Starting phenix.real_space_refine on Tue Dec 31 00:10:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dyt_27781/12_2024/8dyt_27781.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dyt_27781/12_2024/8dyt_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_27781/12_2024/8dyt_27781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dyt_27781/12_2024/8dyt_27781.map" model { file = "/net/cci-nas-00/data/ceres_data/8dyt_27781/12_2024/8dyt_27781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dyt_27781/12_2024/8dyt_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 9.29, per 1000 atoms: 0.64 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: 3.56 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: 2.53 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: 4.75 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3569 1.33 - 1.45: 3330 1.45 - 1.56: 7964 1.56 - 1.68: 1 1.68 - 1.80: 72 Bond restraints: 14936 Sorted by residual: bond pdb=" CB CYS P 88 " pdb=" SG CYS P 88 " ideal model delta sigma weight residual 1.808 1.764 0.044 3.30e-02 9.18e+02 1.76e+00 bond pdb=" CG1 ILE T 27C" pdb=" CD1 ILE T 27C" ideal model delta sigma weight residual 1.513 1.462 0.051 3.90e-02 6.57e+02 1.73e+00 bond pdb=" CB CYS D 88 " pdb=" SG CYS D 88 " ideal model delta sigma weight residual 1.808 1.765 0.043 3.30e-02 9.18e+02 1.70e+00 bond pdb=" CG1 ILE B 27C" pdb=" CD1 ILE B 27C" ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.60e+00 bond pdb=" CB THR C 77 " pdb=" CG2 THR C 77 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.58e+00 ... (remaining 14931 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.86: 17520 0.86 - 1.72: 2147 1.72 - 2.57: 438 2.57 - 3.43: 173 3.43 - 4.29: 48 Bond angle restraints: 20326 Sorted by residual: angle pdb=" N ILE D 27C" pdb=" CA ILE D 27C" pdb=" C ILE D 27C" ideal model delta sigma weight residual 113.53 110.66 2.87 9.80e-01 1.04e+00 8.59e+00 angle pdb=" CA PRO I 2 " pdb=" N PRO I 2 " pdb=" CD PRO I 2 " ideal model delta sigma weight residual 112.00 108.29 3.71 1.40e+00 5.10e-01 7.02e+00 angle pdb=" N THR D 42 " pdb=" CA THR D 42 " pdb=" C THR D 42 " ideal model delta sigma weight residual 111.02 114.08 -3.06 1.25e+00 6.40e-01 5.99e+00 angle pdb=" C PRO L 59 " pdb=" N ASP L 60 " pdb=" CA ASP L 60 " ideal model delta sigma weight residual 120.60 124.46 -3.86 1.60e+00 3.91e-01 5.82e+00 angle pdb=" N THR P 42 " pdb=" CA THR P 42 " pdb=" C THR P 42 " ideal model delta sigma weight residual 111.02 114.01 -2.99 1.25e+00 6.40e-01 5.71e+00 ... (remaining 20321 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 7839 17.95 - 35.90: 639 35.90 - 53.84: 168 53.84 - 71.79: 36 71.79 - 89.74: 22 Dihedral angle restraints: 8704 sinusoidal: 3274 harmonic: 5430 Sorted by residual: dihedral pdb=" CB CYS T 23 " pdb=" SG CYS T 23 " pdb=" SG CYS T 88 " pdb=" CB CYS T 88 " ideal model delta sinusoidal sigma weight residual 93.00 136.26 -43.26 1 1.00e+01 1.00e-02 2.61e+01 dihedral pdb=" CB CYS B 23 " pdb=" SG CYS B 23 " pdb=" SG CYS B 88 " pdb=" CB CYS B 88 " ideal model delta sinusoidal sigma weight residual 93.00 136.23 -43.23 1 1.00e+01 1.00e-02 2.61e+01 dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 88 " pdb=" CB CYS F 88 " ideal model delta sinusoidal sigma weight residual 93.00 134.44 -41.44 1 1.00e+01 1.00e-02 2.40e+01 ... (remaining 8701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1242 0.033 - 0.065: 596 0.065 - 0.098: 213 0.098 - 0.131: 118 0.131 - 0.163: 15 Chirality restraints: 2184 Sorted by residual: chirality pdb=" CA PRO I 10 " pdb=" N PRO I 10 " pdb=" C PRO I 10 " pdb=" CB PRO I 10 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.67e-01 chirality pdb=" CB THR E 87 " pdb=" CA THR E 87 " pdb=" OG1 THR E 87 " pdb=" CG2 THR E 87 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.77e-01 chirality pdb=" CA VAL S 89 " pdb=" N VAL S 89 " pdb=" C VAL S 89 " pdb=" CB VAL S 89 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.88e-01 ... (remaining 2181 not shown) Planarity restraints: 2648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO F 7 " 0.053 5.00e-02 4.00e+02 8.00e-02 1.02e+01 pdb=" N PRO F 8 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO F 8 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO F 8 