Starting phenix.real_space_refine on Fri Jul 3 09:25:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i86_52708/07_2026/9i86_52708.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i86_52708/07_2026/9i86_52708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9i86_52708/07_2026/9i86_52708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i86_52708/07_2026/9i86_52708.map" model { file = "/net/cci-nas-00/data/ceres_data/9i86_52708/07_2026/9i86_52708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i86_52708/07_2026/9i86_52708.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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: 6 Type Number sf(0) Gaussians P 38 5.49 5 S 6 5.16 5 C 4300 2.51 5 N 1100 2.21 5 O 1446 1.98 5 H 6728 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13618 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2057 Classifications: {'peptide': 135} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "Y" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 638 Classifications: {'DNA': 20} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 19} Chain: "Z" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 638 Classifications: {'DNA': 20} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 19} Chain: "B" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2057 Classifications: {'peptide': 135} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "C" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2057 Classifications: {'peptide': 135} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "D" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2057 Classifications: {'peptide': 135} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "E" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2057 Classifications: {'peptide': 135} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "F" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2057 Classifications: {'peptide': 135} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Time building chain proxies: 2.98, per 1000 atoms: 0.22 Number of scatterers: 13618 At special positions: 0 Unit cell: (113.16, 72.98, 140.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 6 16.00 P 38 15.00 O 1446 8.00 N 1100 7.00 C 4300 6.00 H 6728 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 429.8 milliseconds 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1452 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 6 sheets defined 20.0% alpha, 40.0% beta 0 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 73 through 84 Processing helix chain 'A' and resid 121 through 135 removed outlier: 3.852A pdb=" N ALA A 134 " --> pdb=" O GLN A 130 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU A 135 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 84 Processing helix chain 'B' and resid 121 through 135 removed outlier: 3.853A pdb=" N ALA B 134 " --> pdb=" O GLN B 130 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU B 135 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 84 Processing helix chain 'C' and resid 121 through 135 removed outlier: 3.853A pdb=" N ALA C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU C 135 " --> pdb=" O VAL C 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 84 Processing helix chain 'D' and resid 121 through 135 removed outlier: 3.852A pdb=" N ALA D 134 " --> pdb=" O GLN D 130 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU D 135 " --> pdb=" O VAL D 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 84 Processing helix chain 'E' and resid 121 through 135 removed outlier: 3.852A pdb=" N ALA E 134 " --> pdb=" O GLN E 130 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU E 135 " --> pdb=" O VAL E 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 84 Processing helix chain 'F' and resid 121 through 135 removed outlier: 3.853A pdb=" N ALA F 134 " --> pdb=" O GLN F 130 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU F 135 " --> pdb=" O VAL F 131 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 6.215A pdb=" N GLU A 2 " --> pdb=" O ARG A 66 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N GLY A 68 " --> pdb=" O GLU A 2 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ALA A 69 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLY A 52 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE A 71 " --> pdb=" O PHE A 50 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N PHE A 50 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLN A 41 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE A 47 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL A 39 " --> pdb=" O PHE A 47 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LYS A 49 " --> pdb=" O LYS A 37 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS A 