Starting phenix.real_space_refine on Thu Mar 6 05:03:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9czp_46424/03_2025/9czp_46424_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9czp_46424/03_2025/9czp_46424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9czp_46424/03_2025/9czp_46424.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9czp_46424/03_2025/9czp_46424.map" model { file = "/net/cci-nas-00/data/ceres_data/9czp_46424/03_2025/9czp_46424_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9czp_46424/03_2025/9czp_46424_neut.cif" } resolution = 3.3 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: 4.27, per 1000 atoms: 0.85 Number of scatterers: 5020 At special positions: 0 Unit cell: (91.698, 108.562, 52.7, 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: 1.31 Conformation dependent library (CDL) restraints added in 621.8 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 15 sheets defined 0.0% alpha, 50.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 13 removed outlier: 6.530A pdb=" N TYR A 10 " --> pdb=" O GLU C 11 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N HIS C 13 " --> pdb=" O TYR A 10 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL A 12 " --> pdb=" O HIS C 13 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TYR C 10 " --> pdb=" O GLU E 11 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N HIS E 13 " --> pdb=" O TYR C 10 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL C 12 " --> pdb=" O HIS E 13 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TYR E 10 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N HIS G 13 " --> pdb=" O TYR E 10 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL E 12 " --> pdb=" O HIS G 13 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TYR G 10 " --> pdb=" O GLU I 11 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N HIS I 13 " --> pdb=" O TYR G 10 " (cutoff:3.500A) removed outlier: 6.615A 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: 6.610A pdb=" N LEU A 17 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU C 17 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU E 17 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 6.610A 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 31 through 41 removed outlier: 6.276A pdb=" N ILE A 31 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU C 34 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLY A 33 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 10.361A pdb=" N VAL C 36 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N MET A 35 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N GLY C 38 " --> pdb=" O MET A 35 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY A 37 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL C 40 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE C 31 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU E 34 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLY C 33 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 10.361A pdb=" N VAL E 36 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N MET C 35 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N GLY E 38 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY C 37 " --> pdb=" O GLY E 38 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL E 40 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL C 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE E 31 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU G 34 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLY E 33 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 10.361A pdb=" N VAL G 36 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N MET E 35 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N GLY G 38 " --> pdb=" O MET E 35 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY E 37 " --> pdb=" O GLY G 38 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL G 40 " --> pdb=" O GLY E 37 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL E 39 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE G 31 " --> pdb=" O ILE I 32 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU I 34 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLY G 33 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 10.361A pdb=" N VAL I 36 " --> pdb=" O GLY G 33 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N MET G 35 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N GLY I 38 " --> pdb=" O MET G 35 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY G 37 " --> pdb=" O GLY I 38 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL I 40 " --> pdb=" O GLY G 37 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL G 39 " --> pdb=" O VAL I 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.538A pdb=" N TYR B 10 " --> pdb=" O GLU D 11 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N HIS D 13 " --> pdb=" O TYR B 10 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL B 12 " --> pdb=" O HIS D 13 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TYR D 10 " --> pdb=" O GLU F 11 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N HIS F 13 " --> pdb=" O TYR D 10 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL D 12 " --> pdb=" O HIS F 13 