Starting phenix.real_space_refine on Thu Jun 12 21:23:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dyt_27781/06_2025/8dyt_27781.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dyt_27781/06_2025/8dyt_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dyt_27781/06_2025/8dyt_27781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dyt_27781/06_2025/8dyt_27781.map" model { file = "/net/cci-nas-00/data/ceres_data/8dyt_27781/06_2025/8dyt_27781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dyt_27781/06_2025/8dyt_27781.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.04, per 1000 atoms: 0.62 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: 3.52 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 2.77 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: 4.51 Time building geometry restraints manager: 4.21 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: 0.01 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: 0.560 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: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 36.110 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.900 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (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 TRP 0.022 0.002 TRP C 47 HIS 0.006 0.002 HIS M 82A PHE 0.023 0.002 PHE B 96 TYR 0.026 0.002 TYR E 52A ARG 0.006 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.21861 ( 530) hydrogen bonds : angle 9.74501 ( 1314) SS BOND : bond 0.00529 ( 16) SS BOND : angle 1.34848 ( 32) covalent geometry : bond 0.00701 (14936) covalent geometry : angle 0.67236 (20326) *********************** 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 : 1.577 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: 0.3168 time to fit residues: 101.5829 Evaluate side-chains 232 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 228 time to evaluate : 1.621 ------------------------------------------------------------------------------- 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 153 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 142 optimal weight: 0.7980 chunk 55 optimal weight: 0.2980 chunk 86 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3314 r_free = 0.3314 target = 0.108553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.089479 restraints weight = 20420.115| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.47 r_work: 0.2972 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14952 Z= 0.126 Angle : 0.536 4.305 20358 Z= 0.290 Chirality : 0.044 0.173 2184 Planarity : 0.004 0.058 2648 Dihedral : 5.109 52.764 2126 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.49 % Allowed : 14.16 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.19), residues: 1884 helix: None (None), residues: 0 sheet: 0.26 (0.19), residues: 776 loop : -0.56 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 47 HIS 0.004 0.002 HIS C 35 PHE 0.013 0.002 PHE S 29 TYR 0.018 0.001 TYR M 52A ARG 0.003 0.000 ARG Q 16 Details of bonding type rmsd hydrogen bonds : bond 0.03862 ( 530) hydrogen bonds : angle 6.58194 ( 1314) SS BOND : bond 0.00254 ( 16) SS BOND : angle 0.79134 ( 32) covalent geometry : bond 0.00287 (14936) covalent geometry : angle 0.53551 (20326) *********************** 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 : 1.834 Fit side-chains REVERT: B 69 THR cc_start: 0.8280 (p) cc_final: 0.8016 (t) REVERT: B 79 GLN cc_start: 0.8558 (mp10) cc_final: 0.8306 (mp10) REVERT: B 106 VAL cc_start: 0.5359 (m) cc_final: 0.5099 (m) REVERT: A 53 ASP cc_start: 0.8762 (p0) cc_final: 0.8554 (p0) REVERT: A 68 THR cc_start: 0.9388 (t) cc_final: 0.9180 (p) REVERT: A 73 ASN cc_start: 0.9240 (OUTLIER) cc_final: 0.8981 (t0) REVERT: C 3 GLN cc_start: 0.8621 (mt0) cc_final: 0.8378 (mm-40) REVERT: O 3 GLN cc_start: 0.8623 (mt0) cc_final: 0.8381 (mm-40) REVERT: O 73 ASN cc_start: 0.8994 (t0) cc_final: 0.8721 (m-40) REVERT: T 79 GLN cc_start: 0.8614 (mp10) cc_final: 0.8333 (mp10) REVERT: S 73 ASN cc_start: 0.9232 (OUTLIER) cc_final: 0.8987 (t0) outliers start: 39 outliers final: 16 residues processed: 272 average time/residue: 0.3073 time to fit residues: 118.4374 Evaluate side-chains 253 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 235 time to evaluate : 1.664 ------------------------------------------------------------------------------- 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 76 optimal weight: 0.5980 chunk 151 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 83 optimal weight: 0.5980 chunk 163 optimal weight: 8.9990 chunk 154 optimal weight: 2.9990 chunk 72 optimal weight: 0.1980 chunk 67 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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** T 