37 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLU A 51 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE A 96 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N SER A 29 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL A 94 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR A 31 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N PHE A 92 " --> pdb=" O TYR A 31 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG A 33 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL A 90 " --> pdb=" O ARG A 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 2 through 3 removed outlier: 6.215A pdb=" N GLU B 2 " --> pdb=" O ARG B 66 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N GLY B 68 " --> pdb=" O GLU B 2 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ALA B 69 " --> pdb=" O GLY B 52 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLY B 52 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ILE B 71 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N PHE B 50 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLN B 41 " --> pdb=" O GLY B 45 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N PHE B 47 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL B 39 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LYS B 49 " --> pdb=" O LYS B 37 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LYS B 37 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLU B 51 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE B 96 " --> pdb=" O LEU B 27 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N SER B 29 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL B 94 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR B 31 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N PHE B 92 " --> pdb=" O TYR B 31 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG B 33 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL B 90 " --> pdb=" O ARG B 33 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 2 through 3 removed outlier: 6.215A pdb=" N GLU C 2 " --> pdb=" O ARG C 66 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N GLY C 68 " --> pdb=" O GLU C 2 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ALA C 69 " --> pdb=" O GLY C 52 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLY C 52 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ILE C 71 " --> pdb=" O PHE C 50 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N PHE C 50 " --> pdb=" O ILE C 71 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLY C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLN C 41 " --> pdb=" O GLY C 45 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N PHE C 47 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL C 39 " --> pdb=" O PHE C 47 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LYS C 49 " --> pdb=" O LYS C 37 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LYS C 37 " --> pdb=" O LYS C 49 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLU C 51 " --> pdb=" O ARG C 35 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE C 96 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N SER C 29 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL C 94 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR C 31 " --> pdb=" O PHE C 92 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N PHE C 92 " --> pdb=" O TYR C 31 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG C 33 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL C 90 " --> pdb=" O ARG C 33 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 2 through 3 removed outlier: 6.216A pdb=" N GLU D 2 " --> pdb=" O ARG D 66 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N GLY D 68 " --> pdb=" O GLU D 2 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ALA D 69 " --> pdb=" O GLY D 52 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLY D 52 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE D 71 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N PHE D 50 " --> pdb=" O ILE D 71 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLN D 41 " --> pdb=" O GLY D 45 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N PHE D 47 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL D 39 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LYS D 49 " --> pdb=" O LYS D 37 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS D 37 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLU D 51 " --> pdb=" O ARG D 35 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE D 96 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N SER D 29 " --> pdb=" O VAL D 94 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL D 94 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N TYR D 31 " --> pdb=" O PHE D 92 