Starting phenix.real_space_refine on Wed Sep 17 05:18:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9czp_46424/09_2025/9czp_46424_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9czp_46424/09_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_46424/09_2025/9czp_46424.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9czp_46424/09_2025/9czp_46424.map" model { file = "/net/cci-nas-00/data/ceres_data/9czp_46424/09_2025/9czp_46424_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9czp_46424/09_2025/9czp_46424_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 3260 2.51 5 N 840 2.21 5 O 900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5020 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "B" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "C" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "D" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "E" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "F" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "G" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "H" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "I" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "J" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "K" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "L" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "M" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "N" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "O" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "P" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "Q" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "R" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "S" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "T" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Time building chain proxies: 1.21, per 1000 atoms: 0.24 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: 0.39 Conformation dependent library (CDL) restraints added in 194.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1120 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 15 sheets defined 0.0% alpha, 50.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 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: 0.70 Time building geometry restraints manager: 0.56 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.470 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.520 ------------------------------------------------------------------------------- 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= 1.096 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (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 TYR 0.013 0.004 TYR Q 10 PHE 0.012 0.003 PHE R 19 HIS 0.009 0.003 HIS J 14 Details of bonding type rmsd covalent geometry : bond 0.02120 ( 5100) covalent geometry : angle 2.00525 ( 6860) hydrogen bonds : bond 0.12116 ( 80) hydrogen bonds : angle 9.05382 ( 240) *********************** 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 : 0.198 Fit side-chains REVERT: J 10 TYR cc_start: 0.8623 (m-80) cc_final: 0.8374 (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: 0.0777 time to fit residues: 13.1159 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 : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.129932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.112069 restraints weight = 6898.507| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.61 r_work: 0.3521 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2733 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= 0.203 Angle : 0.590 7.647 6860 Z= 0.337 Chirality : 0.059 0.135 780 Planarity : 0.002 0.011 880 Dihedral : 7.163 46.516 700 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 1.00 % Allowed : 7.40 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.31), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.59 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.002 TYR R 10 PHE 0.008 0.001 PHE A 20 HIS 0.005 0.001 HIS O 14 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 5100) covalent geometry : angle 0.58957 ( 6860) hydrogen bonds : bond 0.04576 ( 80) hydrogen bonds : angle 7.54030 ( 240) *********************** 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 135 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 130 time to evaluate : 0.189 Fit side-chains