Starting phenix.real_space_refine on Wed Mar 4 14:42:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dyt_27781/03_2026/8dyt_27781.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dyt_27781/03_2026/8dyt_27781.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 { model { file = "/net/cci-nas-00/data/ceres_data/8dyt_27781/03_2026/8dyt_27781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dyt_27781/03_2026/8dyt_27781.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dyt_27781/03_2026/8dyt_27781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dyt_27781/03_2026/8dyt_27781.map" } 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= 0.005 sd= 0.203 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 56 5.16 5 C 9152 2.51 5 N 2544 2.21 5 O 2826 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14578 Number of models: 1 Model: "" Number of chains: 18 Chain: "I" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 225 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 23} Chain: "J" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 225 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 23} Chain: "L" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 787 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 979 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "B" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 787 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "A" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 979 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "D" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 787 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "C" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 979 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "F" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 787 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "E" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 979 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "N" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 787 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "M" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 979 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "P" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 787 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "O" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 979 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "R" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 787 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "Q" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 979 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "T" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 787 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "S" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 979 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Time building chain proxies: 3.65, per 1000 atoms: 0.25 Number of scatterers: 14578 At special positions: 0 Unit cell: (109.25, 125.35, 92, 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 56 16.00 O 2826 8.00 N 2544 7.00 C 9152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.02 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.02 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 614.3 milliseconds 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3408 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 48 sheets defined 5.6% alpha, 41.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'P' and resid 79 through 83 Processing helix chain 'O' and resid 28 through 32 Processing helix chain 'O' and resid 61 through 64 Processing helix chain 'O' and resid 73 through 75 No H-bonds generated for 'chain 'O' and resid 73 through 75' Processing helix chain 'R' and resid 79 through 83 Processing helix chain 'Q' and resid 28 through 32 Processing helix chain 'Q' and resid 61 through 64 Processing helix chain 'Q' and resid 73 through 75 No H-bonds generated for 'chain 'Q' and resid 73 through 75' Processing helix chain 'T' and resid 79 through 83 Processing helix chain 'S' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'L' and resid 9 through 11 removed outlier: 5.871A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AA3, first strand: chain 'L' and resid 89 through 92 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.544A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.871A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.267A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 9 through 11 removed outlier: 6.515A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 19 through 24 Processing sheet with id=AA9, first strand: chain 'B' and resid 89 through 92 Processing sheet with id=AB1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.631A pdb=" N THR A 77 " --> pdb=" O ASP A 72 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.451A pdb=" N GLY A 10 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N MET A 34 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.451A pdb=" N GLY A 10 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N TYR A 102 " --> pdb=" O ARG A 94 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 9 through 11 removed outlier: 6.598A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AB6, first strand: chain 'D' and resid 89 through 92 Processing sheet with id=AB7, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.570A pdb=" N THR C 77 " --> pdb=" O ASP C 72 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.877A pdb=" N MET C 34 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.200A pdb=" N CYS C 92 " --> pdb=" O TRP C 103 