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TYR F 10 " --> pdb=" O GLU H 11 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N HIS H 13 " --> pdb=" O TYR F 10 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL F 12 " --> pdb=" O HIS H 13 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TYR H 10 " --> pdb=" O GLU J 11 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N HIS J 13 " --> pdb=" O TYR H 10 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL H 12 " --> pdb=" O HIS J 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 18 removed outlier: 6.544A pdb=" N LEU B 17 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU D 17 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU F 17 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 6.543A 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: 6.902A pdb=" N LEU D 34 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N MET B 35 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL D 36 " --> pdb=" O MET B 35 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU F 34 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N MET D 35 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL F 36 " --> pdb=" O MET D 35 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU H 34 " --> pdb=" O GLY F 33 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N MET F 35 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL H 36 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU J 34 " --> pdb=" O GLY H 33 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N MET H 35 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.905A 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 18 removed outlier: 7.091A pdb=" N GLU M 11 " --> pdb=" O TYR K 10 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL K 12 " --> pdb=" O GLU M 11 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N HIS M 13 " --> pdb=" O VAL K 12 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N HIS K 14 " --> pdb=" O HIS M 13 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLU O 11 " --> pdb=" O TYR M 10 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL M 12 " --> pdb=" O GLU O 11 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N HIS O 13 " --> pdb=" O VAL M 12 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N HIS M 14 " --> pdb=" O HIS O 13 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLU Q 11 " --> pdb=" O TYR O 10 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL O 12 " --> pdb=" O GLU Q 11 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N HIS Q 13 " --> pdb=" O VAL O 12 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N HIS O 14 " --> pdb=" O HIS Q 13 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLU S 11 " --> pdb=" O TYR Q 10 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL Q 12 " --> pdb=" O GLU S 11 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N HIS S 13 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N HIS Q 14 " --> pdb=" O HIS S 13 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 23 through 27 removed outlier: 6.368A pdb=" N ASP K 23 " --> pdb=" O VAL M 24 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N SER M 26 " --> pdb=" O ASP K 23 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N GLY K 25 " --> pdb=" O SER M 26 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASP M 23 " --> pdb=" O VAL O 24 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N SER O 26 " --> pdb=" O ASP M 23 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N GLY M 25 " --> pdb=" O SER O 26 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP O 23 " --> pdb=" O VAL Q 24 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N SER Q 26 " --> pdb=" O ASP O 23 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N GLY O 25 " --> pdb=" O SER Q 26 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASP Q 23 " --> pdb=" O VAL S 24 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N SER S 26 " --> pdb=" O ASP Q 23 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N GLY Q 25 " --> pdb=" O SER S 26 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 30 through 35 removed outlier: 6.902A pdb=" N ILE K 31 " --> pdb=" O ALA M 30 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE M 32 " --> pdb=" O ILE K 31 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLY K 33 " --> pdb=" O ILE M 32 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE M 31 " --> pdb=" O ALA O 30 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE O 32 " --> pdb=" O ILE M 31 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLY M 33 " --> pdb=" O ILE O 32 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE O 31 " --> pdb=" O ALA Q 30 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE Q 32 " --> pdb=" O ILE O 31 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLY O 33 " --> pdb=" O ILE Q 32 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE Q 31 " --> pdb=" O ALA S 30 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE S 32 " --> pdb=" O ILE Q 31 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLY Q 33 " --> pdb=" O ILE S 32 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 39 through 41 removed outlier: 6.339A pdb=" N VAL K 40 " --> pdb=" O ILE M 41 