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO N 7 " -0.052 5.00e-02 4.00e+02 7.97e-02 1.02e+01 pdb=" N PRO N 8 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO N 8 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO N 8 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN I 1 " 0.046 5.00e-02 4.00e+02 6.84e-02 7.48e+00 pdb=" N PRO I 2 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO I 2 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO I 2 " 0.038 5.00e-02 4.00e+02 ... (remaining 2645 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 994 2.72 - 3.27: 13717 3.27 - 3.81: 23874 3.81 - 4.36: 30383 4.36 - 4.90: 54389 Nonbonded interactions: 123357 Sorted by model distance: nonbonded pdb=" ND2 ASN I 3 " pdb=" O TYR A 100C" model vdw 2.181 3.120 nonbonded pdb=" ND2 ASN J 15 " pdb=" OD1 ASN Q 97 " model vdw 2.217 3.120 nonbonded pdb=" ND2 ASN J 31 " pdb=" OD1 ASN M 97 " model vdw 2.235 3.120 nonbonded pdb=" NH2 ARG N 61 " pdb=" OD1 ASP N 82 " model vdw 2.244 3.120 nonbonded pdb=" NH2 ARG F 61 " pdb=" OD1 ASP F 82 " model vdw 2.260 3.120 ... (remaining 123352 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'H' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 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: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 36.150 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.320 ------------------------------------------------------------------------------- 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 14936 Z= 0.459 Angle : 0.672 4.289 20326 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 *********************** 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 : 1.754 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: 0.3372 time to fit residues: 107.0549 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 : 1.696 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 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 14936 Z= 0.189 Angle : 0.535 4.305 20326 Z= 0.290 Chirality : 0.044 0.173 2184 Planarity : 0.004 0.058 2648 Dihedral : 5.109 52.767 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 *********************** 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 286 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 247 time to evaluate : 1.579 Fit side-chains REVERT: B 69 THR cc_start: 0.8471 (p) cc_final: 0.8093 (t) REVERT: B 79 GLN cc_start: 0.8432 (mp10) cc_final: 0.8146 (mp10) REVERT: B 106 VAL cc_start: 0.4978 (m) cc_final: 0.4727 (m) REVERT: A 68 THR cc_start: 0.9305 (t) cc_final: 0.9050 (p) REVERT: A 73 ASN cc_start: 0.9260 (OUTLIER) cc_final: 0.8959 (t0) REVERT: C 3 GLN cc_start: 0.8512 (mt0) cc_final: 0.8148 (mm-40) REVERT: N 54 ARG cc_start: 0.8010 (mtp-110) cc_final: 0.7771 (mtp-110) REVERT: O 3 GLN cc_start: 0.8505 (mt0) cc_final: 0.8141 (mm-40) REVERT: O 73 ASN cc_start: 0.9178 (t0) cc_final: 0.8946 (m-40) REVERT: T 69 THR cc_start: 0.8366 (p) cc_final: 0.8062 (t) REVERT: T 79 GLN cc_start: 0.8480 (mp10) cc_final: 0.8161 (mp10) REVERT: S 73 ASN cc_start: 0.9250 (OUTLIER) cc_final: 0.8962 (t0) outliers start: 39 outliers final: 16 residues processed: 273 average time/residue: 0.3006 time to fit residues: 115.9644 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 : 1.804 ------------------------------------------------------------------------------- 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 91 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 165 optimal weight: 0.4980 chunk 178 optimal weight: 5.9990 chunk 147 optimal weight: 0.9980 chunk 164 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14936 Z= 0.259 Angle : 0.532 4.325 20326 Z= 0.286 Chirality : 0.044 0.158 2184 Planarity : 0.004 0.048 2648 Dihedral : 4.836 47.519 2120 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.51 % Allowed : 14.22 % Favored : 82.27 % 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: -0.27 (0.19), residues: 1884 helix: None (None), residues: 0 sheet: 0.24 (0.18), residues: 800 loop : -0.45 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.004 0.002 HIS O 35 PHE 0.012 0.002 PHE B 96 TYR 0.015 0.001 TYR A 79 ARG 0.004 0.000 ARG H 16 *********************** 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 298 