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N TRP C 103 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ARG C 94 " --> pdb=" O ASP C 101 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 9 through 11 removed outlier: 6.718A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 9 through 11 Processing sheet with id=AC3, first strand: chain 'F' and resid 19 through 24 removed outlier: 3.503A pdb=" N SER F 65 " --> pdb=" O SER F 72 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.696A pdb=" N THR E 77 " --> pdb=" O ASP E 72 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.762A pdb=" N MET E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.132A pdb=" N TYR E 102 " --> pdb=" O ARG E 94 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 9 through 11 removed outlier: 6.715A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 9 through 11 Processing sheet with id=AC9, first strand: chain 'N' and resid 19 through 24 removed outlier: 3.504A pdb=" N SER N 65 " --> pdb=" O SER N 72 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.691A pdb=" N THR M 77 " --> pdb=" O ASP M 72 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.763A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 10 through 12 removed outlier: 4.129A pdb=" N TYR M 102 " --> pdb=" O ARG M 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 9 through 11 removed outlier: 6.597A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 19 through 24 Processing sheet with id=AD6, first strand: chain 'P' and resid 89 through 92 Processing sheet with id=AD7, first strand: chain 'O' and resid 3 through 7 removed outlier: 3.575A pdb=" N THR O 77 " --> pdb=" O ASP O 72 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.876A pdb=" N MET O 34 " --> pdb=" O VAL O 50 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N VAL O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.193A pdb=" N CYS O 92 " --> pdb=" O TRP O 103 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TRP O 103 " --> pdb=" O CYS O 92 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG O 94 " --> pdb=" O ASP O 101 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'R' and resid 9 through 11 removed outlier: 5.866A pdb=" N GLN R 37 " --> pdb=" O LEU R 46 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N LEU R 46 " --> pdb=" O GLN R 37 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'R' and resid 19 through 24 Processing sheet with id=AE3, first strand: chain 'R' and resid 89 through 92 Processing sheet with id=AE4, first strand: chain 'Q' and resid 3 through 7 removed outlier: 3.513A pdb=" N THR Q 77 " --> pdb=" O ASP Q 72 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.869A pdb=" N MET Q 34 " --> pdb=" O VAL Q 50 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL Q 50 " --> pdb=" O MET Q 34 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP Q 36 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.268A pdb=" N CYS Q 92 " --> pdb=" O TRP Q 103 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TRP Q 103 " --> pdb=" O CYS Q 92 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG Q 94 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'T' and resid 9 through 11 removed outlier: 6.513A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'T' and resid 19 through 24 Processing sheet with id=AE9, first strand: chain 'T' and resid 89 through 92 Processing sheet with id=AF1, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.630A pdb=" N THR S 77 " --> pdb=" O ASP S 72 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.483A pdb=" N GLY S 10 " --> pdb=" O THR S 110 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N MET S 34 " --> pdb=" O VAL S 50 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.483A pdb=" N GLY S 10 " --> pdb=" O THR S 110 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR S 102 " --> pdb=" O ARG S 94 " (cutoff:3.500A) 586 hydrogen bonds defined for protein. 1314 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: 2.42 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3569 1.33 - 1.45: 3330 1.45 - 1.56: 7964 1.56 - 1.68: 1 1.68 - 1.80: 72 Bond restraints: 14936 Sorted by residual: bond pdb=" CB CYS P 88 " pdb=" SG CYS P 88 " ideal model delta sigma weight residual 1.808 1.764 0.044 3.30e-02 9.18e+02 1.76e+00 bond pdb=" CG1 ILE T 27C" pdb=" CD1 ILE T 27C" ideal model delta sigma weight residual 1.513 1.462 0.051 3.90e-02 6.57e+02 1.73e+00 bond pdb=" CB CYS D 88 " pdb=" SG CYS D 88 " ideal model delta sigma weight residual 1.808 1.765 0.043 3.30e-02 9.18e+02 1.70e+00 bond pdb=" CG1 ILE B 27C" pdb=" CD1 ILE B 27C" ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.60e+00 bond pdb=" CB THR C 77 " pdb=" CG2 THR C 77 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.58e+00 ... (remaining 14931 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.86: 17520 0.86 - 1.72: 2147 1.72 - 2.57: 438 2.57 - 3.43: 173 3.43 - 4.29: 48 Bond angle restraints: 20326 Sorted by residual: angle pdb=" N ILE D 27C" pdb=" CA ILE D 27C" pdb=" C ILE D 27C" ideal model delta sigma weight residual 113.53 110.66 2.87 9.80e-01 1.04e+00 8.59e+00 angle pdb=" CA PRO I 2 " pdb=" N PRO I 2 " pdb=" CD PRO I 2 " ideal model delta sigma weight residual 112.00 108.29 3.71 1.40e+00 5.10e-01 7.02e+00 angle pdb=" N THR D 42 " pdb=" CA THR D 42 " pdb=" C THR D 42 " ideal model delta sigma weight residual 111.02 114.08 -3.06 1.25e+00 6.40e-01 5.99e+00 angle pdb=" C PRO L 59 " pdb=" N ASP L 60 " pdb=" CA ASP L 60 " ideal model delta sigma weight residual 120.60 124.46 -3.86 1.60e+00 3.91e-01 5.82e+00 angle pdb=" N THR P 42 " pdb=" CA THR P 42 " pdb=" C THR P 42 " ideal model