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL M 40 " --> pdb=" O ILE O 41 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL O 40 " --> pdb=" O ILE Q 41 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL Q 40 " --> pdb=" O ILE S 41 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AB4, first strand: chain 'L' and resid 16 through 18 Processing sheet with id=AB5, first strand: chain 'L' and resid 23 through 24 removed outlier: 6.492A pdb=" N ASP L 23 " --> pdb=" O VAL N 24 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASP N 23 " --> pdb=" O VAL P 24 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP P 23 " --> pdb=" O VAL R 24 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP R 23 " --> pdb=" O VAL T 24 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'L' and resid 30 through 41 removed outlier: 6.589A pdb=" N ALA L 30 " --> pdb=" O ILE N 31 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N GLY N 33 " --> pdb=" O ALA L 30 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N ILE L 32 " --> pdb=" O GLY N 33 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N MET N 35 " --> pdb=" O ILE L 32 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N LEU L 34 " --> pdb=" O MET N 35 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N GLY N 37 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL L 36 " --> pdb=" O GLY N 37 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL N 39 " --> pdb=" O VAL L 36 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY L 38 " --> pdb=" O VAL N 39 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE N 41 " --> pdb=" O GLY L 38 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL L 40 " --> pdb=" O ILE N 41 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA N 30 " --> pdb=" O ILE P 31 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N GLY P 33 " --> pdb=" O ALA N 30 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N ILE N 32 " --> pdb=" O GLY P 33 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N MET P 35 " --> pdb=" O ILE N 32 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N LEU N 34 " --> pdb=" O MET P 35 " (cutoff:3.500A) removed outlier: 9.288A pdb=" N GLY P 37 " --> pdb=" O LEU N 34 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL N 36 " --> pdb=" O GLY P 37 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL P 39 " --> pdb=" O VAL N 36 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY N 38 " --> pdb=" O VAL P 39 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE P 41 " --> pdb=" O GLY N 38 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL N 40 " --> pdb=" O ILE P 41 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA P 30 " --> pdb=" O ILE R 31 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N GLY R 33 " --> pdb=" O ALA P 30 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N ILE P 32 " --> pdb=" O GLY R 33 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N MET R 35 " --> pdb=" O ILE P 32 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N LEU P 34 " --> pdb=" O MET R 35 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N GLY R 37 " --> pdb=" O LEU P 34 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL P 36 " --> pdb=" O GLY R 37 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N VAL R 39 " --> pdb=" O VAL P 36 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLY P 38 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE R 41 " --> pdb=" O GLY P 38 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL P 40 " --> pdb=" O ILE R 41 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA R 30 " --> pdb=" O ILE T 31 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N GLY T 33 " --> pdb=" O ALA R 30 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N ILE R 32 " --> pdb=" O GLY T 33 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N MET T 35 " --> pdb=" O ILE R 32 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N LEU R 34 " --> pdb=" O MET T 35 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N GLY T 37 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL R 36 " --> pdb=" O GLY T 37 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL T 39 " --> pdb=" O VAL R 36 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY R 38 " --> pdb=" O VAL T 39 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE T 41 " --> pdb=" O GLY R 38 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL R 40 " --> pdb=" O ILE T 41 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 80 hydrogen bonds defined for protein. 