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N PHE D 92 " --> pdb=" O TYR D 31 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG D 33 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL D 90 " --> pdb=" O ARG D 33 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 2 through 3 removed outlier: 6.216A pdb=" N GLU E 2 " --> pdb=" O ARG E 66 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N GLY E 68 " --> pdb=" O GLU E 2 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ALA E 69 " --> pdb=" O GLY E 52 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLY E 52 " --> pdb=" O ALA E 69 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ILE E 71 " --> pdb=" O PHE E 50 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N PHE E 50 " --> pdb=" O ILE E 71 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLY E 45 " --> pdb=" O GLN E 41 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLN E 41 " --> pdb=" O GLY E 45 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE E 47 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL E 39 " --> pdb=" O PHE E 47 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS E 49 " --> pdb=" O LYS E 37 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LYS E 37 " --> pdb=" O LYS E 49 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLU E 51 " --> pdb=" O ARG E 35 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE E 96 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N SER E 29 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL E 94 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR E 31 " --> pdb=" O PHE E 92 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N PHE E 92 " --> pdb=" O TYR E 31 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG E 33 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL E 90 " --> pdb=" O ARG E 33 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 2 through 3 removed outlier: 6.215A pdb=" N GLU F 2 " --> pdb=" O ARG F 66 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N GLY F 68 " --> pdb=" O GLU F 2 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ALA F 69 " --> pdb=" O GLY F 52 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLY F 52 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE F 71 " --> pdb=" O PHE F 50 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N PHE F 50 " --> pdb=" O ILE F 71 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY F 45 " --> pdb=" O GLN F 41 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N GLN F 41 " --> pdb=" O GLY F 45 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N PHE F 47 " --> pdb=" O VAL F 39 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL F 39 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LYS F 49 " --> pdb=" O LYS F 37 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS F 37 " --> pdb=" O LYS F 49 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLU F 51 " --> pdb=" O ARG F 35 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE F 96 " --> pdb=" O LEU F 27 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N SER F 29 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL F 94 " --> pdb=" O SER F 29 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR F 31 " --> pdb=" O PHE F 92 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N PHE F 92 " --> pdb=" O TYR F 31 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG F 33 " --> pdb=" O VAL F 90 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL F 90 " --> pdb=" O ARG F 33 " (cutoff:3.500A) 222 hydrogen bonds defined for protein. 648 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.71: 13783 1.71 - 2.59: 12 2.59 - 3.47: 0 3.47 - 4.34: 2 4.34 - 5.22: 1 Warning: very large bond lengths. Bond restraints: 13798 Sorted by residual: bond pdb=" C2' DT Y 19 " pdb=" H2' DT Y 19 " ideal model delta sigma weight residual 0.970 5.218 -4.248 2.00e-02 2.50e+03 4.51e+04 bond pdb=" C2' DT Y 18 " pdb="H2'' DT Y 18 " ideal model delta sigma weight residual 0.970 4.233 -3.263 2.00e-02 2.50e+03 2.66e+04 bond pdb=" C2' DT Y 17 " pdb="H2'' DT Y 17 " ideal model delta sigma weight residual 0.970 3.929 -2.959 2.00e-02 2.50e+03 2.19e+04 bond pdb=" N3 DT Y 19 " pdb=" H3 DT Y 19 " ideal model delta sigma weight residual 0.860 1.041 -0.181 2.00e-02 2.50e+03 8.16e+01 bond pdb=" N3 DT Y 18 " pdb=" H3 DT Y 18 " ideal model delta sigma weight residual 0.860 1.041 -0.181 2.00e-02 2.50e+03 8.15e+01 ... (remaining 13793 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.91: 25144 12.91 - 25.82: 2 25.82 - 38.73: 20 38.73 - 51.64: 1 51.64 - 64.56: 1 Bond angle restraints: 25168 Sorted by residual: angle pdb=" H2' DT Y 17 " pdb=" C2' DT Y 17 " pdb="H2'' DT Y 17 " ideal model delta sigma weight residual 109.00 173.56 -64.56 1.50e+00 4.44e-01 1.85e+03 angle pdb=" C1' DT