REVERT: A 27 ASN cc_start: 0.7969 (m110) cc_final: 0.7736 (m110) REVERT: B 15 GLN cc_start: 0.9160 (mp10) cc_final: 0.8371 (mp10) REVERT: C 22 GLU cc_start: 0.8302 (pt0) cc_final: 0.8009 (pt0) REVERT: F 15 GLN cc_start: 0.9338 (mp10) cc_final: 0.8533 (mp10) REVERT: H 10 TYR cc_start: 0.8863 (m-80) cc_final: 0.8305 (m-80) REVERT: K 10 TYR cc_start: 0.7573 (m-80) cc_final: 0.7245 (m-80) REVERT: K 23 ASP cc_start: 0.7944 (m-30) cc_final: 0.7489 (m-30) REVERT: M 10 TYR cc_start: 0.7996 (m-80) cc_final: 0.7655 (m-80) REVERT: M 15 GLN cc_start: 0.9045 (mp10) cc_final: 0.8464 (mp10) REVERT: Q 23 ASP cc_start: 0.7983 (m-30) cc_final: 0.7598 (m-30) REVERT: R 10 TYR cc_start: 0.8748 (m-80) cc_final: 0.8323 (m-10) REVERT: R 11 GLU cc_start: 0.8304 (tt0) cc_final: 0.7387 (mp0) outliers start: 5 outliers final: 4 residues processed: 131 average time/residue: 0.0519 time to fit residues: 9.5238 Evaluate side-chains 115 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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 21 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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 27 ASN ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 ASN R 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.122751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.105407 restraints weight = 7122.985| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.55 r_work: 0.3432 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 5100 Z= 0.290 Angle : 0.648 6.778 6860 Z= 0.365 Chirality : 0.061 0.153 780 Planarity : 0.002 0.012 880 Dihedral : 6.763 42.718 700 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 2.40 % Allowed : 9.80 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.31), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.84 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.025 0.003 TYR M 10 PHE 0.009 0.001 PHE I 19 HIS 0.004 0.001 HIS K 14 Details of bonding type rmsd covalent geometry : bond 0.00686 ( 5100) covalent geometry : angle 0.64800 ( 6860) hydrogen bonds : bond 0.05002 ( 80) hydrogen bonds : angle 7.14711 ( 240) *********************** 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 127 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.198 Fit side-chains REVERT: A 27 ASN cc_start: 0.7866 (m110) cc_final: 0.7547 (m110) REVERT: C 22 GLU cc_start: 0.8441 (pt0) cc_final: 0.8187 (pt0) REVERT: D 16 LYS cc_start: 0.9287 (tttt) cc_final: 0.9056 (tttp) REVERT: H 10 TYR cc_start: 0.8762 (m-80) cc_final: 0.8129 (m-80) REVERT: I 28 LYS cc_start: 0.8359 (mttp) cc_final: 0.7704 (mmmt) REVERT: K 10 TYR cc_start: 0.8136 (m-80) cc_final: 0.7495 (m-80) REVERT: L 35 MET cc_start: 0.8853 (ttp) cc_final: 0.8637 (ptm) REVERT: M 10 TYR cc_start: 0.8116 (m-80) cc_final: 0.7712 (m-80) REVERT: M 15 GLN cc_start: 0.9172 (mp10) cc_final: 0.8548 (mp10) REVERT: O 15 GLN cc_start: 0.9175 (mp10) cc_final: 0.8822 (mp10) REVERT: P 15 GLN cc_start: 0.9287 (pt0) cc_final: 0.9012 (pt0) REVERT: Q 10 TYR cc_start: 0.7425 (m-80) cc_final: 0.7110 (m-80) REVERT: R 10 TYR cc_start: 0.8872 (m-80) cc_final: 0.8303 (m-80) REVERT: R 11 GLU cc_start: 0.8305 (tt0) cc_final: 0.7326 (mp0) REVERT: S 10 TYR cc_start: 0.7844 (m-80) cc_final: 0.7643 (m-80) REVERT: T 10 TYR cc_start: 0.8513 (m-80) cc_final: 0.7892 (m-80) outliers start: 12 outliers final: 7 residues processed: 121 average time/residue: 0.0548 time to fit residues: 9.0029 Evaluate side-chains 113 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.189 ------------------------------------------------------------------------------- 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 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 T residue 15 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 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 = 0.3713 r_free = 0.3713 target = 0.119891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.102703 restraints weight = 7143.314| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.54 r_work: 0.3401 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.044 5100 Z= 0.359 Angle : 0.692 7.671 6860 Z= 0.386 Chirality : 0.062 0.150 780 Planarity : 0.003 0.011 880 Dihedral : 6.670 39.705 700 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.31), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.06 