240 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: 1.42 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1358 1.32 - 1.44: 978 1.44 - 1.57: 2719 1.57 - 1.69: 10 1.69 - 1.82: 35 Bond restraints: 5100 Sorted by residual: bond pdb=" C TYR K 10 " pdb=" N GLU K 11 " ideal model delta sigma weight residual 1.331 1.397 -0.066 1.38e-02 5.25e+03 2.28e+01 bond pdb=" C TYR O 10 " pdb=" N GLU O 11 " ideal model delta sigma weight residual 1.331 1.397 -0.066 1.38e-02 5.25e+03 2.26e+01 bond pdb=" C TYR Q 10 " pdb=" N GLU Q 11 " ideal model delta sigma weight residual 1.331 1.397 -0.066 1.38e-02 5.25e+03 2.26e+01 bond pdb=" C TYR S 10 " pdb=" N GLU S 11 " ideal model delta sigma weight residual 1.331 1.397 -0.066 1.38e-02 5.25e+03 2.25e+01 bond pdb=" C TYR M 10 " pdb=" N GLU M 11 " ideal model delta sigma weight residual 1.331 1.396 -0.065 1.38e-02 5.25e+03 2.19e+01 ... (remaining 5095 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 5612 2.34 - 4.69: 1003 4.69 - 7.03: 184 7.03 - 9.37: 41 9.37 - 11.72: 20 Bond angle restraints: 6860 Sorted by residual: angle pdb=" N VAL H 36 " pdb=" CA VAL H 36 " pdb=" C VAL H 36 " ideal model delta sigma weight residual 110.82 100.97 9.85 9.70e-01 1.06e+00 1.03e+02 angle pdb=" N VAL F 36 " pdb=" CA VAL F 36 " pdb=" C VAL F 36 " ideal model delta sigma weight residual 110.82 100.98 9.84 9.70e-01 1.06e+00 1.03e+02 angle pdb=" N VAL B 36 " pdb=" CA VAL B 36 " pdb=" C VAL B 36 " ideal model delta sigma weight residual 110.82 101.01 9.81 9.70e-01 1.06e+00 1.02e+02 angle pdb=" N VAL J 36 " pdb=" CA VAL J 36 " pdb=" C VAL J 36 " ideal model delta sigma weight residual 110.82 101.01 9.81 9.70e-01 1.06e+00 1.02e+02 angle pdb=" N VAL D 36 " pdb=" CA VAL D 36 " pdb=" C VAL D 36 " ideal model delta sigma weight residual 110.82 101.02 9.80 9.70e-01 1.06e+00 1.02e+02 ... (remaining 6855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.60: 2680 13.60 - 27.19: 85 27.19 - 40.78: 45 40.78 - 54.37: 20 54.37 - 67.97: 10 Dihedral angle restraints: 2840 sinusoidal: 1040 harmonic: 1800 Sorted by residual: dihedral pdb=" CA ASP D 23 " pdb=" CB ASP D 23 " pdb=" CG ASP D 23 " pdb=" OD1 ASP D 23 " ideal model delta sinusoidal sigma weight residual -30.00 -80.93 50.93 1 2.00e+01 2.50e-03 8.87e+00 dihedral pdb=" CA ASP B 23 " pdb=" CB ASP B 23 " pdb=" CG ASP B 23 " pdb=" OD1 ASP B 23 " ideal model delta sinusoidal sigma weight residual -30.00 -80.90 50.90 1 2.00e+01 2.50e-03 8.86e+00 dihedral pdb=" CA ASP H 23 " pdb=" CB ASP H 23 " pdb=" CG ASP H 23 " pdb=" OD1 ASP H 23 " ideal model delta sinusoidal sigma weight residual -30.00 -80.84 50.84 1 2.00e+01 2.50e-03 8.84e+00 ... (remaining 2837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 384 0.075 - 0.150: 249 0.150 - 0.226: 109 0.226 - 0.301: 33 0.301 - 0.376: 5 Chirality restraints: 780 Sorted by residual: chirality pdb=" CA HIS J 13 " pdb=" N HIS J 13 " pdb=" C HIS J 13 " pdb=" CB HIS J 13 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CA HIS F 13 " pdb=" N HIS F 13 " pdb=" C HIS F 13 " pdb=" CB HIS F 13 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CA HIS H 13 " pdb=" N HIS H 13 " pdb=" C HIS H 13 " pdb=" CB HIS H 13 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.50e+00 ... (remaining 777 not shown) Planarity restraints: 880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Q 42 " -0.026 2.00e-02 2.50e+03 5.27e-02 2.78e+01 pdb=" C ALA Q 42 " 0.091 2.00e-02 2.50e+03 pdb=" O ALA Q 42 " -0.033 2.00e-02 2.50e+03 pdb=" OXT ALA Q 42 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA M 42 " -0.026 2.00e-02 2.50e+03 5.27e-02 2.78e+01 pdb=" C ALA M 42 " 0.091 2.00e-02 2.50e+03 pdb=" O ALA M 42 " -0.033 2.00e-02 2.50e+03 pdb=" OXT ALA M 42 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA K 42 " -0.026 2.00e-02 2.50e+03 5.27e-02 2.77e+01 pdb=" C ALA K 42 " 0.091 2.00e-02 2.50e+03 pdb=" O ALA K 42 " -0.033 2.00e-02 2.50e+03 pdb=" OXT ALA K 42 " -0.032 2.00e-02 2.50e+03 ... (remaining 877 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 1996 2.90 - 3.40: 4130 3.40 - 3.90: 9200 3.90 - 4.40: 9524 4.40 - 4.90: 18942 Nonbonded interactions: 43792 Sorted by model distance: nonbonded pdb=" NZ LYS I 16 " pdb=" OE1 GLU I 22 " model vdw 2.402 3.120 nonbonded pdb=" NZ LYS A 16 " pdb=" OE1 GLU A 22 " model vdw 2.402 3.120 nonbonded pdb=" NZ LYS G 16 " pdb=" OE1 GLU G 22 " model vdw 2.402 3.120 nonbonded pdb=" NZ LYS E 16 " pdb=" OE1 GLU E 22 " model vdw 2.403 3.120 nonbonded pdb=" NZ LYS C 16 " pdb=" OE1 GLU C 22 " model vdw 2.403 3.120 ... (remaining 43787 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: 2.920 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.960 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 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 : 0.021 0.112 5100 Z= 1.418 Angle : 2.005 11.715 6860 Z= 1.329 Chirality : 0.115 0.376 780 Planarity : 0.010 0.053 880 Dihedral : 10.683 67.968 1720 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 0.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % 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: -0.29 (0.32), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.21 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS J 14 PHE 0.012 0.003 PHE R 19 TYR 0.013 0.004 TYR Q 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 132 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.552 Fit side-chains REVERT: J 10 TYR cc_start: 0.8623 (m-80) cc_final: 0.8384 (m-80) REVERT: M 23 ASP cc_start: 0.7408 (m-30) cc_final: 0.7140 (m-30) REVERT: R 10 TYR cc_start: 0.9011 (m-80) cc_final: 0.8747 (m-10) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1726 time to fit residues: 28.7965 Evaluate side-chains 91 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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: 2.9990 chunk 25 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 28 optimal weight: 0.2980 chunk 35 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS C 27 ASN D 14 