17 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 = 0.3172 r_free = 0.3172 target = 0.099943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.075893 restraints weight = 21415.558| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 1.81 r_work: 0.2771 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 14952 Z= 0.150 Angle : 0.525 4.313 20358 Z= 0.282 Chirality : 0.044 0.137 2184 Planarity : 0.004 0.049 2648 Dihedral : 4.807 47.876 2120 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.38 % Allowed : 14.22 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.19), residues: 1884 helix: None (None), residues: 0 sheet: 0.24 (0.18), residues: 800 loop : -0.44 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 47 HIS 0.004 0.001 HIS C 35 PHE 0.012 0.002 PHE S 29 TYR 0.014 0.001 TYR A 79 ARG 0.004 0.000 ARG H 16 Details of bonding type rmsd hydrogen bonds : bond 0.03263 ( 530) hydrogen bonds : angle 5.95211 ( 1314) SS BOND : bond 0.00293 ( 16) SS BOND : angle 0.73071 ( 32) covalent geometry : bond 0.00353 (14936) covalent geometry : angle 0.52503 (20326) *********************** 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 295 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 242 time to evaluate : 1.689 Fit side-chains REVERT: B 67 SER cc_start: 0.7554 (OUTLIER) cc_final: 0.7233 (m) REVERT: B 69 THR cc_start: 0.8436 (p) cc_final: 0.8067 (t) REVERT: B 79 GLN cc_start: 0.8421 (mp10) cc_final: 0.8071 (mp10) REVERT: A 68 THR cc_start: 0.9281 (t) cc_final: 0.9047 (p) REVERT: A 73 ASN cc_start: 0.9282 (OUTLIER) cc_final: 0.8969 (t0) REVERT: C 3 GLN cc_start: 0.8667 (mt0) cc_final: 0.8272 (mm-40) REVERT: C 73 ASN cc_start: 0.9075 (t0) cc_final: 0.8853 (m-40) REVERT: N 54 ARG cc_start: 0.8036 (mtp-110) cc_final: 0.7778 (mtp-110) REVERT: O 3 GLN cc_start: 0.8683 (mt0) cc_final: 0.8301 (mm-40) REVERT: O 19 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8035 (ttt-90) REVERT: O 73 ASN cc_start: 0.9065 (m-40) cc_final: 0.8865 (m-40) REVERT: O 102 TYR cc_start: 0.9015 (m-80) cc_final: 0.8773 (m-10) REVERT: Q 13 GLN cc_start: 0.7861 (mp10) cc_final: 0.7656 (mp10) REVERT: T 17 GLN cc_start: 0.8272 (pt0) cc_final: 0.8040 (pt0) REVERT: T 79 GLN cc_start: 0.8446 (mp10) cc_final: 0.8071 (mp10) REVERT: S 73 ASN cc_start: 0.9267 (OUTLIER) cc_final: 0.8953 (t0) outliers start: 53 outliers final: 34 residues processed: 270 average time/residue: 0.3274 time to fit residues: 124.1253 Evaluate side-chains 270 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 232 time to evaluate : 1.716 ------------------------------------------------------------------------------- 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 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 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 87 THR 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 20 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 5 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 176 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 11 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.095468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.071207 restraints weight = 21842.315| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 1.86 r_work: 0.2674 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.045 14952 Z= 0.322 Angle : 0.624 4.414 20358 Z= 0.337 Chirality : 0.047 0.181 2184 Planarity : 0.005 0.050 2648 Dihedral : 5.164 43.539 2120 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.78 % Allowed : 14.48 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.19), residues: 1884 helix: None (None), residues: 0 sheet: 0.19 (0.18), residues: 824 loop : -0.52 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 47 HIS 0.005 0.002 HIS C 35 PHE 0.016 0.003 PHE B 98 TYR 0.021 0.002 TYR H 79 ARG 0.004 0.001 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.03454 ( 530) hydrogen bonds : angle 6.02627 ( 1314) SS BOND : bond 0.00523 ( 16) SS BOND : angle 0.98140 ( 32) covalent geometry : bond 0.00780 (14936) covalent geometry : angle 0.62340 (20326) *********************** 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 308 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 233 time to evaluate : 1.453 Fit side-chains REVERT: L 38 GLN cc_start: 0.9202 (OUTLIER) cc_final: 0.8487 (tt0) REVERT: H 101 ASP cc_start: 0.8496 (p0) cc_final: 0.8209 (p0) REVERT: B 67 SER cc_start: 0.7709 (OUTLIER) cc_final: 0.7366 (m) REVERT: B 69 THR cc_start: 0.8475 (p) cc_final: 0.8092 (t) REVERT: B 79 GLN cc_start: 0.8419 (mp10) cc_final: 0.7973 (mp10) REVERT: B 106 VAL cc_start: 0.5076 (m) cc_final: 0.4850 (m) REVERT: A 52 TYR cc_start: 0.9156 (p90) cc_final: 