Y 18 " pdb=" C2' DT Y 18 " pdb="H2'' DT Y 18 " ideal model delta sigma weight residual 109.00 68.22 40.78 1.50e+00 4.44e-01 7.39e+02 angle pdb=" C3' DT Y 17 " pdb=" C2' DT Y 17 " pdb="H2'' DT Y 17 " ideal model delta sigma weight residual 109.00 71.46 37.54 1.50e+00 4.44e-01 6.26e+02 angle pdb=" C1' DT Y 17 " pdb=" C2' DT Y 17 " pdb="H2'' DT Y 17 " ideal model delta sigma weight residual 109.00 75.52 33.48 1.50e+00 4.44e-01 4.98e+02 angle pdb=" H2' DT Y 18 " pdb=" C2' DT Y 18 " pdb="H2'' DT Y 18 " ideal model delta sigma weight residual 109.00 131.12 -22.12 1.50e+00 4.44e-01 2.18e+02 ... (remaining 25163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.85: 5678 23.85 - 47.71: 367 47.71 - 71.56: 161 71.56 - 95.41: 3 95.41 - 119.27: 1 Dihedral angle restraints: 6210 sinusoidal: 3630 harmonic: 2580 Sorted by residual: dihedral pdb=" C SER D 121 " pdb=" N SER D 121 " pdb=" CA SER D 121 " pdb=" CB SER D 121 " ideal model delta harmonic sigma weight residual -122.60 -131.43 8.83 0 2.50e+00 1.60e-01 1.25e+01 dihedral pdb=" C SER B 121 " pdb=" N SER B 121 " pdb=" CA SER B 121 " pdb=" CB SER B 121 " ideal model delta harmonic sigma weight residual -122.60 -131.40 8.80 0 2.50e+00 1.60e-01 1.24e+01 dihedral pdb=" C SER A 121 " pdb=" N SER A 121 " pdb=" CA SER A 121 " pdb=" CB SER A 121 " ideal model delta harmonic sigma weight residual -122.60 -131.40 8.80 0 2.50e+00 1.60e-01 1.24e+01 ... (remaining 6207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 931 0.069 - 0.139: 171 0.139 - 0.208: 10 0.208 - 0.277: 0 0.277 - 0.347: 6 Chirality restraints: 1118 Sorted by residual: chirality pdb=" CA SER D 121 " pdb=" N SER D 121 " pdb=" C SER D 121 " pdb=" CB SER D 121 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA SER A 121 " pdb=" N SER A 121 " pdb=" C SER A 121 " pdb=" CB SER A 121 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA SER B 121 " pdb=" N SER B 121 " pdb=" C SER B 121 " pdb=" CB SER B 121 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 1115 not shown) Planarity restraints: 1888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 72 " 0.016 5.00e-02 4.00e+02 2.35e-02 8.83e-01 pdb=" N PRO D 73 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO D 73 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO D 73 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 72 " -0.015 5.00e-02 4.00e+02 2.33e-02 8.71e-01 pdb=" N PRO B 73 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO B 73 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 73 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 72 " 0.015 5.00e-02 4.00e+02 2.33e-02 8.65e-01 pdb=" N PRO A 73 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO A 73 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 73 " 0.013 5.00e-02 4.00e+02 ... (remaining 1885 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 414 2.14 - 2.76: 25704 2.76 - 3.37: 34156 3.37 - 3.99: 47451 3.99 - 4.60: 73557 Nonbonded interactions: 181282 Sorted by model distance: nonbonded pdb=" H3 DT Z 5 " pdb=" O LYS B 103 " model vdw 1.531 2.450 nonbonded pdb=" O2 DT Z 3 " pdb=" HG SER E 42 " model vdw 1.561 2.450 nonbonded pdb=" H3 DT Z 11 " pdb=" O LYS C 103 " model vdw 1.578 2.450 nonbonded pdb=" O2 DT Z 9 " pdb=" HG SER B 42 " model vdw 1.600 2.450 nonbonded pdb=" O2 DT Z 15 " pdb=" HG SER C 42 " model vdw 1.631 2.450 ... (remaining 181277 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'Y' selection = chain 'Z' } 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: 4.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.940 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 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 0.041 7070 Z= 0.404 Angle : 0.690 6.184 9714 Z= 0.562 Chirality : 0.054 0.347 1118 Planarity : 0.003 0.023 1120 Dihedral : 15.977 119.266 2678 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.29), residues: 798 helix: -0.40 (0.42), residues: 180 sheet: 1.19 (0.27), residues: 336 loop : -1.34 (0.33), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 128 TYR 0.005 0.001 TYR A 108 PHE 0.004 0.001 PHE D 44 TRP 0.004 0.001 TRP F 97 HIS 0.000 0.000 HIS A 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00728 / 0.40 ( 7070) covalent geometry : angle 0.69020 / 0.56 ( 9714) hydrogen bonds : bond 0.14601 / 10.37 ( 222) hydrogen bonds : angle 9.30650 / 6.42 ( 648) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.7141 (tt0) cc_final: 0.6391 (mp0) REVERT: A 103 LYS cc_start: 0.6921 (mttt) cc_final: 0.6045 (ttpt) REVERT: A 113 LYS cc_start: 0.8399 (mtpm) cc_final: 0.8002 (mttp) REVERT: B 2 GLU cc_start: 0.7387 (tt0) cc_final: 0.6842 (mp0) REVERT: B 103 LYS cc_start: 0.7209 (mttt) cc_final: 0.6091 (ttpt) REVERT: C 39 VAL cc_start: 0.7721 (t) cc_final: 0.7495 (m) REVERT: C 103 LYS cc_start: 