HIS F 14 HIS ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 ASN H 14 HIS ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 14 HIS K 14 HIS M 14 HIS O 14 HIS ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 14 HIS ** Q 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 14 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.134075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.116604 restraints weight = 6818.857| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.53 r_work: 0.3583 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5100 Z= 0.231 Angle : 0.562 7.497 6860 Z= 0.324 Chirality : 0.058 0.136 780 Planarity : 0.002 0.011 880 Dihedral : 7.169 48.199 700 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.80 % Allowed : 7.80 % Favored : 91.40 % 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: -0.68 (0.32), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.51 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS O 14 PHE 0.007 0.001 PHE A 20 TYR 0.015 0.002 TYR R 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 137 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 133 time to evaluate : 0.585 Fit side-chains REVERT: A 27 ASN cc_start: 0.7820 (m110) cc_final: 0.7586 (m110) REVERT: B 15 GLN cc_start: 0.9132 (mp10) cc_final: 0.8425 (mp10) REVERT: C 22 GLU cc_start: 0.8253 (pt0) cc_final: 0.8022 (pt0) REVERT: F 15 GLN cc_start: 0.9314 (mp10) cc_final: 0.8599 (mp10) REVERT: H 10 TYR cc_start: 0.8786 (m-80) cc_final: 0.8142 (m-80) REVERT: K 10 TYR cc_start: 0.7424 (m-80) cc_final: 0.7184 (m-80) REVERT: K 23 ASP cc_start: 0.7845 (m-30) cc_final: 0.7423 (m-30) REVERT: M 15 GLN cc_start: 0.8982 (mp10) cc_final: 0.8416 (mp10) REVERT: R 10 TYR cc_start: 0.8691 (m-80) cc_final: 0.8281 (m-10) REVERT: R 11 GLU cc_start: 0.8257 (tt0) cc_final: 0.7368 (mp0) REVERT: T 10 TYR cc_start: 0.8538 (m-80) cc_final: 0.7842 (m-80) outliers start: 4 outliers final: 4 residues processed: 134 average time/residue: 0.1560 time to fit residues: 28.1258 Evaluate side-chains 119 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain N residue 15 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 31 optimal weight: 0.0030 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 overall best weight: 4.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 ASN ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.122056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.104727 restraints weight = 7053.811| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.54 r_work: 0.3457 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 5100 Z= 0.493 Angle : 0.657 6.902 6860 Z= 0.370 Chirality : 0.061 0.139 780 Planarity : 0.003 0.012 880 Dihedral : 6.802 40.899 700 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 2.20 % Allowed : 10.20 % Favored : 87.60 % 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: -1.04 (0.31), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.78 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS K 14 PHE 0.010 0.001 PHE I 19 TYR 0.017 0.003 TYR Q 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 120 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.568 Fit side-chains REVERT: A 27 ASN cc_start: 0.8158 (m110) cc_final: 0.7902 (m110) REVERT: B 10 TYR cc_start: 0.8311 (m-80) cc_final: 0.8103 (m-80) REVERT: C 22 GLU cc_start: 0.8408 (pt0) cc_final: 0.8199 (pt0) REVERT: D 16 LYS cc_start: 0.9295 (tttt) cc_final: 0.9060 (tttp) REVERT: H 10 TYR cc_start: 0.8800 (m-80) cc_final: 0.8226 (m-80) REVERT: M 15 GLN cc_start: 0.9209 (mp10) cc_final: 0.8699 (mp10) REVERT: R 10 TYR cc_start: 0.8941 (m-80) cc_final: 0.8687 (m-80) REVERT: R 11 GLU cc_start: 0.8308 (tt0) cc_final: 0.8050 (tt0) REVERT: T 10 TYR cc_start: 0.8592 (m-80) cc_final: 0.8201 (m-80) outliers start: 11 outliers final: 8 residues processed: 115 average time/residue: 0.1306 time to fit residues: 20.6359 Evaluate side-chains 111 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain L residue 15 GLN Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain T residue 15 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 19 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.122427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.105252 restraints weight = 7145.229| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.55 r_work: 0.3442 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 5100 Z= 0.467 Angle : 0.640 7.944 6860 Z= 0.357 Chirality : 0.060 0.149 780 Planarity : 0.002 0.011 880 Dihedral : 6.444 37.391 700 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 3.00 % Allowed : 10.40 % Favored : 86.60 % 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: -1.23 (0.32), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.93 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS K 14 PHE 0.008 0.001 PHE I 19 TYR 0.022 0.002 TYR Q 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 127 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 1.018 Fit side-chains REVERT: A 27 ASN cc_start: 0.8019 (m110) cc_final: 0.7741 (m110) REVERT: B 10 TYR cc_start: 0.8233 (m-80) cc_final: 0.7948 (m-80) REVERT: B 15 GLN cc_start: 0.9232 (mp10) cc_final: 0.8281 (mp10) REVERT: C 15 GLN cc_start: 0.9007 (mp10) cc_final: 0.8734 (mp10) REVERT: C 22 GLU