0.8866 (p90) REVERT: A 68 THR cc_start: 0.9276 (t) cc_final: 0.9020 (p) REVERT: A 73 ASN cc_start: 0.9317 (OUTLIER) cc_final: 0.8989 (t0) REVERT: C 3 GLN cc_start: 0.8746 (mt0) cc_final: 0.8229 (mm-40) REVERT: C 85 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8418 (mt-10) REVERT: C 101 ASP cc_start: 0.8726 (p0) cc_final: 0.8298 (p0) REVERT: F 54 ARG cc_start: 0.8215 (mtp-110) cc_final: 0.7929 (mtp-110) REVERT: N 54 ARG cc_start: 0.8110 (mtp-110) cc_final: 0.7761 (mtp-110) REVERT: O 19 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8181 (ttt-90) REVERT: O 85 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8430 (mt-10) REVERT: O 101 ASP cc_start: 0.8791 (p0) cc_final: 0.8436 (p0) REVERT: R 38 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.8458 (tt0) REVERT: Q 13 GLN cc_start: 0.7886 (mp10) cc_final: 0.7642 (mp10) REVERT: Q 101 ASP cc_start: 0.8492 (p0) cc_final: 0.8211 (p0) REVERT: T 79 GLN cc_start: 0.8489 (mp10) cc_final: 0.8035 (mp10) REVERT: S 73 ASN cc_start: 0.9311 (OUTLIER) cc_final: 0.8983 (t0) outliers start: 75 outliers final: 59 residues processed: 281 average time/residue: 0.2815 time to fit residues: 112.9408 Evaluate side-chains 289 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 224 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 11 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 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 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 19 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 A residue 107 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain C residue 24 THR 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 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 20 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 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 20 THR Chi-restraints excluded: chain R residue 38 GLN 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 Chi-restraints excluded: chain S residue 107 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 147 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 chunk 74 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 174 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 81 GLN T 51 ASN S 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.099578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.075555 restraints weight = 21482.984| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 1.83 r_work: 0.2780 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14952 Z= 0.107 Angle : 0.509 4.716 20358 Z= 0.274 Chirality : 0.043 0.150 2184 Planarity : 0.004 0.064 2648 Dihedral : 4.778 38.966 2120 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.93 % Allowed : 17.03 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.19), residues: 1884 helix: None (None), residues: 0 sheet: 0.21 (0.19), residues: 800 loop : -0.39 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 47 HIS 0.003 0.001 HIS O 35 PHE 0.012 0.001 PHE S 29 TYR 0.021 0.001 TYR M 52A ARG 0.003 0.000 ARG H 16 Details of bonding type rmsd hydrogen bonds : bond 0.02819 ( 530) hydrogen bonds : angle 5.57892 ( 1314) SS BOND : bond 0.00237 ( 16) SS BOND : angle 0.52143 ( 32) covalent geometry : bond 0.00240 (14936) covalent geometry : angle 0.50936 (20326) *********************** 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 279 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 233 time to evaluate : 1.457 Fit side-chains REVERT: H 101 ASP cc_start: 0.8429 (p0) cc_final: 0.8151 (p0) REVERT: B 69 THR cc_start: 0.8436 (p) cc_final: 0.8062 (t) REVERT: B 79 GLN cc_start: 0.8440 (mp10) cc_final: 0.7982 (mp10) REVERT: B 106 VAL cc_start: 0.5104 (m) cc_final: 0.4850 (m) REVERT: A 68 THR cc_start: 0.9235 (t) cc_final: 0.9008 (p) REVERT: A 73 ASN cc_start: 0.9281 (OUTLIER) cc_final: 0.8929 (t0) REVERT: D 38 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.7445 (tt0) REVERT: C 3 GLN cc_start: 0.8701 (mt0) cc_final: 0.8220 (mm-40) REVERT: C 101 ASP cc_start: 0.8702 (p0) cc_final: 0.8374 (p0) REVERT: F 54 ARG cc_start: 0.8252 (mtp-110) cc_final: 0.7893 (mtp-110) REVERT: P 38 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.7420 (tt0) REVERT: O 3 GLN cc_start: 0.8679 (mt0) cc_final: 0.8308 (mm-40) REVERT: O 85 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8505 (mt-10) REVERT: O 102 TYR cc_start: 0.9023 (m-80) cc_final: 0.8749 (m-80) REVERT: Q 13 GLN cc_start: 0.7931 (mp10) cc_final: 0.7682 (mp10) REVERT: Q 19 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8346 (ttp-170) REVERT: Q 101 ASP cc_start: 0.8416 (p0) cc_final: 0.8137 (p0) REVERT: T 79 GLN cc_start: 0.8498 (mp10) cc_final: 0.8018 (mp10) REVERT: S 73 ASN cc_start: 