delta sigma weight residual 111.02 114.01 -2.99 1.25e+00 6.40e-01 5.71e+00 ... (remaining 20321 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 7839 17.95 - 35.90: 639 35.90 - 53.84: 168 53.84 - 71.79: 36 71.79 - 89.74: 22 Dihedral angle restraints: 8704 sinusoidal: 3274 harmonic: 5430 Sorted by residual: dihedral pdb=" CB CYS T 23 " pdb=" SG CYS T 23 " pdb=" SG CYS T 88 " pdb=" CB CYS T 88 " ideal model delta sinusoidal sigma weight residual 93.00 136.26 -43.26 1 1.00e+01 1.00e-02 2.61e+01 dihedral pdb=" CB CYS B 23 " pdb=" SG CYS B 23 " pdb=" SG CYS B 88 " pdb=" CB CYS B 88 " ideal model delta sinusoidal sigma weight residual 93.00 136.23 -43.23 1 1.00e+01 1.00e-02 2.61e+01 dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 88 " pdb=" CB CYS F 88 " ideal model delta sinusoidal sigma weight residual 93.00 134.44 -41.44 1 1.00e+01 1.00e-02 2.40e+01 ... (remaining 8701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1242 0.033 - 0.065: 596 0.065 - 0.098: 213 0.098 - 0.131: 118 0.131 - 0.163: 15 Chirality restraints: 2184 Sorted by residual: chirality pdb=" CA PRO I 10 " pdb=" N PRO I 10 " pdb=" C PRO I 10 " pdb=" CB PRO I 10 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.67e-01 chirality pdb=" CB THR E 87 " pdb=" CA THR E 87 " pdb=" OG1 THR E 87 " pdb=" CG2 THR E 87 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.77e-01 chirality pdb=" CA VAL S 89 " pdb=" N VAL S 89 " pdb=" C VAL S 89 " pdb=" CB VAL S 89 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.88e-01 ... (remaining 2181 not shown) Planarity restraints: 2648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO F 7 " 0.053 5.00e-02 4.00e+02 8.00e-02 1.02e+01 pdb=" N PRO F 8 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO F 8 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO F 8 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO N 7 " -0.052 5.00e-02 4.00e+02 7.97e-02 1.02e+01 pdb=" N PRO N 8 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO N 8 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO N 8 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN I 1 " 0.046 5.00e-02 4.00e+02 6.84e-02 7.48e+00 pdb=" N PRO I 2 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO I 2 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO I 2 " 0.038 5.00e-02 4.00e+02 ... (remaining 2645 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 994 2.72 - 3.27: 13717 3.27 - 3.81: 23874 3.81 - 4.36: 30383 4.36 - 4.90: 54389 Nonbonded interactions: 123357 Sorted by model distance: nonbonded pdb=" ND2 ASN I 3 " pdb=" O TYR A 100C" model vdw 2.181 3.120 nonbonded pdb=" ND2 ASN J 15 " pdb=" OD1 ASN Q 97 " model vdw 2.217 3.120 nonbonded pdb=" ND2 ASN J 31 " pdb=" OD1 ASN M 97 " model vdw 2.235 3.120 nonbonded pdb=" NH2 ARG N 61 " pdb=" OD1 ASP N 82 " model vdw 2.244 3.120 nonbonded pdb=" NH2 ARG F 61 " pdb=" OD1 ASP F 82 " model vdw 2.260 3.120 ... (remaining 123352 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 'C' selection = chain 'E' selection = chain 'H' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'I' selection = chain 'J' } 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: 0.910 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.440 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 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 : 0.007 0.061 14952 Z= 0.298 Angle : 0.674 4.289 20358 Z= 0.387 Chirality : 0.047 0.163 2184 Planarity : 0.006 0.080 2648 Dihedral : 15.304 89.740 5248 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.45 % Allowed : 17.22 % Favored : 82.33 % 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 are not related in a simple way. whole: -0.40 (0.19), residues: 1884 helix: None (None), residues: 0 sheet: 0.16 (0.19), residues: 824 loop : -0.57 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 19 TYR 0.026 0.002 TYR E 52A PHE 0.023 0.002 PHE B 96 TRP 0.022 0.002 TRP C 47 HIS 0.006 0.002 HIS M 82A Details of bonding type rmsd covalent geometry : bond 0.00701 (14936) covalent geometry : angle 0.67236 (20326) SS BOND : bond 0.00529 ( 16) SS BOND : angle 1.34848 ( 32) hydrogen bonds : bond 0.21861 ( 530) hydrogen bonds : angle 9.74501 ( 1314) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 229 time to evaluate : 0.482 Fit side-chains REVERT: A 68 THR cc_start: 0.9310 (t) cc_final: 0.9084 (p) outliers start: 7 outliers final: 4 residues processed: 230 average time/residue: 0.1441 time to fit residues: 46.1997 Evaluate side-chains 231 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 227 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain R residue 105 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.099805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.075261 restraints weight = 21656.024| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 1.89 r_work: 0.2757 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14952 Z= 0.123 Angle : 0.538 4.186 20358 Z= 0.292 Chirality : 0.044 0.177 2184 Planarity : 0.004 0.059 2648 Dihedral : 5.107 52.792 2126 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.49 % Allowed : 14.09 % Favored : 83.42 % 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 are not related in a simple way. whole: -0.34 (0.19), residues: 1884 helix: None (None), residues: 0 sheet: 0.27 (0.19), residues: 776 loop : -0.55 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 16 TYR 0.017 0.001 TYR M 52A PHE 0.012 0.002 PHE S 29 TRP 0.014 0.001 TRP O 47 HIS 0.004 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00273 (14936) covalent geometry : angle 0.53709 (20326) SS BOND : bond 0.00277 ( 16) SS BOND : angle 0.76867 ( 32) hydrogen bonds : bond 0.03867 ( 