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 243 time to evaluate : 1.718 Fit side-chains REVERT: H 13 GLN cc_start: 0.7786 (mp10) cc_final: 0.7581 (mp10) REVERT: H 101 ASP cc_start: 0.8660 (p0) cc_final: 0.8319 (p0) REVERT: B 67 SER cc_start: 0.7583 (OUTLIER) cc_final: 0.7264 (m) REVERT: B 69 THR cc_start: 0.8441 (p) cc_final: 0.8083 (t) REVERT: B 79 GLN cc_start: 0.8473 (mp10) cc_final: 0.8144 (mp10) REVERT: B 106 VAL cc_start: 0.4994 (OUTLIER) cc_final: 0.4723 (m) REVERT: A 68 THR cc_start: 0.9280 (t) cc_final: 0.9029 (p) REVERT: A 73 ASN cc_start: 0.9300 (OUTLIER) cc_final: 0.8992 (t0) REVERT: C 3 GLN cc_start: 0.8526 (mt0) cc_final: 0.8159 (mm-40) REVERT: C 73 ASN cc_start: 0.9181 (t0) cc_final: 0.8951 (m-40) REVERT: N 54 ARG cc_start: 0.8015 (mtp-110) cc_final: 0.7678 (mtp-110) REVERT: O 3 GLN cc_start: 0.8546 (mt0) cc_final: 0.8189 (mm-40) REVERT: O 19 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.8199 (ttt-90) REVERT: O 73 ASN cc_start: 0.9175 (m-40) cc_final: 0.8965 (m-40) REVERT: O 102 TYR cc_start: 0.9147 (m-80) cc_final: 0.8895 (m-10) REVERT: Q 13 GLN cc_start: 0.7795 (mp10) cc_final: 0.7582 (mp10) REVERT: T 17 GLN cc_start: 0.8271 (pt0) cc_final: 0.8065 (pt0) REVERT: T 79 GLN cc_start: 0.8470 (mp10) cc_final: 0.8092 (mp10) REVERT: S 73 ASN cc_start: 0.9285 (OUTLIER) cc_final: 0.8974 (t0) outliers start: 55 outliers final: 34 residues processed: 271 average time/residue: 0.3329 time to fit residues: 125.2709 Evaluate side-chains 275 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 236 time to evaluate : 1.815 ------------------------------------------------------------------------------- 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 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 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 163 optimal weight: 6.9990 chunk 124 optimal weight: 0.6980 chunk 85 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 166 optimal weight: 9.9990 chunk 175 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 157 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14936 Z= 0.273 Angle : 0.530 4.386 20326 Z= 0.285 Chirality : 0.044 0.161 2184 Planarity : 0.004 0.042 2648 Dihedral : 4.807 42.514 2120 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.95 % Allowed : 14.60 % Favored : 81.44 % 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: 0.19 (0.18), residues: 848 loop : -0.33 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.004 0.002 HIS C 35 PHE 0.013 0.002 PHE S 29 TYR 0.019 0.001 TYR E 52A ARG 0.003 0.000 ARG F 54 *********************** 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 297 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 235 time to evaluate : 1.652 Fit side-chains REVERT: H 13 GLN cc_start: 0.7787 (mp10) cc_final: 0.7541 (mp10) REVERT: B 17 GLN cc_start: 0.8154 (pt0) cc_final: 0.7832 (pt0) REVERT: B 67 SER cc_start: 0.7715 (OUTLIER) cc_final: 0.7373 (m) REVERT: B 69 THR cc_start: 0.8441 (p) cc_final: 0.8085 (t) REVERT: B 79 GLN cc_start: 0.8483 (mp10) cc_final: 0.8110 (mp10) REVERT: B 106 VAL cc_start: 0.5061 (m) cc_final: 0.4796 (m) REVERT: A 68 THR cc_start: 0.9263 (t) cc_final: 0.8987 (p) REVERT: A 73 ASN cc_start: 0.9306 (OUTLIER) cc_final: 0.8987 (t0) REVERT: C 3 GLN cc_start: 0.8542 (mt0) cc_final: 0.8177 (mm-40) REVERT: C 101 ASP cc_start: 0.8940 (p0) cc_final: 0.8534 (p0) REVERT: E 92 CYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8014 (p) REVERT: N 54 ARG cc_start: 0.8067 (mtp-110) cc_final: 0.7680 (mtp-110) REVERT: O 3 GLN cc_start: 0.8549 (mt0) cc_final: 0.8182 (mm-40) REVERT: O 19 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.8220 (ttt-90) REVERT: O 73 ASN cc_start: 0.9151 (m-40) cc_final: 0.8930 (m-40) REVERT: O 101 ASP cc_start: 0.8992 (p0) cc_final: 0.8722 (p0) REVERT: O 102 TYR cc_start: 0.9069 (m-80) cc_final: 0.8858 (m-80) REVERT: Q 13 GLN cc_start: 0.7796 (mp10) cc_final: 0.7544 (mp10) REVERT: Q 101 ASP cc_start: 0.8742 (p0) cc_final: 0.8479 (p0) REVERT: T 79 GLN cc_start: 0.8513 (mp10) cc_final: 0.8120 (mp10) REVERT: S 73 ASN cc_start: 0.9281 (OUTLIER) cc_final: 0.8962 (t0) outliers start: 62 outliers final: 48 residues processed: 272 average time/residue: 0.3168 time to fit residues: 121.4878 Evaluate side-chains 282 