0.9265 (OUTLIER) cc_final: 0.8913 (t0) outliers start: 46 outliers final: 31 residues processed: 264 average time/residue: 0.3016 time to fit residues: 111.0464 Evaluate side-chains 258 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 222 time to evaluate : 1.484 ------------------------------------------------------------------------------- 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 87 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 71 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 38 GLN 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 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 38 GLN 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 95 SER Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain Q residue 19 ARG 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 0 optimal weight: 10.0000 chunk 181 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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** S 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.096177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.073112 restraints weight = 21951.591| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 1.83 r_work: 0.2647 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2519 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.042 14952 Z= 0.312 Angle : 0.607 4.468 20358 Z= 0.327 Chirality : 0.046 0.192 2184 Planarity : 0.005 0.050 2648 Dihedral : 5.069 30.794 2120 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.91 % Allowed : 15.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.19), residues: 1884 helix: None (None), residues: 0 sheet: -0.02 (0.18), residues: 848 loop : -0.38 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Q 47 HIS 0.006 0.002 HIS S 82A PHE 0.014 0.002 PHE B 98 TYR 0.020 0.002 TYR Q 79 ARG 0.012 0.001 ARG N 54 Details of bonding type rmsd hydrogen bonds : bond 0.03235 ( 530) hydrogen bonds : angle 5.81171 ( 1314) SS BOND : bond 0.00500 ( 16) SS BOND : angle 1.19475 ( 32) covalent geometry : bond 0.00753 (14936) covalent geometry : angle 0.60584 (20326) *********************** 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 306 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 229 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 38 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.8447 (tt0) REVERT: H 101 ASP cc_start: 0.8460 (p0) cc_final: 0.8202 (p0) REVERT: B 67 SER cc_start: 0.7706 (OUTLIER) cc_final: 0.7348 (m) REVERT: B 69 THR cc_start: 0.8526 (p) cc_final: 0.8148 (t) REVERT: B 106 VAL cc_start: 0.5150 (m) cc_final: 0.4932 (m) REVERT: A 68 THR cc_start: 0.9275 (t) cc_final: 0.8994 (p) REVERT: A 73 ASN cc_start: 0.9318 (OUTLIER) cc_final: 0.9004 (t0) REVERT: D 38 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.7643 (tt0) REVERT: C 19 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8099 (ttt-90) REVERT: C 61 ASP cc_start: 0.8597 (t70) cc_final: 0.8247 (t0) REVERT: C 101 ASP cc_start: 0.8741 (p0) cc_final: 0.8507 (p0) REVERT: F 54 ARG cc_start: 0.8316 (mtp-110) cc_final: 0.7891 (mtp-110) REVERT: E 92 CYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8110 (p) REVERT: M 92 CYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8110 (p) REVERT: P 38 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.7634 (tt0) REVERT: O 19 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8210 (ttt-90) REVERT: O 61 ASP cc_start: 0.8585 (t70) cc_final: 0.8240 (t0) REVERT: R 38 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8418 (tt0) REVERT: Q 13 GLN cc_start: 0.7936 (mp10) cc_final: 0.7691 (mp10) REVERT: Q 101 ASP cc_start: 0.8469 (p0) cc_final: 0.8209 (p0) REVERT: S 73 ASN cc_start: 0.9311 (OUTLIER) cc_final: 0.8976 (t0) outliers start: 77 outliers final: 57 residues processed: 283 average time/residue: 0.3072 time to fit residues: 121.4250 Evaluate side-chains 290 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 222 time to evaluate : 1.691 ------------------------------------------------------------------------------- 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 24 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 H residue 107 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 66 LYS 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 24 THR Chi-restraints excluded: chain C residue 38 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 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 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 38 GLN 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 38 ARG 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 48 ILE Chi-restraints excluded: chain R residue 95 SER 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 87 THR 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 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 112 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 78 optimal weight: 8.