530) hydrogen bonds : angle 6.62241 ( 1314) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 246 time to evaluate : 0.444 Fit side-chains REVERT: B 69 THR cc_start: 0.8490 (p) cc_final: 0.8079 (t) REVERT: B 79 GLN cc_start: 0.8339 (mp10) cc_final: 0.8039 (mp10) REVERT: B 106 VAL cc_start: 0.4833 (m) cc_final: 0.4574 (m) REVERT: A 53 ASP cc_start: 0.8899 (p0) cc_final: 0.8695 (p0) REVERT: A 68 THR cc_start: 0.9292 (t) cc_final: 0.9047 (p) REVERT: A 73 ASN cc_start: 0.9240 (OUTLIER) cc_final: 0.8939 (t0) REVERT: C 3 GLN cc_start: 0.8649 (mt0) cc_final: 0.8220 (mm-40) REVERT: N 54 ARG cc_start: 0.8094 (mtp-110) cc_final: 0.7870 (mtp-110) REVERT: O 3 GLN cc_start: 0.8659 (mt0) cc_final: 0.8248 (mm-40) REVERT: O 73 ASN cc_start: 0.9072 (t0) cc_final: 0.8857 (m-40) REVERT: T 69 THR cc_start: 0.8400 (p) cc_final: 0.8063 (t) REVERT: T 79 GLN cc_start: 0.8392 (mp10) cc_final: 0.8068 (mp10) REVERT: S 73 ASN cc_start: 0.9229 (OUTLIER) cc_final: 0.8936 (t0) outliers start: 39 outliers final: 16 residues processed: 272 average time/residue: 0.1304 time to fit residues: 50.3539 Evaluate side-chains 254 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 236 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain O residue 57 LYS Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 73 ASN Chi-restraints excluded: chain S residue 87 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 37 optimal weight: 0.6980 chunk 45 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 87 optimal weight: 0.0670 chunk 105 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 95 optimal weight: 0.9980 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.100838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.076499 restraints weight = 21537.394| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 1.85 r_work: 0.2782 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14952 Z= 0.129 Angle : 0.514 4.445 20358 Z= 0.276 Chirality : 0.044 0.150 2184 Planarity : 0.004 0.048 2648 Dihedral : 4.739 47.423 2120 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.38 % Allowed : 14.16 % Favored : 82.46 % 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 are not related in a simple way. whole: -0.19 (0.19), residues: 1884 helix: None (None), residues: 0 sheet: 0.28 (0.19), residues: 800 loop : -0.39 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 16 TYR 0.013 0.001 TYR A 58 PHE 0.012 0.002 PHE S 29 TRP 0.012 0.001 TRP Q 47 HIS 0.004 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00301 (14936) covalent geometry : angle 0.51411 (20326) SS BOND : bond 0.00266 ( 16) SS BOND : angle 0.70285 ( 32) hydrogen bonds : bond 0.03177 ( 530) hydrogen bonds : angle 5.86828 ( 1314) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 246 time to evaluate : 0.556 Fit side-chains REVERT: H 13 GLN cc_start: 0.7876 (mp10) cc_final: 0.7664 (mp10) REVERT: B 69 THR cc_start: 0.8446 (p) cc_final: 0.8061 (t) REVERT: B 79 GLN cc_start: 0.8373 (mp10) cc_final: 0.8027 (mp10) REVERT: A 68 THR cc_start: 0.9315 (t) cc_final: 0.9043 (p) REVERT: A 73 ASN cc_start: 0.9267 (OUTLIER) cc_final: 0.8948 (t0) REVERT: C 3 GLN cc_start: 0.8656 (mt0) cc_final: 0.8251 (mm-40) REVERT: C 73 ASN cc_start: 0.9053 (t0) cc_final: 0.8830 (m-40) REVERT: N 54 ARG cc_start: 0.8051 (mtp-110) cc_final: 0.7746 (mtp-110) REVERT: O 3 GLN cc_start: 0.8680 (mt0) cc_final: 0.8273 (mm-40) REVERT: O 19 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8060 (ttt-90) REVERT: O 101 ASP cc_start: 0.8612 (p0) cc_final: 0.8374 (p0) REVERT: O 102 TYR cc_start: 0.8997 (m-80) cc_final: 0.8699 (m-80) REVERT: Q 13 GLN cc_start: 0.7871 (mp10) cc_final: 0.7662 (mp10) REVERT: T 69 THR cc_start: 0.8370 (p) cc_final: 0.8161 (t) REVERT: T 79 GLN cc_start: 0.8429 (mp10) cc_final: 0.8059 (mp10) REVERT: S 73 ASN cc_start: 0.9255 (OUTLIER) cc_final: 0.8948 (t0) outliers start: 53 outliers final: 31 residues processed: 273 average time/residue: 0.1339 time to fit residues: 50.9543 Evaluate side-chains 266 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 232 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain O residue 19 ARG Chi-restraints excluded: chain O residue 57 LYS Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain Q residue 57 LYS Chi-restraints excluded: chain Q residue 105 GLN Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 73 ASN Chi-restraints excluded: chain S residue 87 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 75 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 55 optimal weight: 0.0010 chunk 149 optimal weight: 7.9990 chunk 163 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 167 optimal weight: 3.9990 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** 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 = 0.3128 r_free = 0.3128 target = 0.097197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.073485 restraints weight = 22033.058| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 1.87 r_work: 0.2728 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 14952 Z= 0.226 Angle : 0.558 4.400 20358 Z= 0.300 Chirality : 0.045 0.155 2184 Planarity : 0.004 0.042 2648 Dihedral : 4.893 42.390 2120 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.02 % Allowed : 14.86 % Favored : 81.12 % 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 are not related in a simple way. whole: -0.22 (0.19), residues: 1884 helix: None (None), residues: 0 sheet: 0.16 (0.18), residues: 848 loop : -0.34 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 16 TYR 0.018 0.002 TYR H 79 PHE 0.014 0.002 PHE S 29 TRP 0.013 0.002 TRP H 47 HIS 0.004 0.002 HIS O 35 Details of bonding type rmsd covalent geometry : bond 