0.7191 (mttt) cc_final: 0.6355 (ttpt) REVERT: D 2 GLU cc_start: 0.6843 (tt0) cc_final: 0.6403 (mp0) REVERT: D 49 LYS cc_start: 0.7896 (tttt) cc_final: 0.7686 (ttpt) REVERT: D 103 LYS cc_start: 0.6824 (mttt) cc_final: 0.6077 (ttpt) REVERT: E 2 GLU cc_start: 0.7460 (tt0) cc_final: 0.6840 (mp0) REVERT: E 103 LYS cc_start: 0.6783 (mttt) cc_final: 0.6068 (ttpt) REVERT: F 2 GLU cc_start: 0.6939 (tt0) cc_final: 0.6499 (mp0) REVERT: F 103 LYS cc_start: 0.6859 (mttt) cc_final: 0.6268 (ttpt) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 1.3446 time to fit residues: 290.3350 Evaluate side-chains 125 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.2980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 105 ASN D 24 ASN D 41 GLN D 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.223115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.205902 restraints weight = 17680.534| |-----------------------------------------------------------------------------| r_work (start): 0.4391 rms_B_bonded: 1.08 r_work: 0.4252 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.4145 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7070 Z= 0.146 Angle : 0.656 8.223 9714 Z= 0.381 Chirality : 0.055 0.370 1118 Planarity : 0.004 0.026 1120 Dihedral : 19.356 121.060 1238 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.04 % Allowed : 22.96 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.29), residues: 798 helix: -0.22 (0.41), residues: 186 sheet: 1.53 (0.26), residues: 336 loop : -1.17 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 66 TYR 0.006 0.001 TYR B 108 PHE 0.008 0.001 PHE C 47 TRP 0.006 0.001 TRP B 97 HIS 0.001 0.001 HIS D 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.15 ( 7070) covalent geometry : angle 0.65588 / 0.38 ( 9714) hydrogen bonds : bond 0.04033 / 2.67 ( 222) hydrogen bonds : angle 7.20311 / 4.95 ( 648) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7351 (mm-30) REVERT: A 84 VAL cc_start: 0.6423 (p) cc_final: 0.5952 (m) REVERT: A 103 LYS cc_start: 0.7238 (mttt) cc_final: 0.6872 (mmtm) REVERT: A 113 LYS cc_start: 0.8519 (mtpm) cc_final: 0.8264 (mttm) REVERT: B 17 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7174 (mmtt) REVERT: B 63 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7235 (mt-10) REVERT: B 103 LYS cc_start: 0.7268 (mttt) cc_final: 0.6572 (ttpp) REVERT: C 39 VAL cc_start: 0.7671 (t) cc_final: 0.7420 (m) REVERT: C 103 LYS cc_start: 0.7287 (mttt) cc_final: 0.6514 (ttpt) REVERT: D 1 MET cc_start: 0.7366 (tmm) cc_final: 0.7160 (tmm) REVERT: D 2 GLU cc_start: 0.7253 (tt0) cc_final: 0.6684 (mp0) REVERT: D 103 LYS cc_start: 0.7311 (mttt) cc_final: 0.6746 (ttpt) REVERT: E 63 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7080 (mt-10) REVERT: F 2 GLU cc_start: 0.7494 (tt0) cc_final: 0.6937 (mp0) outliers start: 13 outliers final: 4 residues processed: 128 average time/residue: 1.3208 time to fit residues: 176.7603 Evaluate side-chains 120 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 LYS Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain E residue 53 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 22 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 ASN E 105 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.215038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.196726 restraints weight = 17759.514| |-----------------------------------------------------------------------------| r_work (start): 0.4304 rms_B_bonded: 1.14 r_work: 0.4169 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.4063 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7070 Z= 0.184 Angle : 0.658 8.421 9714 Z= 0.383 Chirality : 0.054 0.359 1118 Planarity : 0.004 0.029 1120 Dihedral : 19.894 122.205 1238 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.52 % Allowed : 22.64 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.28), residues: 798 helix: -0.07 (0.40), residues: 186 sheet: 1.61 (0.26), residues: 336 loop : -1.19 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG F 33 TYR 0.011 0.002 TYR C 31 PHE 0.009 0.001 PHE C 47 TRP 0.007 0.001 TRP E 97 HIS 0.003 0.001 HIS E 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 ( 7070) covalent geometry : angle 0.65792 / 0.38 ( 9714) hydrogen bonds : bond 0.03645 / 2.40 ( 222) hydrogen bonds : angle 6.46786 / 4.41 ( 648) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7309 (mm-30) REVERT: A 103 LYS cc_start: 0.7447 (mttt) cc_final: 0.6930 (tttm) REVERT: A 113 LYS cc_start: 0.8581 (mtpm) cc_final: 0.8361 (mttm) REVERT: B 63 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7280 (mt-10) REVERT: B 103 LYS cc_start: 0.7392 (mttt) cc_final: 0.6737 (ttpt) REVERT: C 31 TYR cc_start: 0.8444 (p90) cc_final: 0.8086 (p90) REVERT: C 39 VAL cc_start: 0.7748 (t) cc_final: 