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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** S 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.098912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.076232 restraints weight = 21479.251| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.78 r_work: 0.2828 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14952 Z= 0.143 Angle : 0.522 5.084 20358 Z= 0.279 Chirality : 0.043 0.162 2184 Planarity : 0.004 0.044 2648 Dihedral : 4.822 25.870 2120 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.08 % Allowed : 16.33 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.19), residues: 1884 helix: None (None), residues: 0 sheet: 0.15 (0.19), residues: 800 loop : -0.39 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Q 47 HIS 0.004 0.001 HIS O 35 PHE 0.012 0.002 PHE A 29 TYR 0.013 0.001 TYR C 52A ARG 0.007 0.000 ARG N 54 Details of bonding type rmsd hydrogen bonds : bond 0.02809 ( 530) hydrogen bonds : angle 5.52599 ( 1314) SS BOND : bond 0.00265 ( 16) SS BOND : angle 0.71596 ( 32) covalent geometry : bond 0.00335 (14936) covalent geometry : angle 0.52131 (20326) *********************** 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 296 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 232 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 101 ASP cc_start: 0.8466 (p0) cc_final: 0.8226 (p0) REVERT: B 38 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.6512 (tp40) REVERT: B 69 THR cc_start: 0.8504 (p) cc_final: 0.8141 (t) REVERT: B 106 VAL cc_start: 0.5290 (m) cc_final: 0.5067 (m) REVERT: A 68 THR cc_start: 0.9271 (t) cc_final: 0.9006 (p) REVERT: A 73 ASN cc_start: 0.9296 (OUTLIER) cc_final: 0.8973 (t0) REVERT: D 38 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.7489 (tt0) REVERT: C 61 ASP cc_start: 0.8516 (t70) cc_final: 0.8150 (t0) REVERT: F 54 ARG cc_start: 0.8314 (mtp-110) cc_final: 0.7870 (mtp-110) REVERT: E 92 CYS cc_start: 0.8304 (OUTLIER) cc_final: 0.8007 (p) REVERT: M 87 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8560 (t) REVERT: M 92 CYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7991 (p) REVERT: P 38 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.7483 (tt0) REVERT: O 19 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8197 (ttt-90) REVERT: O 61 ASP cc_start: 0.8527 (t70) cc_final: 0.8164 (t0) REVERT: O 81 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.7753 (tp-100) REVERT: Q 13 GLN cc_start: 0.7922 (mp10) cc_final: 0.7682 (mp10) REVERT: Q 101 ASP cc_start: 0.8466 (p0) cc_final: 0.8219 (p0) REVERT: T 38 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.6536 (tp40) REVERT: S 73 ASN cc_start: 0.9293 (OUTLIER) cc_final: 0.8935 (t0) outliers start: 64 outliers final: 49 residues processed: 277 average time/residue: 0.3864 time to fit residues: 149.1962 Evaluate side-chains 277 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 217 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 95 SER 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 107 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 71 VAL 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 38 GLN Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain C residue 38 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 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 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 67 SER Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 92 CYS 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 19 ARG Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain O residue 57 LYS Chi-restraints excluded: chain O residue 81 GLN 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 95 SER 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 107 VAL Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 38 GLN 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 82 MET Chi-restraints excluded: chain S residue 87 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 66 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 chunk 153 optimal weight: 4.9990 chunk 11 optimal weight: 0.0770 chunk 86 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 30 optimal weight: 0.0870 chunk 159 optimal weight: 3.9990 overall best weight: 1.1720 ------------------------------------------------------------------------------- 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 = 0.3184 r_free = 0.3184 target = 0.100316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.076634 