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 229 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain O residue 19 ARG Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 57 LYS Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 57 LYS Chi-restraints excluded: chain Q residue 107 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 146 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 150 optimal weight: 0.0070 chunk 121 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 44 optimal weight: 0.0030 overall best weight: 0.7410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14936 Z= 0.148 Angle : 0.487 4.392 20326 Z= 0.259 Chirality : 0.042 0.128 2184 Planarity : 0.004 0.039 2648 Dihedral : 4.543 36.105 2120 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.25 % Allowed : 15.82 % Favored : 80.93 % 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: 0.03 (0.19), residues: 1884 helix: None (None), residues: 0 sheet: 0.40 (0.20), residues: 720 loop : -0.16 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS C 35 PHE 0.012 0.001 PHE S 29 TYR 0.016 0.001 TYR E 52A ARG 0.004 0.000 ARG F 54 *********************** 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 289 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 238 time to evaluate : 1.788 Fit side-chains revert: symmetry clash REVERT: L 38 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8335 (tt0) REVERT: H 13 GLN cc_start: 0.7838 (mp10) cc_final: 0.7563 (mp10) REVERT: H 19 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8480 (ttp-170) REVERT: H 101 ASP cc_start: 0.8732 (p0) cc_final: 0.8474 (p0) REVERT: B 17 GLN cc_start: 0.8099 (pt0) cc_final: 0.7782 (pt0) REVERT: B 67 SER cc_start: 0.7667 (OUTLIER) cc_final: 0.7319 (m) REVERT: B 69 THR cc_start: 0.8431 (p) cc_final: 0.8086 (t) REVERT: B 79 GLN cc_start: 0.8521 (mp10) cc_final: 0.8153 (mp10) REVERT: B 106 VAL cc_start: 0.5127 (OUTLIER) cc_final: 0.4869 (m) REVERT: A 73 ASN cc_start: 0.9235 (OUTLIER) cc_final: 0.8937 (t0) REVERT: C 3 GLN cc_start: 0.8521 (mt0) cc_final: 0.8218 (mm-40) REVERT: C 101 ASP cc_start: 0.8941 (p0) cc_final: 0.8621 (p0) REVERT: E 92 CYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7940 (p) REVERT: N 54 ARG cc_start: 0.8079 (mtp-110) cc_final: 0.7729 (mtp-110) REVERT: M 92 CYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7892 (p) REVERT: O 3 GLN cc_start: 0.8507 (mt0) cc_final: 0.8248 (mm-40) REVERT: O 102 TYR cc_start: 0.9071 (m-80) cc_final: 0.8832 (m-80) REVERT: R 38 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8297 (tt0) REVERT: Q 13 GLN cc_start: 0.7846 (mp10) cc_final: 0.7588 (mp10) REVERT: Q 101 ASP cc_start: 0.8698 (p0) cc_final: 0.8484 (p0) REVERT: T 17 GLN cc_start: 0.8057 (pt0) cc_final: 0.7568 (pt0) REVERT: T 79 GLN cc_start: 0.8556 (mp10) cc_final: 0.8157 (mp10) REVERT: S 73 ASN cc_start: 0.9266 (OUTLIER) cc_final: 0.8921 (t0) outliers start: 51 outliers final: 29 residues processed: 274 average time/residue: 0.3189 time to fit residues: 122.8597 Evaluate side-chains 255 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 217 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 67 SER 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 C residue 87 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 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 O residue 57 LYS Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 38 GLN Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 73 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 176 optimal weight: 7.9990 chunk 146 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN O 81 GLN T 17 GLN ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14936 Z= 0.205 Angle : 0.495 4.429 20326 Z= 0.264 Chirality : 0.043 0.167 2184 Planarity : 0.004 0.037 2648 Dihedral : 4.498 29.602 2120 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.95 % Allowed : 16.01 % 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: 0.05 (0.20), residues: 1884 helix: None (None), residues: 0 sheet: 0.24 (0.19), residues: 768 loop : -0.02 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.004 0.001 HIS O 35 PHE 0.012 0.001 PHE S 29 TYR 0.015 0.001 TYR C 52A ARG 0.003 0.000 ARG F 54 *********************** 