0.7504 (m) REVERT: C 103 LYS cc_start: 0.7621 (mttt) cc_final: 0.6858 (ttpt) REVERT: D 1 MET cc_start: 0.7566 (tmm) cc_final: 0.7190 (tmm) REVERT: D 63 GLU cc_start: 0.7390 (mm-30) cc_final: 0.7147 (mt-10) REVERT: D 78 SER cc_start: 0.7962 (p) cc_final: 0.7757 (m) REVERT: D 103 LYS cc_start: 0.7519 (mttt) cc_final: 0.6935 (ttpt) REVERT: E 63 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7191 (mt-10) REVERT: E 80 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7094 (tt) REVERT: F 48 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8138 (mm) REVERT: F 78 SER cc_start: 0.8058 (p) cc_final: 0.7798 (m) outliers start: 16 outliers final: 4 residues processed: 118 average time/residue: 1.4740 time to fit residues: 180.8282 Evaluate side-chains 107 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 3 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.216011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.198435 restraints weight = 17671.355| |-----------------------------------------------------------------------------| r_work (start): 0.4320 rms_B_bonded: 1.10 r_work: 0.4183 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.4077 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7070 Z= 0.139 Angle : 0.603 7.585 9714 Z= 0.352 Chirality : 0.052 0.355 1118 Planarity : 0.003 0.027 1120 Dihedral : 19.836 128.541 1238 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.52 % Allowed : 22.64 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.28), residues: 798 helix: 0.18 (0.40), residues: 186 sheet: 1.50 (0.26), residues: 336 loop : -1.18 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 33 TYR 0.007 0.001 TYR F 108 PHE 0.006 0.001 PHE C 47 TRP 0.007 0.001 TRP B 97 HIS 0.001 0.001 HIS A 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 ( 7070) covalent geometry : angle 0.60335 / 0.35 ( 9714) hydrogen bonds : bond 0.03285 / 2.17 ( 222) hydrogen bonds : angle 6.04319 / 4.11 ( 648) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7320 (mm-30) REVERT: A 103 LYS cc_start: 0.7396 (mttt) cc_final: 0.6906 (tttm) REVERT: A 113 LYS cc_start: 0.8630 (mtpm) cc_final: 0.8373 (mttm) REVERT: B 63 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7287 (mt-10) REVERT: B 103 LYS cc_start: 0.7556 (mttt) cc_final: 0.6910 (ttpt) REVERT: C 31 TYR cc_start: 0.8284 (p90) cc_final: 0.7940 (p90) REVERT: C 39 VAL cc_start: 0.7777 (t) cc_final: 0.7550 (m) REVERT: C 53 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7323 (tt0) REVERT: C 55 GLU cc_start: 0.8174 (tt0) cc_final: 0.7961 (tt0) REVERT: C 103 LYS cc_start: 0.7555 (mttt) cc_final: 0.6784 (ttpt) REVERT: D 1 MET cc_start: 0.7619 (tmm) cc_final: 0.7289 (tmm) REVERT: D 63 GLU cc_start: 0.7348 (mm-30) cc_final: 0.7102 (mt-10) REVERT: D 103 LYS cc_start: 0.7524 (mttt) cc_final: 0.6927 (ttpt) REVERT: E 63 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7181 (mt-10) REVERT: E 80 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6955 (tt) REVERT: F 63 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.6416 (mt-10) REVERT: F 78 SER cc_start: 0.8028 (p) cc_final: 0.7764 (m) outliers start: 16 outliers final: 3 residues processed: 110 average time/residue: 1.5302 time to fit residues: 174.6139 Evaluate side-chains 109 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain F residue 63 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 72 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 43 optimal weight: 0.1980 chunk 67 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.216911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.199130 restraints weight = 18009.348| |-----------------------------------------------------------------------------| r_work (start): 0.4324 rms_B_bonded: 1.13 r_work: 0.4191 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.4087 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7070 Z= 0.128 Angle : 0.585 7.361 9714 Z= 0.341 Chirality : 0.052 0.353 1118 Planarity : 0.003 0.025 1120 Dihedral : 19.801 131.030 1238 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.20 % Allowed : 23.43 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.28), residues: 798 helix: 0.44 (0.39), residues: 186 sheet: 1.43 (0.26), residues: 336 loop : -1.12 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 33 TYR 0.005 0.001 TYR F 108 PHE 0.006 0.001 PHE B 54 TRP 0.006 0.001 TRP C 97 HIS 0.001 0.001 HIS E 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.13 ( 7070) covalent geometry : angle 0.58476 / 0.34 ( 9714) hydrogen bonds : bond 0.03094 / 2.04 ( 222) hydrogen bonds : angle 5.75992 / 3.90 ( 648) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7307 (mm-30) REVERT: A 103 LYS cc_start: 0.7406 (mttt) cc_final: 0.6901 (tttm) REVERT: A 113 LYS cc_start: 0.8612 (mtpm) cc_final: 