restraints weight = 21290.711| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.81 r_work: 0.2854 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14952 Z= 0.130 Angle : 0.514 5.192 20358 Z= 0.275 Chirality : 0.043 0.182 2184 Planarity : 0.004 0.038 2648 Dihedral : 4.663 23.768 2120 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.15 % Allowed : 16.77 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.19), residues: 1884 helix: None (None), residues: 0 sheet: 0.21 (0.19), residues: 800 loop : -0.33 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Q 47 HIS 0.004 0.001 HIS C 35 PHE 0.012 0.001 PHE S 29 TYR 0.016 0.001 TYR S 58 ARG 0.004 0.000 ARG N 54 Details of bonding type rmsd hydrogen bonds : bond 0.02690 ( 530) hydrogen bonds : angle 5.35149 ( 1314) SS BOND : bond 0.00255 ( 16) SS BOND : angle 0.67115 ( 32) covalent geometry : bond 0.00304 (14936) covalent geometry : angle 0.51336 (20326) *********************** 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 300 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 235 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 101 ASP cc_start: 0.8427 (p0) cc_final: 0.8215 (p0) REVERT: B 38 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.6519 (tp40) REVERT: B 69 THR cc_start: 0.8456 (p) cc_final: 0.8146 (t) REVERT: B 106 VAL cc_start: 0.5348 (m) cc_final: 0.5102 (m) REVERT: A 68 THR cc_start: 0.9292 (t) cc_final: 0.9040 (p) REVERT: A 73 ASN cc_start: 0.9292 (OUTLIER) cc_final: 0.8966 (t0) REVERT: D 38 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.7510 (tt0) REVERT: C 3 GLN cc_start: 0.8701 (mt0) cc_final: 0.8479 (mm-40) REVERT: C 19 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8663 (ttp-170) REVERT: C 61 ASP cc_start: 0.8471 (t70) cc_final: 0.8122 (t0) REVERT: F 54 ARG cc_start: 0.8306 (mtp-110) cc_final: 0.7876 (mtp-110) REVERT: E 83 ARG cc_start: 0.8801 (mtm-85) cc_final: 0.8488 (ttp-110) REVERT: E 92 CYS cc_start: 0.8287 (OUTLIER) cc_final: 0.8050 (p) REVERT: M 83 ARG cc_start: 0.8816 (mtm-85) cc_final: 0.8281 (ttp-110) REVERT: M 92 CYS cc_start: 0.8273 (OUTLIER) cc_final: 0.8044 (p) REVERT: P 38 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.7486 (tt0) REVERT: O 3 GLN cc_start: 0.8704 (mt0) cc_final: 0.8477 (mm-40) REVERT: O 19 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8172 (ttt-90) REVERT: O 61 ASP cc_start: 0.8476 (t70) cc_final: 0.8119 (t0) REVERT: O 81 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.7741 (tp-100) REVERT: Q 13 GLN cc_start: 0.7928 (mp10) cc_final: 0.7695 (mp10) REVERT: Q 101 ASP cc_start: 0.8416 (p0) cc_final: 0.8177 (p0) REVERT: T 38 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.6513 (tp40) REVERT: S 73 ASN cc_start: 0.9281 (OUTLIER) cc_final: 0.8956 (t0) outliers start: 65 outliers final: 47 residues processed: 281 average time/residue: 0.3344 time to fit residues: 130.7461 Evaluate side-chains 280 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 222 time to evaluate : 1.608 ------------------------------------------------------------------------------- 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 87 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 66 LYS 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 38 GLN Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 38 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 27 ASN Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 67 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 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 92 CYS 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 19 ARG Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain O residue 57 LYS Chi-restraints excluded: chain O residue 81 GLN 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 20 THR Chi-restraints excluded: chain R residue 95 SER 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 107 VAL Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 38 GLN 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 82 MET 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 35 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3200 r_free = 0.3200 target = 0.101298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.077755 restraints weight = 21120.925| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.80 r_work: 0.2928 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1837 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= 0.126 Angle : 0.515 5.075 20358 Z= 0.274 Chirality : 0.043 0.188 2184 Planarity : 0.004 0.037 2648 Dihedral : 4.589 23.453 2120 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.34 % Allowed : 16.39 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.19), residues: 