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 287 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 225 time to evaluate : 1.522 Fit side-chains REVERT: L 38 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8421 (tt0) REVERT: H 13 GLN cc_start: 0.7806 (mp10) cc_final: 0.7547 (mp10) REVERT: H 19 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8513 (ttp-170) REVERT: H 101 ASP cc_start: 0.8725 (p0) cc_final: 0.8460 (p0) REVERT: B 67 SER cc_start: 0.7669 (OUTLIER) cc_final: 0.7309 (m) REVERT: B 69 THR cc_start: 0.8456 (p) cc_final: 0.8109 (t) REVERT: B 79 GLN cc_start: 0.8530 (mp10) cc_final: 0.8120 (mp10) REVERT: B 106 VAL cc_start: 0.5192 (OUTLIER) cc_final: 0.4928 (m) REVERT: A 73 ASN cc_start: 0.9270 (OUTLIER) cc_final: 0.8943 (t0) REVERT: D 38 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.7705 (tt0) REVERT: C 85 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8264 (mt-10) REVERT: C 101 ASP cc_start: 0.8932 (p0) cc_final: 0.8683 (p0) REVERT: E 92 CYS cc_start: 0.8282 (OUTLIER) cc_final: 0.8045 (p) REVERT: N 54 ARG cc_start: 0.8159 (mtp-110) cc_final: 0.7857 (mtp-110) REVERT: M 34 MET cc_start: 0.9133 (mmt) cc_final: 0.8864 (mmt) REVERT: M 92 CYS cc_start: 0.8255 (OUTLIER) cc_final: 0.8035 (p) REVERT: P 38 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.7703 (tt0) REVERT: O 85 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8269 (mt-10) REVERT: R 38 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.8403 (tt0) REVERT: Q 13 GLN cc_start: 0.7814 (mp10) cc_final: 0.7579 (mp10) REVERT: Q 19 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8516 (ttp-170) REVERT: Q 101 ASP cc_start: 0.8708 (p0) cc_final: 0.8486 (p0) REVERT: T 79 GLN cc_start: 0.8580 (mp10) cc_final: 0.8185 (mp10) REVERT: S 73 ASN cc_start: 0.9238 (OUTLIER) cc_final: 0.8914 (t0) outliers start: 62 outliers final: 44 residues processed: 268 average time/residue: 0.3219 time to fit residues: 120.3670 Evaluate side-chains 273 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 217 time to evaluate : 1.811 ------------------------------------------------------------------------------- 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 19 ARG 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 20 THR Chi-restraints excluded: chain B residue 67 SER 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 D residue 38 GLN Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain 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 38 GLN Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain O residue 57 LYS Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 38 GLN Chi-restraints excluded: chain R residue 48 ILE 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 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 102 THR Chi-restraints excluded: chain S residue 46 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 100 optimal weight: 0.2980 chunk 128 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 98 optimal weight: 0.4980 chunk 175 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 14936 Z= 0.321 Angle : 0.539 4.480 20326 Z= 0.288 Chirality : 0.044 0.167 2184 Planarity : 0.004 0.047 2648 Dihedral : 4.666 23.395 2120 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.95 % Allowed : 15.94 % Favored : 80.10 % 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: -0.13 (0.19), residues: 1884 helix: None (None), residues: 0 sheet: 0.13 (0.18), residues: 848 loop : -0.18 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.004 0.002 HIS A 82A PHE 0.012 0.002 PHE A 29 TYR 0.015 0.002 TYR A 79 ARG 0.003 0.000 ARG F 54 *********************** 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 291 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 229 time to evaluate : 1.622 Fit side-chains REVERT: L 38 GLN cc_start: 0.9193 (OUTLIER) cc_final: 0.8510 (tt0) REVERT: H 13 GLN cc_start: 0.7824 (mp10) cc_final: 0.7565 (mp10) REVERT: H 19 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8589 (ttp-170) REVERT: H 101 ASP cc_start: 0.8783 (p0) cc_final: 0.8498 (p0) REVERT: B 67 SER cc_start: 0.7687 (OUTLIER) cc_final: 0.7310 (m) REVERT: B 69 THR cc_start: 0.8467 (p) cc_final: 0.8107 (t) REVERT: B 79 GLN cc_start: 0.8510 (mp10) cc_final: 0.7990 (mp10) REVERT: B 106 VAL