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.026 0.003 TYR Q 10 PHE 0.008 0.002 PHE N 19 HIS 0.005 0.002 HIS K 14 Details of bonding type rmsd covalent geometry : bond 0.00855 ( 5100) covalent geometry : angle 0.69194 ( 6860) hydrogen bonds : bond 0.05031 ( 80) hydrogen bonds : angle 6.90718 ( 240) *********************** 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 125 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.147 Fit side-chains REVERT: A 27 ASN cc_start: 0.8021 (m110) cc_final: 0.7688 (m110) REVERT: C 15 GLN cc_start: 0.9038 (mp10) cc_final: 0.8802 (mp10) REVERT: C 22 GLU cc_start: 0.8467 (pt0) cc_final: 0.8019 (pt0) REVERT: I 28 LYS cc_start: 0.8517 (mttp) cc_final: 0.7808 (mmmt) REVERT: L 35 MET cc_start: 0.8877 (ttp) cc_final: 0.8455 (ptm) REVERT: M 15 GLN cc_start: 0.9231 (mp10) cc_final: 0.8747 (mp10) REVERT: P 15 GLN cc_start: 0.9333 (OUTLIER) cc_final: 0.9092 (pm20) REVERT: Q 10 TYR cc_start: 0.7834 (m-80) cc_final: 0.7607 (m-80) REVERT: R 11 GLU cc_start: 0.8308 (tt0) cc_final: 0.8047 (tt0) REVERT: S 15 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.7440 (mp10) outliers start: 15 outliers final: 9 residues processed: 116 average time/residue: 0.0517 time to fit residues: 8.4409 Evaluate side-chains 115 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.186 ------------------------------------------------------------------------------- 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 Q residue 11 GLU 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 58 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 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 = 0.3812 r_free = 0.3812 target = 0.127350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.110367 restraints weight = 7029.362| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.53 r_work: 0.3516 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5100 Z= 0.153 Angle : 0.538 7.678 6860 Z= 0.297 Chirality : 0.057 0.142 780 Planarity : 0.002 0.011 880 Dihedral : 5.850 32.635 700 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 3.40 % Allowed : 12.00 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 TYR 0.014 0.002 TYR Q 10 PHE 0.007 0.001 PHE G 20 HIS 0.003 0.001 HIS Q 13 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 5100) covalent geometry : angle 0.53801 ( 6860) hydrogen bonds : bond 0.03676 ( 80) hydrogen bonds : angle 6.57203 ( 240) *********************** 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 138 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.167 Fit side-chains REVERT: A 22 GLU cc_start: 0.7808 (pt0) cc_final: 0.7383 (pm20) REVERT: A 27 ASN cc_start: 0.7760 (m110) cc_final: 0.7507 (m110) REVERT: B 15 GLN cc_start: 0.9188 (mp10) cc_final: 0.8061 (mp10) REVERT: C 22 GLU cc_start: 0.8546 (pt0) cc_final: 0.8075 (pt0) REVERT: F 15 GLN cc_start: 0.9388 (mp10) cc_final: 0.8243 (mp10) REVERT: H 10 TYR cc_start: 0.8774 (m-80) cc_final: 0.8343 (m-80) REVERT: I 28 LYS cc_start: 0.8475 (mttp) cc_final: 0.7738 (mmmt) REVERT: M 15 GLN cc_start: 0.9134 (mp10) cc_final: 0.8537 (mp10) REVERT: O 15 GLN cc_start: 0.9179 (mp10) cc_final: 0.8810 (mp10) REVERT: P 15 GLN cc_start: 0.9263 (pt0) cc_final: 0.8992 (pm20) REVERT: Q 15 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.7575 (mp10) REVERT: R 11 GLU cc_start: 0.8309 (tt0) cc_final: 0.7292 (mp0) REVERT: S 15 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.7263 (mp10) outliers start: 17 outliers final: 12 residues processed: 127 average time/residue: 0.0546 time to fit residues: 9.4384 Evaluate side-chains 129 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain H 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 N residue 26 SER Chi-restraints excluded: chain O residue 35 MET 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 T residue 15 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 11 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 35 optimal weight: 0.0060 chunk 38 optimal weight: 8.9990 overall best weight: 6.2004 ------------------------------------------------------------------------------- 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 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 = 0.3723 r_free = 0.3723 target = 0.119578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.102375 restraints weight = 