1884 helix: None (None), residues: 0 sheet: 0.22 (0.19), residues: 800 loop : -0.28 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Q 47 HIS 0.004 0.001 HIS O 35 PHE 0.012 0.001 PHE S 29 TYR 0.016 0.001 TYR S 58 ARG 0.004 0.000 ARG N 54 Details of bonding type rmsd hydrogen bonds : bond 0.02639 ( 530) hydrogen bonds : angle 5.26525 ( 1314) SS BOND : bond 0.00256 ( 16) SS BOND : angle 0.62035 ( 32) covalent geometry : bond 0.00295 (14936) covalent geometry : angle 0.51461 (20326) *********************** 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 297 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 229 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 38 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8191 (tt0) REVERT: H 38 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8554 (ttp-170) REVERT: H 101 ASP cc_start: 0.8429 (p0) cc_final: 0.8199 (p0) REVERT: B 38 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.6512 (tp40) REVERT: B 69 THR cc_start: 0.8456 (p) cc_final: 0.8154 (t) REVERT: B 106 VAL cc_start: 0.5270 (OUTLIER) cc_final: 0.5025 (m) REVERT: A 73 ASN cc_start: 0.9287 (OUTLIER) cc_final: 0.8927 (t0) REVERT: D 38 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.7548 (tt0) REVERT: C 3 GLN cc_start: 0.8678 (mt0) cc_final: 0.8441 (mm-40) REVERT: C 19 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8672 (ttp-170) REVERT: F 54 ARG cc_start: 0.8178 (mtp-110) cc_final: 0.7698 (mtp-110) REVERT: E 83 ARG cc_start: 0.8719 (mtm-85) cc_final: 0.8487 (ttp-110) REVERT: E 92 CYS cc_start: 0.8248 (OUTLIER) cc_final: 0.8032 (p) REVERT: M 83 ARG cc_start: 0.8825 (mtm-85) cc_final: 0.8527 (ttp-110) REVERT: M 92 CYS cc_start: 0.8260 (OUTLIER) cc_final: 0.8045 (p) REVERT: P 38 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.7524 (tt0) REVERT: O 3 GLN cc_start: 0.8687 (mt0) cc_final: 0.8458 (mm-40) REVERT: O 19 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8131 (ttt-90) REVERT: R 38 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8168 (tt0) REVERT: Q 13 GLN cc_start: 0.7905 (mp10) cc_final: 0.7665 (mp10) REVERT: Q 101 ASP cc_start: 0.8430 (p0) cc_final: 0.8204 (p0) REVERT: T 38 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.6513 (tp40) REVERT: S 73 ASN cc_start: 0.9288 (OUTLIER) cc_final: 0.8922 (t0) outliers start: 68 outliers final: 50 residues processed: 278 average time/residue: 0.3186 time to fit residues: 122.8252 Evaluate side-chains 286 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 222 time to evaluate : 1.667 ------------------------------------------------------------------------------- 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 38 GLN Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain H residue 38 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 B residue 38 GLN Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 106 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 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 19 ARG Chi-restraints excluded: chain C residue 38 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 27 ASN Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 67 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 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 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 19 ARG Chi-restraints excluded: chain O residue 38 ARG 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 20 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 57 LYS 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 T residue 38 GLN 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 82 MET 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 46 optimal weight: 9.9990 chunk 164 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 148 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 170 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 = 0.3236 r_free = 0.3236 target = 0.103284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.081815 restraints weight = 20983.381| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 1.70 r_work: 0.2656 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2537 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 14952 Z= 0.209 Angle : 0.548 4.459 20358 Z= 0.292 Chirality : 0.044 0.201 2184 Planarity : 0.004 0.035 2648 Dihedral : 4.744 23.930 2120 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.40 % Allowed : 16.39 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.20), residues: 1884 helix: None (None), residues: 0 sheet: 0.05 (0.18), residues: 848 loop : -0.21 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 47 HIS 0.004 0.001 HIS C 35 PHE 0.013 0.002 PHE A 29 TYR 0.018 0.002 TYR S 58 