chirality : 0.060 0.133 780 Planarity : 0.003 0.010 880 Dihedral : 13.791 88.557 700 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.20 % Allowed : 14.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.34), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.86 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS K 13 PHE 0.020 0.006 PHE K 19 TYR 0.015 0.003 TYR N 10 *********************** 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 144 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.601 Fit side-chains REVERT: H 10 TYR cc_start: 0.8144 (m-80) cc_final: 0.7914 (m-80) REVERT: I 26 SER cc_start: 0.8852 (p) cc_final: 0.8462 (m) REVERT: K 28 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.7882 (mtmm) REVERT: M 28 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8222 (mtmm) REVERT: O 28 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8218 (mtmm) REVERT: O 34 LEU cc_start: 0.9291 (tt) cc_final: 0.9050 (tt) outliers start: 16 outliers final: 7 residues processed: 133 average time/residue: 1.5956 time to fit residues: 219.9080 Evaluate side-chains 135 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain Q 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 1 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 55 optimal weight: 0.3980 chunk 15 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 overall best weight: 2.0382 ------------------------------------------------------------------------------- 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 = 0.3967 r_free = 0.3967 target = 0.145084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.134635 restraints weight = 4752.083| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 0.72 r_work: 0.3724 rms_B_bonded: 1.01 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 1.82 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5100 Z= 0.223 Angle : 0.517 4.573 6860 Z= 0.307 Chirality : 0.056 0.128 780 Planarity : 0.002 0.008 880 Dihedral : 13.154 87.167 700 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.60 % Allowed : 18.00 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.35), 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 HIS 0.004 0.002 HIS K 13 PHE 0.012 0.003 PHE A 19 TYR 0.012 0.002 TYR N 10 *********************** 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 139 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 1.625 Fit side-chains REVERT: G 10 TYR cc_start: 0.8604 (m-80) cc_final: 0.8357 (m-80) REVERT: H 10 TYR cc_start: 0.8041 (m-80) cc_final: 0.7782 (m-80) REVERT: I 26 SER cc_start: 0.8850 (p) cc_final: 0.8512 (m) REVERT: K 28 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.7965 (mtmm) REVERT: M 28 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8342 (mtmm) REVERT: O 28 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8114 (mtmm) REVERT: O 34 LEU cc_start: 0.9200 (tt) cc_final: 0.8991 (tt) REVERT: R 10 TYR cc_start: 0.7904 (m-80) cc_final: 0.7690 (m-80) outliers start: 8 outliers final: 2 residues processed: 132 average time/residue: 2.1933 time to fit residues: 297.1145 Evaluate side-chains 134 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 129 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 16 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 31 optimal weight: 0.0870 chunk 1 optimal weight: 0.0270 chunk 26 optimal weight: 0.8980 overall best weight: 1.4020 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.147087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.136555 restraints weight = 4795.994| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 0.72 r_work: 0.3750 rms_B_bonded: 1.01 restraints_weight: 0.5000 r_work: 0.3664 rms_B_bonded: 1.81 restraints_weight: 0.2500 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5100 Z= 0.173 Angle : 0.478 4.100 6860 Z= 0.284 Chirality : 0.056 0.136 780 Planarity : 0.002 0.007 880 Dihedral : 12.530 85.984 700 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.00 % Allowed : 18.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.35), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.72 (0.27), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 13 PHE 0.010 0.003 PHE T 19 TYR 0.010 0.002 TYR C 10 *********************** 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 137 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 132 time to evaluate : 1.066 Fit side-chains REVERT: C 26 SER cc_start: 0.8743 (p) cc_final: 0.8301 (m) REVERT: G 10 TYR cc_start: 0.8542 (m-80) cc_final: 0.8198 (m-80) REVERT: G 26 SER cc_start: 0.8519 (p) cc_final: 0.8135 (m) REVERT: H 10 TYR cc_start: 0.8027 (m-80) cc_final: 0.7784 (m-80) REVERT: I 26 SER cc_start: 0.8865 (p) cc_final: 0.8580 (m) REVERT: K 28 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8018 (mtmm) REVERT: M 28 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8390 (mtmm) REVERT: O 26 SER cc_start: 0.8698 (p) cc_final: 0.8311 (t) REVERT: O 28 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8122 (mtmm) REVERT: R 10 TYR cc_start: 0.7885 (m-80) cc_final: 0.7684 (m-80) outliers start: 5 outliers final: 0 residues processed: 132 average time/residue: 1.5155 time to fit residues: 207.4987 Evaluate side-chains 130 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 127 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 9 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.140496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.129712 restraints weight = 4705.119| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 0.74 r_work: 0.3632 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 2.01 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 5100 Z= 0.517 Angle : 0.693 6.557 6860 Z= 0.401 Chirality : 0.060 0.133 780 Planarity : 0.003 0.010 880 Dihedral : 13.422 87.149 700 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.20 % Allowed : 18.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.006 0.002 HIS E 13 PHE 0.021 0.006 PHE B 19 TYR 0.020 0.003 TYR C 10 *********************** 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 135 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 129 time to evaluate : 0.659 Fit side-chains REVERT: H 10 TYR cc_start: 0.8145 (m-80) cc_final: 0.7923 (m-80) REVERT: I 26 SER cc_start: 0.8845 (p) cc_final: 0.8491 (m) REVERT: K 28 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.7864 (mtmm) REVERT: M 28 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8187 (mtmm) REVERT: O 28 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8165 (mtmm) outliers start: 6 outliers final: 2 residues processed: 131 average time/residue: 1.3309 time to fit residues: 180.7639 Evaluate side-chains 130 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 125 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 28 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 26 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.143720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.133029 restraints weight = 4711.741| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 0.73 r_work: 0.3681 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 2.01 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5100 Z= 0.261 Angle : 0.557 7.102 6860 Z= 0.324 Chirality : 0.057 0.128 780 Planarity : 0.002 0.008 880 Dihedral : 12.974 87.576 700 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.00 % Allowed : 18.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.35), 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 HIS 0.004 0.002 HIS O 13 PHE 0.013 0.004 PHE B 19 TYR 0.015 0.002 TYR C 10 ********************** 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 133 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 0.731 Fit side-chains REVERT: G 10 TYR cc_start: 0.8566 (m-80) cc_final: 0.8279 (m-80) REVERT: H 10 TYR cc_start: 0.8090 (m-80) cc_final: 0.7833 (m-80) REVERT: I 26 SER cc_start: 0.8890 (p) cc_final: 0.8547 (m) REVERT: K 28 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.7900 (mtmm) REVERT: M 28 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8306 (mtmm) REVERT: O 28 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8124 (mtmm) outliers start: 5 outliers final: 0 residues processed: 128 average time/residue: 1.6078 time to fit residues: 213.6320 Evaluate side-chains 130 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 127 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 40 optimal weight: 9.9990 chunk 33 optimal weight: 0.3980 chunk 39 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.5980 chunk 2 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 35 optimal weight: 0.5980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3983 r_free = 0.3983 target = 0.146887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.136105 restraints weight = 4818.916| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 0.74 r_work: 0.3734 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 1.96 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5100 Z= 0.175 Angle : 0.497 7.813 6860 Z= 0.288 Chirality : 0.056 0.128 780 Planarity : 0.002 0.007 880 Dihedral : 12.314 88.191 700 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.20 % Allowed : 19.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.35), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.77 (0.27), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 13 PHE 0.009 0.002 PHE T 19 TYR 0.008 0.002 TYR N 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5477.59 seconds wall clock time: 100 minutes 6.91 seconds (6006.91 seconds total)