7208.551| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.57 r_work: 0.3404 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.044 5100 Z= 0.367 Angle : 0.695 8.044 6860 Z= 0.386 Chirality : 0.061 0.141 780 Planarity : 0.003 0.013 880 Dihedral : 6.308 35.060 700 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 3.40 % Allowed : 13.00 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.32), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.029 0.003 TYR M 10 PHE 0.008 0.001 PHE I 20 HIS 0.005 0.002 HIS H 13 Details of bonding type rmsd covalent geometry : bond 0.00874 ( 5100) covalent geometry : angle 0.69536 ( 6860) hydrogen bonds : bond 0.04988 ( 80) hydrogen bonds : angle 6.74421 ( 240) *********************** 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 129 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.197 Fit side-chains REVERT: A 22 GLU cc_start: 0.7615 (pt0) cc_final: 0.7347 (pm20) REVERT: A 27 ASN cc_start: 0.8028 (m110) cc_final: 0.7739 (m110) REVERT: B 10 TYR cc_start: 0.8358 (m-80) cc_final: 0.7935 (m-80) REVERT: C 22 GLU cc_start: 0.8576 (pt0) cc_final: 0.8249 (pt0) REVERT: H 10 TYR cc_start: 0.8954 (m-80) cc_final: 0.8365 (m-80) REVERT: I 28 LYS cc_start: 0.8564 (mttp) cc_final: 0.7808 (mmmt) REVERT: M 15 GLN cc_start: 0.9184 (mp10) cc_final: 0.8946 (mp10) REVERT: P 15 GLN cc_start: 0.9339 (OUTLIER) cc_final: 0.9136 (pm20) REVERT: R 11 GLU cc_start: 0.8350 (tt0) cc_final: 0.8079 (tt0) REVERT: S 10 TYR cc_start: 0.6996 (m-80) cc_final: 0.5612 (m-80) outliers start: 17 outliers final: 15 residues processed: 119 average time/residue: 0.0481 time to fit residues: 8.3050 Evaluate side-chains 125 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain K residue 11 GLU 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 N residue 26 SER Chi-restraints excluded: chain O residue 26 SER 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 R residue 26 SER 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: 7.9990 chunk 9 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 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 = 0.3822 r_free = 0.3822 target = 0.127375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.110251 restraints weight = 6940.451| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.54 r_work: 0.3554 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5100 Z= 0.151 Angle : 0.539 8.213 6860 Z= 0.294 Chirality : 0.057 0.137 780 Planarity : 0.002 0.012 880 Dihedral : 5.576 31.104 700 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 3.40 % Allowed : 13.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.32), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.06 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR F 10 PHE 0.005 0.001 PHE G 20 HIS 0.003 0.001 HIS F 13 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 5100) covalent geometry : angle 0.53867 ( 6860) hydrogen bonds : bond 0.03575 ( 80) hydrogen bonds : angle 6.46444 ( 240) *********************** 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 134 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.146 Fit side-chains REVERT: B 15 GLN cc_start: 0.9270 (mp10) cc_final: 0.9045 (mp10) REVERT: C 15 GLN cc_start: 0.9048 (mp10) cc_final: 0.8826 (mp10) REVERT: C 22 GLU cc_start: 0.8500 (pt0) cc_final: 0.8159 (pt0) REVERT: H 10 TYR cc_start: 0.8862 (m-80) cc_final: 0.8560 (m-80) REVERT: I 28 LYS cc_start: 0.8559 (mttp) cc_final: 0.7801 (mmmt) REVERT: M 15 GLN cc_start: 0.9140 (mp10) cc_final: 0.8630 (mp10) REVERT: O 15 GLN cc_start: 0.9132 (mp10) cc_final: 0.8787 (mp10) REVERT: P 15 GLN cc_start: 0.9263 (OUTLIER) cc_final: 0.9038 (pm20) REVERT: Q 15 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.7649 (mp10) REVERT: R 11 GLU cc_start: 0.8305 (tt0) cc_final: 0.7416 (mp0) REVERT: S 10 TYR cc_start: 0.6839 (m-80) cc_final: 0.5673 (m-80) REVERT: S 15 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.7337 (mp10) outliers start: 17 outliers final: 13 residues processed: 122 average time/residue: 0.0493 time to fit residues: 8.5272 Evaluate side-chains 130 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 15 GLN 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 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 T residue 15 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 19 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 chunk 10 optimal weight: 0.4980 chunk 50 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 29 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.134649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.118038 restraints weight = 6867.730| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.51 r_work: 0.3639 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 5100 Z= 0.085 Angle : 0.491 8.248 6860 Z= 0.263 Chirality : 0.056 0.132 780 Planarity : 0.002 0.010 880 Dihedral : 4.794 27.221 700 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 3.40 % Allowed : 14.