cc_start: 0.8466 (pt0) cc_final: 0.8201 (pt0) REVERT: D 16 LYS cc_start: 0.9310 (tttt) cc_final: 0.9090 (tttp) REVERT: H 10 TYR cc_start: 0.8736 (m-80) cc_final: 0.8180 (m-80) REVERT: I 28 LYS cc_start: 0.8441 (mttp) cc_final: 0.7715 (mmmt) REVERT: M 15 GLN cc_start: 0.9172 (mp10) cc_final: 0.8675 (mp10) REVERT: O 15 GLN cc_start: 0.9188 (mp10) cc_final: 0.8630 (mp10) REVERT: R 11 GLU cc_start: 0.8321 (tt0) cc_final: 0.7993 (tt0) REVERT: S 15 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.7322 (mp10) outliers start: 15 outliers final: 9 residues processed: 121 average time/residue: 0.1280 time to fit residues: 21.4087 Evaluate side-chains 120 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain L residue 15 GLN Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain O residue 35 MET Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain T residue 15 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 53 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.124092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.107005 restraints weight = 7099.608| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.55 r_work: 0.3469 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5100 Z= 0.361 Angle : 0.589 7.703 6860 Z= 0.329 Chirality : 0.058 0.156 780 Planarity : 0.002 0.013 880 Dihedral : 6.075 33.952 700 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 2.80 % Allowed : 12.80 % 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: -1.28 (0.32), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.97 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS Q 13 PHE 0.007 0.001 PHE J 19 TYR 0.013 0.002 TYR O 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 132 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.574 Fit side-chains REVERT: A 22 GLU cc_start: 0.8024 (pt0) cc_final: 0.7569 (pm20) REVERT: A 27 ASN cc_start: 0.7831 (m110) cc_final: 0.7541 (m110) REVERT: B 10 TYR cc_start: 0.8156 (m-80) cc_final: 0.7854 (m-80) REVERT: B 15 GLN cc_start: 0.9218 (mp10) cc_final: 0.8178 (mp10) REVERT: C 22 GLU cc_start: 0.8549 (pt0) cc_final: 0.8029 (pt0) REVERT: D 16 LYS cc_start: 0.9293 (tttt) cc_final: 0.9072 (tttp) REVERT: H 10 TYR cc_start: 0.8713 (m-80) cc_final: 0.8234 (m-80) REVERT: I 28 LYS cc_start: 0.8448 (mttp) cc_final: 0.7705 (mmmt) REVERT: M 15 GLN cc_start: 0.9185 (mp10) cc_final: 0.8563 (mp10) REVERT: O 15 GLN cc_start: 0.9175 (mp10) cc_final: 0.8817 (mp10) REVERT: R 11 GLU cc_start: 0.8308 (tt0) cc_final: 0.7310 (mp0) REVERT: S 10 TYR cc_start: 0.7655 (m-80) cc_final: 0.5693 (m-80) REVERT: S 15 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.7280 (mp10) outliers start: 14 outliers final: 11 residues processed: 125 average time/residue: 0.1496 time to fit residues: 24.9792 Evaluate side-chains 124 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain L residue 15 GLN Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain O residue 35 MET Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain R residue 15 GLN Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain T residue 15 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 24 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.123926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.107003 restraints weight = 7080.754| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.54 r_work: 0.3470 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5100 Z= 0.357 Angle : 0.587 7.459 6860 Z= 0.325 Chirality : 0.058 0.151 780 Planarity : 0.002 0.012 880 Dihedral : 5.837 32.214 700 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 3.60 % Allowed : 12.60 % Favored : 83.80 % 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: -1.34 (0.32), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS O 13 PHE 0.007 0.001 PHE J 19 TYR 0.011 0.002 TYR F 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 131 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.571 Fit side-chains REVERT: A 22 GLU cc_start: 0.7522 (pt0) cc_final: 0.7258 (pm20) REVERT: A 27 ASN cc_start: 0.8294 (m-40) cc_final: 0.8062 (m110) REVERT: B 15 GLN cc_start: 0.9195 (mp10) cc_final: 0.8128 (mp10) REVERT: C 22 GLU cc_start: 0.8561 (pt0) cc_final: 0.8018 (pt0) REVERT: I 28 LYS cc_start: 0.8490 (mttp) cc_final: 0.7731 (mmmt) REVERT: K 15 GLN cc_start: 0.9256 (mp10) cc_final: 0.8999 (mp10) REVERT: M 15 GLN cc_start: 0.9144 (mp10) cc_final: 0.8551 (mp10) REVERT: Q 15 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.7523 (mp10) REVERT: R 11 GLU cc_start: 0.8309 (tt0) cc_final: 0.7297 (mp0) REVERT: S 10 TYR cc_start: 0.7635 (m-80) cc_final: 0.5830 (m-80) REVERT: S 15 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.7258 (mp10) outliers start: 18 outliers final: 15 residues processed: 122 average time/residue: 0.1722 time to fit residues: 29.2492 Evaluate side-chains 124 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain L residue 15 GLN Chi-restraints excluded: chain M residue 11 GLU Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain O residue 35 MET Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain Q residue 11 GLU Chi-restraints excluded: chain Q residue 15 GLN Chi-restraints excluded: chain R residue 15 GLN Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain S residue 26 SER