0.00543 (14936) covalent geometry : angle 0.55738 (20326) SS BOND : bond 0.00403 ( 16) SS BOND : angle 0.84730 ( 32) hydrogen bonds : bond 0.03150 ( 530) hydrogen bonds : angle 5.81078 ( 1314) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 231 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: H 13 GLN cc_start: 0.7887 (mp10) cc_final: 0.7646 (mp10) REVERT: H 101 ASP cc_start: 0.8453 (p0) cc_final: 0.8187 (p0) REVERT: B 67 SER cc_start: 0.7693 (OUTLIER) cc_final: 0.7331 (m) REVERT: B 69 THR cc_start: 0.8454 (p) cc_final: 0.8086 (t) REVERT: B 79 GLN cc_start: 0.8446 (mp10) cc_final: 0.8047 (mp10) REVERT: B 106 VAL cc_start: 0.5072 (m) cc_final: 0.4828 (m) REVERT: A 68 THR cc_start: 0.9275 (t) cc_final: 0.9019 (p) REVERT: A 73 ASN cc_start: 0.9275 (OUTLIER) cc_final: 0.8962 (t0) REVERT: C 3 GLN cc_start: 0.8718 (mt0) cc_final: 0.8223 (mm-40) REVERT: C 101 ASP cc_start: 0.8677 (p0) cc_final: 0.8318 (p0) REVERT: E 92 CYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8056 (p) REVERT: N 54 ARG cc_start: 0.8186 (mtp-110) cc_final: 0.7816 (mtp-110) REVERT: M 92 CYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8043 (p) REVERT: O 3 GLN cc_start: 0.8730 (mt0) cc_final: 0.8240 (mm-40) REVERT: O 19 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8126 (ttt-90) REVERT: Q 13 GLN cc_start: 0.7894 (mp10) cc_final: 0.7646 (mp10) REVERT: Q 101 ASP cc_start: 0.8438 (p0) cc_final: 0.8164 (p0) REVERT: T 69 THR cc_start: 0.8387 (p) cc_final: 0.8052 (t) REVERT: T 79 GLN cc_start: 0.8495 (mp10) cc_final: 0.8079 (mp10) REVERT: S 73 ASN cc_start: 0.9267 (OUTLIER) cc_final: 0.8964 (t0) outliers start: 63 outliers final: 50 residues processed: 268 average time/residue: 0.1304 time to fit residues: 49.4644 Evaluate side-chains 280 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 224 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain O residue 19 ARG Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 57 LYS Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 57 LYS Chi-restraints excluded: chain Q residue 105 GLN Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 73 ASN Chi-restraints excluded: chain S residue 87 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 18 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 21 optimal weight: 0.0980 chunk 3 optimal weight: 8.9990 chunk 134 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN A 6 GLN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.101737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.077962 restraints weight = 21361.522| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.80 r_work: 0.2827 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14952 Z= 0.101 Angle : 0.489 4.406 20358 Z= 0.261 Chirality : 0.042 0.129 2184 Planarity : 0.004 0.039 2648 Dihedral : 4.601 36.503 2120 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.25 % Allowed : 16.07 % Favored : 80.68 % 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 are not related in a simple way. whole: -0.00 (0.19), residues: 1884 helix: None (None), residues: 0 sheet: 0.36 (0.20), residues: 720 loop : -0.18 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 54 TYR 0.020 0.001 TYR M 52A PHE 0.011 0.001 PHE S 29 TRP 0.011 0.001 TRP O 47 HIS 0.003 0.001 HIS O 35 Details of bonding type rmsd covalent geometry : bond 0.00225 (14936) covalent geometry : angle 0.48895 (20326) SS BOND : bond 0.00215 ( 16) SS BOND : angle 0.44466 ( 32) hydrogen bonds : bond 0.02714 ( 530) hydrogen bonds : angle 5.38510 ( 1314) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 235 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 38 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8211 (tt0) REVERT: H 13 GLN cc_start: 0.7922 (mp10) cc_final: 0.7682 (mp10) REVERT: H 19 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8218 (ttp-170) REVERT: H 101 ASP cc_start: 0.8385 (p0) cc_final: 0.8152 (p0) REVERT: B 69 THR cc_start: 0.8428 (p) cc_final: 0.8059 (t) REVERT: B 79 GLN cc_start: 0.8462 (mp10) cc_final: 0.8042 (mp10) REVERT: B 106 VAL cc_start: 0.5021 (m) cc_final: 0.4785 (m) REVERT: A 68 THR cc_start: 0.9286 (t) cc_final: 0.9019 (p) REVERT: A 73 ASN cc_start: 0.9243 (OUTLIER) cc_final: 0.8894 (t0) REVERT: C 3 GLN cc_start: 0.8688 (mt0) cc_final: 0.8330 (mm-40) REVERT: C 101 ASP cc_start: 0.8669 (p0) cc_final: 0.8343 (p0) REVERT: E 92 CYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7920 (p) REVERT: N 54 ARG cc_start: 0.8187 (mtp-110) cc_final: 0.7864 (mtp-110) REVERT: M 92 CYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7918 (p) REVERT: O 3 GLN cc_start: 0.8694 (mt0) cc_final: 0.8336 (mm-40) REVERT: O 85 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8502 (mt-10) REVERT: O 101 ASP cc_start: 0.8631 (p0) cc_final: 0.8360 (p0) REVERT: R 38 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8197 (tt0) REVERT: Q 13 GLN cc_start: 0.7926 (mp10) cc_final: 0.7683 (mp10) REVERT: Q 101 ASP cc_start: 0.8369 (p0) cc_final: 0.8124 (p0) REVERT: T 69 THR cc_start: 0.8384 (p) cc_final: 0.8043 (t) REVERT: T 79 GLN cc_start: 0.8511 (mp10) cc_final: 0.8044 (mp10) REVERT: S 73 ASN cc_start: 0.9243 (OUTLIER) cc_final: 0.8896 (t0) outliers start: 51 outliers final: 32 residues processed: 270 average time/residue: 0.1304 time to fit residues: 49.5117 Evaluate side-chains 254 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 215 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain O residue 57 LYS Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 38 GLN Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 73 ASN Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 107 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 