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.33), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.94 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR H 10 PHE 0.004 0.001 PHE G 20 HIS 0.002 0.001 HIS Q 13 Details of bonding type rmsd covalent geometry : bond 0.00191 ( 5100) covalent geometry : angle 0.49067 ( 6860) hydrogen bonds : bond 0.02863 ( 80) hydrogen bonds : angle 6.22719 ( 240) *********************** 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 144 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.211 Fit side-chains REVERT: B 15 GLN cc_start: 0.9140 (mp10) cc_final: 0.8169 (mp10) REVERT: C 15 GLN cc_start: 0.9023 (mp10) cc_final: 0.8755 (mp10) REVERT: C 22 GLU cc_start: 0.8290 (pt0) cc_final: 0.7855 (pt0) REVERT: F 15 GLN cc_start: 0.9313 (mp10) cc_final: 0.8071 (mp10) REVERT: G 16 LYS cc_start: 0.8539 (tttt) cc_final: 0.8302 (tttp) REVERT: G 26 SER cc_start: 0.8184 (p) cc_final: 0.7707 (t) REVERT: I 28 LYS cc_start: 0.8537 (mttp) cc_final: 0.7734 (mmmt) REVERT: K 11 GLU cc_start: 0.8250 (tt0) cc_final: 0.7928 (tp30) REVERT: M 15 GLN cc_start: 0.9025 (mp10) cc_final: 0.8433 (mp10) REVERT: O 15 GLN cc_start: 0.9161 (mp10) cc_final: 0.8764 (mp10) REVERT: P 15 GLN cc_start: 0.9188 (OUTLIER) cc_final: 0.8910 (pm20) REVERT: Q 15 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.7534 (mp10) REVERT: R 11 GLU cc_start: 0.8255 (tt0) cc_final: 0.7375 (mp0) REVERT: S 10 TYR cc_start: 0.6394 (m-80) cc_final: 0.5561 (m-80) REVERT: S 15 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7127 (mp10) REVERT: T 11 GLU cc_start: 0.8260 (tt0) cc_final: 0.7857 (mp0) outliers start: 17 outliers final: 9 residues processed: 132 average time/residue: 0.0582 time to fit residues: 10.4638 Evaluate side-chains 132 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H 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 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 15 GLN Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain T residue 15 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 39 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 58 optimal weight: 0.0370 chunk 26 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 0.3980 overall best weight: 1.0460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN C 27 ASN ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.135185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.118502 restraints weight = 6891.229| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.53 r_work: 0.3676 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5100 Z= 0.097 Angle : 0.504 8.165 6860 Z= 0.267 Chirality : 0.056 0.131 780 Planarity : 0.002 0.010 880 Dihedral : 4.623 24.864 700 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 3.00 % Allowed : 15.80 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.33), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.91 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.001 TYR F 10 PHE 0.003 0.000 PHE G 20 HIS 0.002 0.001 HIS Q 13 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 5100) covalent geometry : angle 0.50411 ( 6860) hydrogen bonds : bond 0.02958 ( 80) hydrogen bonds : angle 6.14294 ( 240) *********************** 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 137 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.198 Fit side-chains REVERT: B 15 GLN cc_start: 0.9172 (mp10) cc_final: 0.8317 (mp10) REVERT: C 15 GLN cc_start: 0.9029 (mp10) cc_final: 0.8792 (mp10) REVERT: C 22 GLU cc_start: 0.8247 (pt0) cc_final: 0.7870 (pt0) REVERT: G 26 SER cc_start: 0.8292 (p) cc_final: 0.7805 (t) REVERT: I 28 LYS cc_start: 0.8580 (mttp) cc_final: 0.7819 (mmmt) REVERT: M 15 GLN cc_start: 0.9039 (mp10) cc_final: 0.8548 (mp10) REVERT: N 