Chi-restraints excluded: chain T residue 15 GLN 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: 5.9990 chunk 59 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.120585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.103501 restraints weight = 7125.145| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.56 r_work: 0.3415 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.041 5100 Z= 0.512 Angle : 0.661 8.050 6860 Z= 0.366 Chirality : 0.060 0.150 780 Planarity : 0.002 0.012 880 Dihedral : 6.045 33.679 700 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 4.00 % Allowed : 12.80 % 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: -1.47 (0.32), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.11 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 13 PHE 0.008 0.001 PHE J 19 TYR 0.026 0.003 TYR H 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 130 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.572 Fit side-chains REVERT: A 22 GLU cc_start: 0.7396 (pt0) cc_final: 0.7155 (pm20) REVERT: A 27 ASN cc_start: 0.8319 (m-40) cc_final: 0.8063 (m110) REVERT: C 22 GLU cc_start: 0.8609 (pt0) cc_final: 0.8245 (pt0) REVERT: H 10 TYR cc_start: 0.8743 (m-80) cc_final: 0.8461 (m-80) REVERT: I 28 LYS cc_start: 0.8541 (mttp) cc_final: 0.7760 (mmmt) REVERT: M 10 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.7189 (m-80) REVERT: M 15 GLN cc_start: 0.9169 (mp10) cc_final: 0.8921 (mp10) REVERT: P 15 GLN cc_start: 0.9347 (OUTLIER) cc_final: 0.8994 (pm20) REVERT: Q 15 GLN cc_start: 0.9055 (OUTLIER) cc_final: 0.7720 (mp10) REVERT: R 11 GLU cc_start: 0.8347 (tt0) cc_final: 0.7954 (tt0) REVERT: S 10 TYR cc_start: 0.7132 (m-80) cc_final: 0.5884 (m-80) REVERT: S 15 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.7367 (mp10) outliers start: 20 outliers final: 15 residues processed: 120 average time/residue: 0.1153 time to fit residues: 19.4850 Evaluate side-chains 127 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain L residue 15 GLN Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain O residue 35 MET Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain Q residue 11 GLU Chi-restraints excluded: chain Q residue 15 GLN Chi-restraints excluded: chain R residue 15 GLN Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain S residue 26 SER Chi-restraints excluded: chain T residue 15 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 16 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.129257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.112543 restraints weight = 6993.755| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.53 r_work: 0.3583 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5100 Z= 0.185 Angle : 0.514 7.948 6860 Z= 0.279 Chirality : 0.057 0.144 780 Planarity : 0.002 0.010 880 Dihedral : 5.292 30.262 700 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 3.00 % Allowed : 14.60 % 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: -1.34 (0.32), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS T 14 PHE 0.005 0.001 PHE G 20 TYR 0.013 0.001 TYR H 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 136 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.661 Fit side-chains REVERT: B 15 GLN cc_start: 0.9224 (mp10) cc_final: 0.8340 (mp10) REVERT: C 22 GLU cc_start: 0.8539 (pt0) cc_final: 0.8159 (pt0) REVERT: F 15 GLN cc_start: 0.9372 (mp10) cc_final: 0.8304 (mp10) REVERT: G 16 LYS cc_start: 0.8743 (tttt) cc_final: 0.8525 (tttp) REVERT: I 28 LYS cc_start: 0.8509 (mttp) cc_final: 0.7773 (mmmt) REVERT: K 11 GLU cc_start: 0.8149 (tt0) cc_final: 0.7905 (tp30) REVERT: M 15 GLN cc_start: 0.9099 (mp10) cc_final: 0.8599 (mp10) REVERT: O 15 GLN cc_start: 0.9114 (mp10) cc_final: 0.8659 (mp10) REVERT: Q 15 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.7547 (mp10) REVERT: R 11 GLU cc_start: 0.8275 (tt0) cc_final: 0.7429 (mp0) REVERT: S 10 TYR cc_start: 0.6989 (m-80) cc_final: 0.5932 (m-80) REVERT: S 15 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7235 (mp10) REVERT: T 11 GLU cc_start: 0.8289 (tt0) cc_final: 0.7922 (mp0) outliers start: 15 outliers final: 11 residues processed: 126 average time/residue: 0.1590 time to fit residues: 27.0362 Evaluate side-chains 129 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain L residue 15 GLN Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain O residue 10 TYR Chi-restraints excluded: chain O residue 35 MET Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain Q residue 15 GLN Chi-restraints excluded: chain R residue 15 GLN Chi-restraints excluded: chain S residue 15 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 9 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.127293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.110578 restraints weight = 6908.029| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.52 r_work: 0.3532 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5100 Z= 0.257 Angle : 0.544 7.935 6860 Z= 0.296 Chirality : 0.057 0.142 780 Planarity : 0.002 0.011 880 Dihedral : 5.259 30.279 700 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 4.20 % Allowed : 13.80 % Favored : 82.00 % 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: -1.33 (0.32), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 