42 optimal weight: 0.0070 chunk 143 optimal weight: 0.0670 chunk 57 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 81 GLN S 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.114308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.093865 restraints weight = 19896.156| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.46 r_work: 0.2922 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14952 Z= 0.100 Angle : 0.480 4.441 20358 Z= 0.255 Chirality : 0.042 0.128 2184 Planarity : 0.004 0.037 2648 Dihedral : 4.385 28.903 2120 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.51 % Allowed : 16.58 % Favored : 79.91 % 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 are not related in a simple way. whole: 0.09 (0.20), residues: 1884 helix: None (None), residues: 0 sheet: 0.40 (0.20), residues: 720 loop : -0.09 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 16 TYR 0.016 0.001 TYR M 52A PHE 0.009 0.001 PHE S 29 TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS Q 35 Details of bonding type rmsd covalent geometry : bond 0.00226 (14936) covalent geometry : angle 0.48035 (20326) SS BOND : bond 0.00245 ( 16) SS BOND : angle 0.48564 ( 32) hydrogen bonds : bond 0.02596 ( 530) hydrogen bonds : angle 5.15619 ( 1314) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 233 time to evaluate : 0.345 Fit side-chains REVERT: L 38 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8366 (tt0) REVERT: H 13 GLN cc_start: 0.7887 (mp10) cc_final: 0.7679 (mp10) REVERT: H 101 ASP cc_start: 0.8253 (p0) cc_final: 0.8035 (p0) REVERT: B 67 SER cc_start: 0.7603 (OUTLIER) cc_final: 0.7271 (m) REVERT: B 69 THR cc_start: 0.8317 (p) cc_final: 0.8072 (t) REVERT: B 79 GLN cc_start: 0.8599 (mp10) cc_final: 0.8221 (mp10) REVERT: B 106 VAL cc_start: 0.5332 (m) cc_final: 0.5068 (m) REVERT: A 73 ASN cc_start: 0.9196 (OUTLIER) cc_final: 0.8915 (t0) REVERT: D 38 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.7496 (tt0) REVERT: C 85 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8421 (mt-10) REVERT: F 54 ARG cc_start: 0.8230 (mtp-110) cc_final: 0.7984 (mtp-110) REVERT: E 34 MET cc_start: 0.8889 (mmt) cc_final: 0.8684 (mmt) REVERT: N 54 ARG cc_start: 0.8082 (mtp-110) cc_final: 0.7842 (mtp-110) REVERT: M 34 MET cc_start: 0.8902 (mmt) cc_final: 0.8653 (mmt) REVERT: P 38 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.7496 (tt0) REVERT: O 101 ASP cc_start: 0.8574 (p0) cc_final: 0.8339 (p0) REVERT: R 38 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8336 (tt0) REVERT: Q 13 GLN cc_start: 0.7896 (mp10) cc_final: 0.7687 (mp10) REVERT: Q 101 ASP cc_start: 0.8244 (p0) cc_final: 0.8011 (p0) REVERT: T 69 THR cc_start: 0.8305 (p) cc_final: 0.8072 (t) REVERT: T 79 GLN cc_start: 0.8656 (mp10) cc_final: 0.8259 (mp10) REVERT: S 73 ASN cc_start: 0.9198 (OUTLIER) cc_final: 0.8903 (t0) outliers start: 55 outliers final: 37 residues processed: 270 average time/residue: 0.1325 time to fit residues: 50.0754 Evaluate side-chains 269 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 225 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 38 GLN Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain O residue 57 LYS Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 38 GLN Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain Q residue 57 LYS Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 105 GLN Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 73 ASN Chi-restraints excluded: chain S residue 107 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 84 optimal weight: 0.0980 chunk 98 optimal weight: 0.0670 chunk 149 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 32 optimal weight: 0.0270 chunk 178 optimal weight: 7.9990 chunk 146 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.115700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.095228 restraints weight = 19850.248| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.48 r_work: 0.3020 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14952 Z= 0.089 Angle : 0.478 4.426 20358 Z= 0.253 Chirality : 0.042 0.150 2184 Planarity : 0.004 0.040 2648 Dihedral : 4.288 23.985 2120 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.93 % Allowed : 16.90 % Favored : 80.17 % 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 are not related in a simple way. whole: 0.17 (0.20), residues: 1884 helix: None (None), residues: 0 sheet: 0.33 (0.19), residues: 760 loop : 0.05 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 19 TYR 0.015 0.001 TYR M 52A PHE 0.011 0.001 PHE S 29 TRP 0.008 0.001 TRP O 103 HIS 0.003 0.001 HIS Q 35 Details of bonding type rmsd covalent geometry : bond 0.00194 (14936) covalent geometry : angle 0.47701 (20326) SS BOND : bond 0.00187 ( 16) SS BOND : angle 0.85804 ( 32) hydrogen bonds : bond 0.02490 ( 530) hydrogen bonds : angle 4.98027 ( 1314) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 238 time to evaluate : 0.443 Fit side-chains REVERT: L 38 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8360 (tt0) REVERT: H 101 ASP cc_start: 0.8190 (p0) cc_final: 0.7976 (p0) REVERT: B 67 SER cc_start: 0.7566 (OUTLIER) cc_final: 0.7252 (m) REVERT: B 79 GLN cc_start: 0.8624 (mp10) cc_final: 0.8302 (mp10) REVERT: B 106 VAL cc_start: 0.5383 (m) cc_final: 0.5160 (m) REVERT: A 73 ASN cc_start: 0.9178 (OUTLIER) cc_final: 0.8913 (t0) REVERT: D 38 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.7528 (tt0) REVERT: F 54 ARG cc_start: 0.8063 (mtp-110) cc_final: 0.7793 (mtp-110) REVERT: F 69 THR cc_start: 0.8826 (p) cc_final: 0.8568 (t) REVERT: E 34 MET cc_start: 0.8884 (mmt) cc_final: 0.8674 (mmt) REVERT: N 54 ARG cc_start: 0.8062 (mtp-110) cc_final: 0.7847 (mtp-110) REVERT: N 69 THR cc_start: 0.8846 (p) cc_final: 0.8589 (t) REVERT: P 38 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.7520 (tt0) REVERT: O 101 ASP cc_start: 0.8504 (p0) cc_final: 0.8257 (p0) REVERT: R 38 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8321 (tt0) REVERT: Q 101 ASP cc_start: 0.8178 (p0) cc_final: 0.7963 (p0) REVERT: S 73 ASN cc_start: 0.9177 (OUTLIER) cc_final: 0.8909 (t0) outliers start: 46 outliers final: 35 residues processed: 268 average time/residue: 0.1294 time to fit residues: 49.0039 Evaluate side-chains 272 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 230 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain P residue 38 GLN Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain O residue 57 LYS Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 38 GLN Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 73 ASN Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 107 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 22 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 149 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 81 GLN ** 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 = 0.3217 r_free = 0.3217 target = 0.102088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.078296 restraints weight = 21088.498| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.84 r_work: 0.2897 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 14952 Z= 0.222 Angle : 0.552 4.499 20358 Z= 0.295 Chirality : 0.044 0.189 2184 Planarity : 0.004 0.049 2648 Dihedral : 4.591 22.739 2120 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.70 % Allowed : 16.65 % Favored : 79.66 % 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 are not related in a simple way. whole: 0.04 (0.20), residues: 1884 helix: None (None), residues: 0 sheet: 0.19 (0.19), residues: 768 loop : 0.00 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 94 TYR 0.016 0.002 TYR Q 79 PHE 0.012 0.002 PHE A 29 TRP 0.011 0.001 TRP C 103 HIS 0.004 0.002 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00532 (14936) covalent geometry : angle 0.54860 (20326) SS BOND : bond 0.00387 ( 16) SS BOND : angle 1.56597 ( 32) hydrogen bonds : bond 0.02834 ( 530) hydrogen bonds : angle 5.31285 ( 1314) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 230 time to evaluate : 0.548 Fit side-chains REVERT: L 38 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8438 (tt0) REVERT: H 101 ASP cc_start: 0.8483 (p0) cc_final: 0.8251 (p0) REVERT: B 67 SER cc_start: 0.7637 (OUTLIER) cc_final: 0.7265 (m) REVERT: B 79 GLN cc_start: 0.8542 (mp10) cc_final: 0.8141 (mp10) REVERT: A 68 THR cc_start: 0.9317 (t) cc_final: 0.9070 (p) REVERT: A 73 ASN cc_start: 0.9260 (OUTLIER) cc_final: 0.8935 (t0) REVERT: D 38 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.7712 (tt0) REVERT: C 3 GLN cc_start: 0.8724 (mt0) cc_final: 0.8481 (mm-40) REVERT: C 19 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8046 (ttt-90) REVERT: F 54 ARG cc_start: 0.8224 (mtp-110) cc_final: 0.7856 (mtp-110) REVERT: N 54 ARG cc_start: 0.8289 (mtp-110) cc_final: 0.7994 (mtp-110) REVERT: P 38 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.7723 (tt0) REVERT: O 3 GLN cc_start: 0.8724 (mt0) cc_final: 0.8492 (mm-40) REVERT: O 101 ASP cc_start: 0.8777 (p0) cc_final: 0.8507 (p0) REVERT: R 38 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8386 (tt0) REVERT: Q 101 ASP cc_start: 0.8470 (p0) cc_final: 0.8235 (p0) REVERT: S 73 ASN cc_start: 0.9246 (OUTLIER) cc_final: 0.8934 (t0) outliers start: 58 outliers final: 44 residues processed: 269 average time/residue: 0.1361 time to fit residues: 51.3738 Evaluate side-chains 275 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 223 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 38 GLN Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain O residue 57 LYS Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 38 GLN Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 105 GLN Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 73 ASN Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 107 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 127 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 178 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.113270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.093069 restraints weight = 20248.051| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.57 r_work: 0.2972 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14952 Z= 0.112 Angle : 0.512 6.844 20358 Z= 0.272 Chirality : 0.043 0.173 2184 Planarity : 0.004 0.044 2648 Dihedral : 4.458 23.026 2120 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.25 % Allowed : 17.28 % Favored : 79.46 % 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 are not related in a simple way. whole: 0.09 (0.20), residues: 1884 helix: None (None), residues: 0 sheet: 0.22 (0.19), residues: 768 loop : 0.05 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 19 TYR 0.015 0.001 TYR S 58 PHE 0.010 0.001 PHE S 29 TRP 0.010 0.001 TRP O 47 HIS 0.003 0.001 HIS O 35 Details of bonding type rmsd covalent geometry : bond 0.00256 (14936) covalent geometry : angle 0.51131 (20326) SS BOND : bond 0.00237 ( 16) SS BOND : angle 0.98973 ( 32) hydrogen bonds : bond 0.02565 ( 530) hydrogen bonds : angle 5.11936 ( 1314) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 229 time to evaluate : 0.547 Fit side-chains REVERT: L 38 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8120 (tt0) REVERT: H 101 ASP cc_start: 0.8214 (p0) cc_final: 0.7980 (p0) REVERT: B 67 SER cc_start: 0.7550 (OUTLIER) cc_final: 0.7236 (m) REVERT: B 79 GLN cc_start: 0.8606 (mp10) cc_final: 0.8146 (mp10) REVERT: A 73 ASN cc_start: 0.9232 (OUTLIER) cc_final: 0.8955 (t0) REVERT: D 38 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.7476 (tt0) REVERT: N 54 ARG cc_start: 0.8120 (mtp-110) cc_final: 0.7873 (mtp-110) REVERT: P 38 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.7471 (tt0) REVERT: R 38 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8093 (tt0) REVERT: Q 101 ASP cc_start: 0.8209 (p0) cc_final: 0.7974 (p0) REVERT: S 73 ASN cc_start: 0.9222 (OUTLIER) cc_final: 0.8942 (t0) outliers start: 51 outliers final: 39 residues processed: 263 average time/residue: 0.1436 time to fit residues: 52.3964 Evaluate side-chains 267 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 221 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 38 GLN Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain O residue 57 LYS Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 38 GLN Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 73 ASN Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 107 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 44 optimal weight: 2.9990 chunk 117 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 172 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 81 GLN ** 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 = 0.3178 r_free = 0.3178 target = 0.099704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.075850 restraints weight = 21382.337| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.82 r_work: 0.2881 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 14952 Z= 0.247 Angle : 0.571 5.023 20358 Z= 0.305 Chirality : 0.045 0.215 2184 Planarity : 0.004 0.051 2648 Dihedral : 4.721 23.304 2120 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.25 % Allowed : 17.41 % Favored : 79.34 % 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 are not related in a simple way. whole: -0.01 (0.20), residues: 1884 helix: None (None), residues: 0 sheet: 0.18 (0.19), residues: 768 loop : -0.05 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Q 19 TYR 0.019 0.002 TYR Q 79 PHE 0.013 0.002 PHE B 98 TRP 0.012 0.002 TRP O 103 HIS 0.006 0.002 HIS S 82A Details of bonding type rmsd covalent geometry : bond 0.00590 (14936) covalent geometry : angle 0.56884 (20326) SS BOND : bond 0.00401 ( 16) SS BOND : angle 1.45253 ( 32) hydrogen bonds : bond 0.02890 ( 530) hydrogen bonds : angle 5.37197 ( 1314) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 228 time to evaluate : 0.577 Fit side-chains REVERT: L 38 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8423 (tt0) REVERT: H 101 ASP cc_start: 0.8498 (p0) cc_final: 0.8251 (p0) REVERT: B 67 SER cc_start: 0.7661 (OUTLIER) cc_final: 0.7293 (m) REVERT: B 79 GLN cc_start: 0.8551 (mp10) cc_final: 0.8058 (mp10) REVERT: A 68 THR cc_start: 0.9302 (t) cc_final: 0.9089 (p) REVERT: A 73 ASN cc_start: 0.9286 (OUTLIER) cc_final: 0.8965 (t0) REVERT: D 38 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.7689 (tt0) REVERT: C 3 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8323 (mm-40) REVERT: C 61 ASP cc_start: 0.8515 (t70) cc_final: 0.8162 (t0) REVERT: N 54 ARG cc_start: 0.8202 (mtp-110) cc_final: 0.7895 (mtp-110) REVERT: P 38 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.7683 (tt0) REVERT: O 61 ASP cc_start: 0.8500 (t70) cc_final: 0.8145 (t0) REVERT: R 38 GLN cc_start: 0.9149 (OUTLIER) cc_final: 0.8395 (tt0) REVERT: Q 101 ASP cc_start: 0.8493 (p0) cc_final: 0.8248 (p0) REVERT: S 73 ASN cc_start: 0.9263 (OUTLIER) cc_final: 0.8952 (t0) REVERT: S 100 TYR cc_start: 0.8351 (t80) cc_final: 0.8007 (t80) outliers start: 51 outliers final: 42 residues processed: 261 average time/residue: 0.1312 time to fit residues: 47.9772 Evaluate side-chains 273 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 223 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 38 GLN Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain O residue 57 LYS Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 38 GLN Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 73 ASN Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 107 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 17 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 152 optimal weight: 0.9990 chunk 87 optimal weight: 0.0170 chunk 96 optimal weight: 8.9990 chunk 116 optimal weight: 0.6980 chunk 155 optimal weight: 0.6980 chunk 30 optimal weight: 0.0470 chunk 99 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.114161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.094387 restraints weight = 19918.245| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.50 r_work: 0.2986 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14952 Z= 0.094 Angle : 0.507 5.972 20358 Z= 0.270 Chirality : 0.042 0.187 2184 Planarity : 0.004 0.040 2648 Dihedral : 4.455 22.942 2120 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.93 % Allowed : 17.73 % Favored : 79.34 % 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 are not related in a simple way. whole: 0.12 (0.20), residues: 1884 helix: None (None), residues: 0 sheet: 0.41 (0.20), residues: 720 loop : -0.06 (0.19), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 19 TYR 0.024 0.001 TYR E 52A PHE 0.010 0.001 PHE S 29 TRP 0.012 0.001 TRP H 47 HIS 0.004 0.001 HIS O 35 Details of bonding type rmsd covalent geometry : bond 0.00201 (14936) covalent geometry : angle 0.50705 (20326) SS BOND : bond 0.00255 ( 16) SS BOND : angle 0.68798 ( 32) hydrogen bonds : bond 0.02521 ( 530) hydrogen bonds : angle 5.05931 ( 1314) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3159.46 seconds wall clock time: 55 minutes 2.92 seconds (3302.92 seconds total)