0.8387 (mttm) REVERT: B 63 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7276 (mt-10) REVERT: B 103 LYS cc_start: 0.7581 (mttt) cc_final: 0.6885 (ttpt) REVERT: C 31 TYR cc_start: 0.8308 (p90) cc_final: 0.7934 (p90) REVERT: C 39 VAL cc_start: 0.7827 (t) cc_final: 0.7601 (m) REVERT: C 53 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7312 (tt0) REVERT: C 103 LYS cc_start: 0.7510 (mttt) cc_final: 0.6753 (ttpt) REVERT: D 1 MET cc_start: 0.7641 (tmm) cc_final: 0.7246 (tmm) REVERT: D 48 ILE cc_start: 0.8205 (mt) cc_final: 0.7944 (mm) REVERT: D 63 GLU cc_start: 0.7325 (mm-30) cc_final: 0.7099 (mt-10) REVERT: D 103 LYS cc_start: 0.7498 (mttt) cc_final: 0.6917 (ttpt) REVERT: E 63 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7177 (mt-10) REVERT: E 80 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6820 (tt) REVERT: F 63 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6492 (mt-10) REVERT: F 78 SER cc_start: 0.8016 (p) cc_final: 0.7743 (m) outliers start: 14 outliers final: 6 residues processed: 109 average time/residue: 1.5641 time to fit residues: 176.9200 Evaluate side-chains 111 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain F residue 63 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 43 optimal weight: 0.6980 chunk 1 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 19 optimal weight: 0.0060 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 40 optimal weight: 0.3980 chunk 31 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.224336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.207594 restraints weight = 17820.695| |-----------------------------------------------------------------------------| r_work (start): 0.4404 rms_B_bonded: 1.08 r_work: 0.4269 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.4170 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7070 Z= 0.108 Angle : 0.560 6.018 9714 Z= 0.327 Chirality : 0.051 0.351 1118 Planarity : 0.003 0.025 1120 Dihedral : 19.663 140.837 1238 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.04 % Allowed : 24.21 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.28), residues: 798 helix: 0.80 (0.40), residues: 186 sheet: 1.49 (0.26), residues: 336 loop : -1.00 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 33 TYR 0.004 0.001 TYR F 108 PHE 0.005 0.001 PHE C 54 TRP 0.005 0.001 TRP C 97 HIS 0.001 0.000 HIS E 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.11 ( 7070) covalent geometry : angle 0.55964 / 0.33 ( 9714) hydrogen bonds : bond 0.02815 / 1.84 ( 222) hydrogen bonds : angle 5.31129 / 3.59 ( 648) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7421 (pt0) REVERT: A 103 LYS cc_start: 0.7359 (mttt) cc_final: 0.6899 (tttm) REVERT: B 63 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7211 (mt-10) REVERT: B 103 LYS cc_start: 0.7570 (mttt) cc_final: 0.6868 (ttpt) REVERT: C 31 TYR cc_start: 0.8253 (p90) cc_final: 0.7990 (p90) REVERT: C 103 LYS cc_start: 0.7354 (mttt) cc_final: 0.6629 (ttpt) REVERT: D 1 MET cc_start: 0.7651 (tmm) cc_final: 0.7217 (tmm) REVERT: D 48 ILE cc_start: 0.8157 (mt) cc_final: 0.7909 (mm) REVERT: D 103 LYS cc_start: 0.7480 (mttt) cc_final: 0.6906 (ttpt) REVERT: E 63 GLU cc_start: 0.7400 (mt-10) cc_final: 0.7182 (mt-10) REVERT: E 80 LEU cc_start: 0.7187 (OUTLIER) cc_final: 0.6839 (tt) REVERT: F 48 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.8106 (mm) REVERT: F 78 SER cc_start: 0.8023 (p) cc_final: 0.7742 (m) REVERT: F 128 ARG cc_start: 0.6612 (OUTLIER) cc_final: 0.4746 (mmm160) outliers start: 13 outliers final: 1 residues processed: 116 average time/residue: 1.5779 time to fit residues: 190.1337 Evaluate side-chains 108 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 128 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 45 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.217817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.200742 restraints weight = 17611.004| |-----------------------------------------------------------------------------| r_work (start): 0.4346 rms_B_bonded: 1.06 r_work: 0.4209 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.4106 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7070 Z= 0.170 Angle : 0.623 8.330 9714 Z= 0.361 Chirality : 0.053 0.354 1118 Planarity : 0.003 0.025 1120 Dihedral : 19.678 126.240 1238 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.83 % Allowed : 24.21 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.28), residues: 798 helix: 0.73 (0.39), residues: 186 sheet: 1.29 (0.26), residues: 336 loop : -1.08 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 66 TYR 0.008 0.002 TYR D 108 PHE 0.007 0.001 PHE B 54 TRP 0.008 0.001 TRP B 97 HIS 0.002 0.001 HIS A 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 ( 7070) covalent geometry : angle 