13 PHE 0.006 0.001 PHE J 19 TYR 0.023 0.002 TYR F 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 140 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.496 Fit side-chains REVERT: B 15 GLN cc_start: 0.9245 (mp10) cc_final: 0.8364 (mp10) REVERT: C 22 GLU cc_start: 0.8315 (pt0) cc_final: 0.7832 (pt0) REVERT: D 10 TYR cc_start: 0.8251 (m-80) cc_final: 0.7929 (m-80) REVERT: I 28 LYS cc_start: 0.8533 (mttp) cc_final: 0.7778 (mmmt) REVERT: K 11 GLU cc_start: 0.8138 (tt0) cc_final: 0.7866 (tp30) REVERT: M 15 GLN cc_start: 0.9096 (mp10) cc_final: 0.8623 (mp10) REVERT: O 15 GLN cc_start: 0.9120 (mp10) cc_final: 0.8635 (mp10) REVERT: Q 15 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.7665 (mp10) REVERT: R 11 GLU cc_start: 0.8283 (tt0) cc_final: 0.7274 (mp0) REVERT: S 10 TYR cc_start: 0.7048 (m-80) cc_final: 0.5946 (m-80) REVERT: S 15 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.7408 (mp10) REVERT: T 10 TYR cc_start: 0.8365 (m-80) cc_final: 0.7976 (m-80) REVERT: T 11 GLU cc_start: 0.8293 (tt0) cc_final: 0.7938 (mp0) outliers start: 21 outliers final: 19 residues processed: 125 average time/residue: 0.1602 time to fit residues: 27.0253 Evaluate side-chains 136 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain L residue 15 GLN Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 11 GLU Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 35 MET Chi-restraints excluded: chain O residue 10 TYR Chi-restraints excluded: chain O residue 35 MET Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain Q residue 10 TYR Chi-restraints excluded: chain Q residue 15 GLN Chi-restraints excluded: chain R residue 15 GLN Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain S residue 26 SER Chi-restraints excluded: chain T residue 15 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 26 optimal weight: 0.3980 chunk 14 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 15 GLN T 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.125267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.108502 restraints weight = 6991.351| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.51 r_work: 0.3503 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 5100 Z= 0.315 Angle : 0.573 8.124 6860 Z= 0.313 Chirality : 0.058 0.142 780 Planarity : 0.002 0.011 880 Dihedral : 5.363 29.930 700 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 4.20 % Allowed : 14.20 % Favored : 81.60 % 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: -1.38 (0.32), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.04 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS T 14 PHE 0.007 0.001 PHE J 19 TYR 0.022 0.002 TYR F 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 135 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 1.223 Fit side-chains REVERT: B 15 GLN cc_start: 0.9224 (mp10) cc_final: 0.8220 (mp10) REVERT: C 22 GLU cc_start: 0.8436 (pt0) cc_final: 0.7928 (pt0) REVERT: D 10 TYR cc_start: 0.8247 (m-80) cc_final: 0.7810 (m-80) REVERT: G 26 SER cc_start: 0.8093 (p) cc_final: 0.7592 (t) REVERT: I 28 LYS cc_start: 0.8539 (mttp) cc_final: 0.7721 (mmmt) REVERT: M 15 GLN cc_start: 0.9093 (mp10) cc_final: 0.8482 (mp10) REVERT: Q 15 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.7568 (mp10) REVERT: R 11 GLU cc_start: 0.8266 (tt0) cc_final: 0.7246 (mp0) REVERT: S 10 TYR cc_start: 0.7037 (m-80) cc_final: 0.5855 (m-80) REVERT: S 15 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.7234 (mp10) outliers start: 21 outliers final: 18 residues processed: 121 average time/residue: 0.2402 time to fit residues: 41.0136 Evaluate side-chains 132 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain L residue 15 GLN Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 11 GLU Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain O residue 10 TYR Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain Q residue 10 TYR Chi-restraints excluded: chain Q residue 11 GLU Chi-restraints excluded: chain Q residue 15 GLN Chi-restraints excluded: chain R residue 15 GLN Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain S residue 26 SER Chi-restraints excluded: chain T residue 15 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 40 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 35 optimal weight: 0.0020 overall best weight: 4.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 15 GLN T 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.122489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.105534 restraints weight = 7188.196| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.57 r_work: 0.3491 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 5100 Z= 0.426 Angle : 0.623 8.306 6860 Z= 0.343 Chirality : 0.059 0.141 780 Planarity : 0.002 0.011 880 Dihedral : 5.582 30.529 700 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Rotamer: Outliers : 4.00 % Allowed : 15.20 % Favored : 80.80 % 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: -1.46 (0.32), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.10 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS R 14 PHE 0.008 0.001 PHE J 19 TYR 0.027 0.002 TYR F 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3051.95 seconds wall clock time: 55 minutes 30.65 seconds (3330.65 seconds total)