10 TYR cc_start: 0.8631 (m-80) cc_final: 0.8337 (m-80) REVERT: O 15 GLN cc_start: 0.9143 (mp10) cc_final: 0.8810 (mp10) REVERT: Q 15 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.7690 (mp10) REVERT: R 11 GLU cc_start: 0.8249 (tt0) cc_final: 0.7447 (mp0) REVERT: R 16 LYS cc_start: 0.9037 (tttt) cc_final: 0.8743 (tttt) REVERT: S 10 TYR cc_start: 0.6406 (m-80) cc_final: 0.5692 (m-80) REVERT: S 15 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7275 (mp10) REVERT: T 11 GLU cc_start: 0.8177 (tt0) cc_final: 0.7921 (mp0) outliers start: 15 outliers final: 11 residues processed: 126 average time/residue: 0.0547 time to fit residues: 9.4700 Evaluate side-chains 130 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain E residue 11 GLU 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 35 MET 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 Q residue 15 GLN Chi-restraints excluded: chain S residue 15 GLN 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 15 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- 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** E 27 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.121851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.104857 restraints weight = 7121.264| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.56 r_work: 0.3454 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.043 5100 Z= 0.315 Angle : 0.678 8.670 6860 Z= 0.369 Chirality : 0.060 0.145 780 Planarity : 0.002 0.014 880 Dihedral : 5.669 30.952 700 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 2.20 % Allowed : 17.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.32), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.07 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.029 0.003 TYR F 10 PHE 0.008 0.001 PHE J 19 HIS 0.006 0.002 HIS H 13 Details of bonding type rmsd covalent geometry : bond 0.00751 ( 5100) covalent geometry : angle 0.67787 ( 6860) hydrogen bonds : bond 0.04511 ( 80) hydrogen bonds : angle 6.57723 ( 240) ********************** 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 123 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.140 Fit side-chains REVERT: C 22 GLU cc_start: 0.8396 (pt0) cc_final: 0.7970 (pt0) REVERT: G 26 SER cc_start: 0.8094 (p) cc_final: 0.7566 (t) REVERT: I 28 LYS cc_start: 0.8555 (mttp) cc_final: 0.7733 (mmmt) REVERT: K 10 TYR cc_start: 0.7255 (m-80) cc_final: 0.5160 (p90) REVERT: K 11 GLU cc_start: 0.8159 (tp30) cc_final: 0.7053 (tm-30) REVERT: M 15 GLN cc_start: 0.9092 (mp10) cc_final: 0.8790 (mp10) REVERT: O 15 GLN cc_start: 0.9163 (mp10) cc_final: 0.8725 (mp10) REVERT: R 11 GLU cc_start: 0.8350 (tt0) cc_final: 0.7245 (mp0) REVERT: S 10 TYR cc_start: 0.7112 (m-80) cc_final: 0.5740 (m-80) REVERT: S 15 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.7218 (mp10) outliers start: 11 outliers final: 7 residues processed: 117 average time/residue: 0.0460 time to fit residues: 7.7536 Evaluate side-chains 119 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 15 GLN 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 S residue 15 GLN 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 36 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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** ** F 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 = 0.3842 r_free = 0.3842 target = 0.127560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.110587 restraints weight = 7059.998| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.56 r_work: 0.3569 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5100 Z= 0.165 Angle : 0.570 8.533 6860 Z= 0.304 Chirality : 0.057 0.137 780 Planarity : 0.002 0.011 880 Dihedral : 5.274 29.505 700 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 1.80 % Allowed : 18.60 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.32), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.07 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.023 0.002 TYR F 10 PHE 0.004 0.001 PHE J 19 HIS 0.003 0.001 HIS F 13 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 5100) covalent geometry : angle 0.57040 ( 6860) hydrogen bonds : bond 0.03560 ( 80) hydrogen bonds : angle 6.34774 ( 240) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1245.60 seconds wall clock time: 22 minutes 4.83 seconds (1324.83 seconds total)