cc_start: 0.5276 (OUTLIER) cc_final: 0.5037 (m) REVERT: A 68 THR cc_start: 0.9263 (t) cc_final: 0.9031 (p) REVERT: A 73 ASN cc_start: 0.9285 (OUTLIER) cc_final: 0.8963 (t0) REVERT: D 38 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.7734 (tt0) REVERT: C 19 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.8116 (ttt-90) REVERT: C 85 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8270 (mt-10) REVERT: C 101 ASP cc_start: 0.8943 (p0) cc_final: 0.8687 (p0) REVERT: F 54 ARG cc_start: 0.7939 (mtp-110) cc_final: 0.7622 (mtp-110) REVERT: E 92 CYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8085 (p) REVERT: N 54 ARG cc_start: 0.8146 (mtp-110) cc_final: 0.7817 (mtp-110) REVERT: M 92 CYS cc_start: 0.8310 (OUTLIER) cc_final: 0.8051 (p) REVERT: P 38 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.7727 (tt0) REVERT: O 85 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8284 (mt-10) REVERT: R 38 GLN cc_start: 0.9204 (OUTLIER) cc_final: 0.8492 (tt0) REVERT: Q 13 GLN cc_start: 0.7833 (mp10) cc_final: 0.7569 (mp10) REVERT: Q 101 ASP cc_start: 0.8744 (p0) cc_final: 0.8514 (p0) REVERT: T 17 GLN cc_start: 0.7765 (pt0) cc_final: 0.7180 (pt0) REVERT: S 73 ASN cc_start: 0.9276 (OUTLIER) cc_final: 0.8974 (t0) outliers start: 62 outliers final: 47 residues processed: 272 average time/residue: 0.3308 time to fit residues: 124.3694 Evaluate side-chains 282 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 223 time to evaluate : 1.720 ------------------------------------------------------------------------------- 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 19 ARG 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 20 THR Chi-restraints excluded: chain B residue 67 SER 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 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 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 chunk 34 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 137 optimal weight: 0.6980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 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 : 0.003 0.024 14936 Z= 0.217 Angle : 0.508 4.566 20326 Z= 0.271 Chirality : 0.043 0.174 2184 Planarity : 0.004 0.041 2648 Dihedral : 4.558 23.201 2120 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.02 % Allowed : 16.20 % Favored : 79.78 % 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: -0.12 (0.20), residues: 1884 helix: None (None), residues: 0 sheet: 0.12 (0.18), residues: 848 loop : -0.14 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Q 47 HIS 0.004 0.001 HIS O 35 PHE 0.011 0.001 PHE S 29 TYR 0.021 0.001 TYR M 52A ARG 0.004 0.000 ARG Q 19 *********************** 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 281 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 218 time to evaluate : 1.810 Fit side-chains REVERT: L 38 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8404 (tt0) REVERT: H 13 GLN cc_start: 0.7818 (mp10) cc_final: 0.7564 (mp10) REVERT: H 19 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8490 (ttp-170) REVERT: H 101 ASP cc_start: 0.8721 (p0) cc_final: 0.8475 (p0) REVERT: B 69 THR cc_start: 0.8457 (p) cc_final: 0.8093 (t) REVERT: B 106 VAL cc_start: 0.5254 (OUTLIER) cc_final: 0.5018 (m) REVERT: A 68 THR cc_start: 0.9248 (t) cc_final: 0.9023 (p) REVERT: A 73 ASN cc_start: 0.9285 (OUTLIER) cc_final: 0.8980 (t0) REVERT: D 38 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.7694 (tt0) REVERT: C 3 GLN cc_start: 0.8603 (mt0) cc_final: 0.8387 (mm-40) REVERT: C 85 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8252 (mt-10) REVERT: C 101 ASP cc_start: 0.8899 (p0) cc_final: 0.8663 (p0) REVERT: F 54 ARG cc_start: 0.8009 (mtp-110) cc_final: 0.7649 (mtp-110) REVERT: F 61 ARG cc_start: 0.8448 (mtm180) cc_final: 0.8240 (mtm180) REVERT: E 83 ARG cc_start: 0.8649 (mtm-85) cc_final: 0.8417 (ttp-110) REVERT: E 92 CYS cc_start: 0.8299 (OUTLIER) cc_final: 0.8062 (p) REVERT: N 54 ARG cc_start: 0.8063 (mtp-110) cc_final: 0.7698 (mtp-110) REVERT: M 92 CYS cc_start: 0.8263 (OUTLIER) cc_final: 0.8029 (p) REVERT: P 38 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.7691 (tt0) REVERT: O 3 GLN cc_start: 0.8593 (mt0) cc_final: 0.8348 (mm-40) REVERT: O 85 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8271 (mt-10) REVERT: R 38 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8383 (tt0) REVERT: Q 13 GLN cc_start: 0.7822 (mp10) cc_final: 0.7559 (mp10) REVERT: Q 101 ASP cc_start: 0.8731 (p0) cc_final: 0.8500 (p0) REVERT: T 17 GLN cc_start: 0.7657 (pt0) cc_final: 0.7079 (pt0) REVERT: S 73 ASN cc_start: 0.9263 (OUTLIER) cc_final: 0.8943 (t0) outliers start: 63 outliers final: 48 residues processed: 264 average time/residue: 0.3348 time to fit residues: 122.6907 Evaluate side-chains 273 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 215 time to evaluate : 1.718 ------------------------------------------------------------------------------- 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 19 ARG 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 107 VAL Chi-restraints excluded: chain B residue 20 THR 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 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 27 ASN Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 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 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 107 VAL Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 73 ASN Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 107 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 2.9990 chunk 168 optimal weight: 0.6980 chunk 153 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 147 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 162 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14936 Z= 0.152 Angle : 0.484 4.442 20326 Z= 0.257 Chirality : 0.042 0.153 2184 Planarity : 0.004 0.034 2648 Dihedral : 4.386 22.665 2120 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.38 % Allowed : 16.65 % Favored : 79.97 % 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: 0.13 (0.20), residues: 1884 helix: None (None), residues: 0 sheet: 0.40 (0.20), residues: 720 loop : -0.05 (0.19), residues: 1164 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 0.011 0.001 PHE S 29 TYR 0.019 0.001 TYR M 52A ARG 0.003 0.000 ARG Q 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 227 time to evaluate : 1.643 Fit side-chains REVERT: L 38 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8686 (tt0) REVERT: H 13 GLN cc_start: 0.7824 (mp10) cc_final: 0.7584 (mp10) REVERT: H 19 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8475 (ttp-170) REVERT: H 101 ASP cc_start: 0.8694 (p0) cc_final: 0.8451 (p0) REVERT: B 67 SER cc_start: 0.7661 (OUTLIER) cc_final: 0.7300 (m) REVERT: B 69 THR cc_start: 0.8443 (p) cc_final: 0.8098 (t) REVERT: B 106 VAL cc_start: 0.5137 (OUTLIER) cc_final: 0.4880 (m) REVERT: A 68 THR cc_start: 0.9264 (t) cc_final: 0.9033 (p) REVERT: A 73 ASN cc_start: 0.9263 (OUTLIER) cc_final: 0.8964 (t0) REVERT: C 3 GLN cc_start: 0.8581 (mt0) cc_final: 0.8366 (mm-40) REVERT: C 85 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8226 (mt-10) REVERT: C 101 ASP cc_start: 0.8863 (p0) cc_final: 0.8644 (p0) REVERT: F 54 ARG cc_start: 0.8046 (mtp-110) cc_final: 0.7693 (mtp-110) REVERT: F 61 ARG cc_start: 0.8473 (mtm180) cc_final: 0.8221 (mtm180) REVERT: E 83 ARG cc_start: 0.8741 (mtm-85) cc_final: 0.8513 (ttp-110) REVERT: N 54 ARG cc_start: 0.7943 (mtp-110) cc_final: 0.7574 (mtp-110) REVERT: O 3 GLN cc_start: 0.8565 (mt0) cc_final: 0.8342 (mm-40) REVERT: O 85 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8255 (mt-10) REVERT: R 38 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8504 (tt0) REVERT: Q 13 GLN cc_start: 0.7828 (mp10) cc_final: 0.7584 (mp10) REVERT: Q 101 ASP cc_start: 0.8696 (p0) cc_final: 0.8476 (p0) REVERT: S 73 ASN cc_start: 0.9256 (OUTLIER) cc_final: 0.8956 (t0) outliers start: 53 outliers final: 40 residues processed: 263 average time/residue: 0.3304 time to fit residues: 120.5268 Evaluate side-chains 267 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 220 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain 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 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 27 ASN Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain O residue 57 LYS Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 38 GLN Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 73 ASN Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 