ARG 0.004 0.001 ARG Q 19 Details of bonding type rmsd hydrogen bonds : bond 0.02840 ( 530) hydrogen bonds : angle 5.42000 ( 1314) SS BOND : bond 0.00357 ( 16) SS BOND : angle 0.84339 ( 32) covalent geometry : bond 0.00503 (14936) covalent geometry : angle 0.54706 (20326) ********************** 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 293 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 224 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 38 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8307 (tt0) REVERT: H 38 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8592 (ttp-170) REVERT: H 101 ASP cc_start: 0.8438 (p0) cc_final: 0.8201 (p0) REVERT: B 38 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.6659 (tt0) REVERT: B 69 THR cc_start: 0.8511 (p) cc_final: 0.8174 (t) REVERT: B 106 VAL cc_start: 0.5196 (OUTLIER) cc_final: 0.4969 (m) REVERT: A 73 ASN cc_start: 0.9277 (OUTLIER) cc_final: 0.8933 (t0) REVERT: D 38 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.7505 (tt0) REVERT: C 3 GLN cc_start: 0.8727 (mt0) cc_final: 0.8464 (mm-40) REVERT: C 19 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8075 (ttt-90) REVERT: C 61 ASP cc_start: 0.8449 (t70) cc_final: 0.8073 (t0) REVERT: F 54 ARG cc_start: 0.8283 (mtp-110) cc_final: 0.7903 (mtp-110) REVERT: E 92 CYS cc_start: 0.8275 (OUTLIER) cc_final: 0.8005 (p) REVERT: M 92 CYS cc_start: 0.8292 (OUTLIER) cc_final: 0.8023 (p) REVERT: P 38 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.7521 (tt0) REVERT: O 3 GLN cc_start: 0.8761 (mt0) cc_final: 0.8484 (mm-40) REVERT: O 19 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8091 (ttt-90) REVERT: O 61 ASP cc_start: 0.8453 (t70) cc_final: 0.8073 (t0) REVERT: R 38 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.8288 (tt0) REVERT: Q 13 GLN cc_start: 0.7875 (mp10) cc_final: 0.7612 (mp10) REVERT: Q 101 ASP cc_start: 0.8443 (p0) cc_final: 0.8203 (p0) REVERT: T 38 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.6642 (tt0) REVERT: S 73 ASN cc_start: 0.9262 (OUTLIER) cc_final: 0.8927 (t0) outliers start: 69 outliers final: 53 residues processed: 271 average time/residue: 0.3227 time to fit residues: 120.1573 Evaluate side-chains 289 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 222 time to evaluate : 1.695 ------------------------------------------------------------------------------- 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 38 GLN Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain H residue 38 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 19 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 106 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 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 38 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 27 ASN Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 67 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 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 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 19 ARG Chi-restraints excluded: chain O residue 38 ARG 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 20 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 57 LYS 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 T residue 38 GLN 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 82 MET 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 57 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 161 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 174 optimal weight: 8.9990 chunk 76 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.102467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.078940 restraints weight = 21139.125| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.81 r_work: 0.2921 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14952 Z= 0.126 Angle : 0.516 4.982 20358 Z= 0.275 Chirality : 0.043 0.191 2184 Planarity : 0.004 0.039 2648 Dihedral : 4.616 23.746 2120 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.15 % Allowed : 16.84 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.19), residues: 1884 helix: None (None), residues: 0 sheet: 0.20 (0.19), residues: 800 loop : -0.30 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Q 47 HIS 0.004 0.001 HIS C 35 PHE 0.012 0.001 PHE A 29 TYR 0.024 0.001 TYR E 52A ARG 0.003 0.000 ARG N 54 Details of bonding type rmsd hydrogen bonds : bond 0.02637 ( 530) hydrogen bonds : angle 5.26238 ( 1314) SS BOND : bond 0.00247 ( 16) SS BOND : angle 0.58122 ( 32) covalent geometry : bond 0.00293 (14936) covalent geometry : angle 0.51601 (20326) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7281.19 seconds wall clock time: 128 minutes 42.04 seconds (7722.04 seconds total)