107 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 181 optimal weight: 0.9980 chunk 166 optimal weight: 10.0000 chunk 144 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14936 Z= 0.237 Angle : 0.516 4.708 20326 Z= 0.275 Chirality : 0.043 0.174 2184 Planarity : 0.004 0.034 2648 Dihedral : 4.474 22.632 2120 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.44 % Allowed : 16.71 % Favored : 79.85 % 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: 0.11 (0.20), residues: 1884 helix: None (None), residues: 0 sheet: 0.23 (0.19), residues: 768 loop : 0.06 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS S 82A PHE 0.012 0.002 PHE A 29 TYR 0.020 0.001 TYR M 52A ARG 0.004 0.000 ARG T 18 ********************** 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 274 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 220 time to evaluate : 1.809 Fit side-chains REVERT: L 38 GLN cc_start: 0.9108 (OUTLIER) cc_final: 0.8407 (tt0) REVERT: H 13 GLN cc_start: 0.7799 (mp10) cc_final: 0.7559 (mp10) REVERT: H 101 ASP cc_start: 0.8729 (p0) cc_final: 0.8511 (p0) REVERT: B 67 SER cc_start: 0.7669 (OUTLIER) cc_final: 0.7301 (m) REVERT: B 69 THR cc_start: 0.8472 (p) cc_final: 0.8130 (t) REVERT: B 106 VAL cc_start: 0.5192 (OUTLIER) cc_final: 0.4955 (m) REVERT: A 68 THR cc_start: 0.9248 (t) cc_final: 0.9021 (p) REVERT: A 73 ASN cc_start: 0.9280 (OUTLIER) cc_final: 0.8965 (t0) REVERT: D 38 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.7714 (tt0) REVERT: C 3 GLN cc_start: 0.8623 (mt0) cc_final: 0.8383 (mm-40) REVERT: C 85 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8252 (mt-10) REVERT: C 101 ASP cc_start: 0.8881 (p0) cc_final: 0.8656 (p0) REVERT: F 54 ARG cc_start: 0.8029 (mtp-110) cc_final: 0.7660 (mtp-110) REVERT: F 61 ARG cc_start: 0.8414 (mtm180) cc_final: 0.8214 (mtm180) REVERT: N 54 ARG cc_start: 0.7977 (mtp-110) cc_final: 0.7598 (mtp-110) REVERT: P 38 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.7706 (tt0) REVERT: O 3 GLN cc_start: 0.8594 (mt0) cc_final: 0.8355 (mm-40) REVERT: O 85 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8272 (mt-10) REVERT: R 38 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8375 (tt0) REVERT: Q 13 GLN cc_start: 0.7832 (mp10) cc_final: 0.7576 (mp10) REVERT: Q 101 ASP cc_start: 0.8715 (p0) cc_final: 0.8491 (p0) REVERT: S 73 ASN cc_start: 0.9262 (OUTLIER) cc_final: 0.8959 (t0) outliers start: 54 outliers final: 45 residues processed: 256 average time/residue: 0.3351 time to fit residues: 118.7763 Evaluate side-chains 268 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 215 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain B residue 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 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 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 27 ASN Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 38 GLN Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain O residue 57 LYS Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 38 GLN Chi-restraints excluded: chain R residue 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 87 THR Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 73 ASN Chi-restraints excluded: chain S residue 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 114 optimal weight: 0.7980 chunk 153 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.113533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.093009 restraints weight = 20053.353| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.48 r_work: 0.2982 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14936 Z= 0.160 Angle : 0.489 4.434 20326 Z= 0.260 Chirality : 0.042 0.168 2184 Planarity : 0.004 0.061 2648 Dihedral : 4.388 22.765 2120 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.19 % Allowed : 16.77 % 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: 0.15 (0.20), residues: 1884 helix: None (None), residues: 0 sheet: 0.25 (0.19), residues: 768 loop : 0.09 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS C 35 PHE 0.011 0.001 PHE A 29 TYR 0.020 0.001 TYR M 52A ARG 0.007 0.000 ARG H 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3146.83 seconds wall clock time: 58 minutes 57.04 seconds (3537.04 seconds total)