0.62346 / 0.36 ( 9714) hydrogen bonds : bond 0.03334 / 2.19 ( 222) hydrogen bonds : angle 5.45053 / 3.68 ( 648) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.7020 (mm-30) REVERT: A 103 LYS cc_start: 0.7423 (mttt) cc_final: 0.6943 (tttm) REVERT: B 63 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7165 (mt-10) REVERT: B 103 LYS cc_start: 0.7678 (mttt) cc_final: 0.6967 (tttm) REVERT: C 103 LYS cc_start: 0.7600 (mttt) cc_final: 0.6819 (ttpt) REVERT: D 63 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6576 (mt-10) REVERT: D 103 LYS cc_start: 0.7533 (mttt) cc_final: 0.6993 (ttpt) REVERT: E 53 GLU cc_start: 0.8153 (pt0) cc_final: 0.7779 (pm20) REVERT: E 63 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7182 (mt-10) REVERT: E 80 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.6937 (tt) REVERT: F 63 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6499 (mt-10) REVERT: F 78 SER cc_start: 0.8095 (p) cc_final: 0.7857 (m) REVERT: F 128 ARG cc_start: 0.6842 (OUTLIER) cc_final: 0.4802 (mmm160) outliers start: 18 outliers final: 4 residues processed: 110 average time/residue: 1.7881 time to fit residues: 203.9803 Evaluate side-chains 109 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 128 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 30 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.218678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.201466 restraints weight = 17738.399| |-----------------------------------------------------------------------------| r_work (start): 0.4293 rms_B_bonded: 1.07 r_work: 0.4139 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.4031 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7070 Z= 0.140 Angle : 0.594 7.421 9714 Z= 0.346 Chirality : 0.052 0.351 1118 Planarity : 0.003 0.024 1120 Dihedral : 19.706 131.046 1238 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.04 % Allowed : 24.84 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.28), residues: 798 helix: 0.79 (0.39), residues: 186 sheet: 1.22 (0.26), residues: 336 loop : -1.07 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 33 TYR 0.006 0.001 TYR E 31 PHE 0.007 0.001 PHE C 54 TRP 0.007 0.001 TRP C 97 HIS 0.002 0.001 HIS C 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 ( 7070) covalent geometry : angle 0.59377 / 0.35 ( 9714) hydrogen bonds : bond 0.03079 / 2.02 ( 222) hydrogen bonds : angle 5.35433 / 3.61 ( 648) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7024 (mm-30) REVERT: A 103 LYS cc_start: 0.7457 (mttt) cc_final: 0.6935 (tttm) REVERT: B 63 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7185 (mt-10) REVERT: B 103 LYS cc_start: 0.7656 (mttt) cc_final: 0.6857 (ttpp) REVERT: C 103 LYS cc_start: 0.7620 (mttt) cc_final: 0.6801 (ttpt) REVERT: D 103 LYS cc_start: 0.7561 (mttt) cc_final: 0.6980 (ttpt) REVERT: E 53 GLU cc_start: 0.8183 (pt0) cc_final: 0.7795 (pm20) REVERT: E 63 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7269 (mt-10) REVERT: E 80 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6954 (tt) REVERT: F 48 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.8106 (mm) REVERT: F 63 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6468 (mt-10) REVERT: F 78 SER cc_start: 0.8072 (p) cc_final: 0.7830 (m) REVERT: F 128 ARG cc_start: 0.6817 (OUTLIER) cc_final: 0.4637 (mmm160) outliers start: 13 outliers final: 5 residues processed: 102 average time/residue: 1.6930 time to fit residues: 179.1178 Evaluate side-chains 104 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 128 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 43 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.219556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.202368 restraints weight = 17818.575| |-----------------------------------------------------------------------------| r_work (start): 0.4362 rms_B_bonded: 1.11 r_work: 0.4229 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.4130 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7070 Z= 0.130 Angle : 0.580 7.250 9714 Z= 0.338 Chirality : 0.052 0.351 1118 Planarity : 0.003 0.023 1120 Dihedral : 19.698 132.649 1238 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.42 % Allowed : 26.10 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.28), residues: 798 helix: 0.92 (0.39), residues: 186 sheet: 1.19 (0.26), residues: 336 loop : -1.03 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 33 TYR 0.005 0.001 TYR B 110 PHE 0.006 0.001 PHE A 54 TRP 0.007 0.001 TRP C 97 HIS 0.002 0.001 HIS E 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 ( 7070) covalent geometry : angle 0.58049 / 0.34 ( 9714) hydrogen bonds : bond 0.02978 / 1.95 ( 222) hydrogen bonds : angle 5.20797 / 3.51 ( 648) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6935 (mm-30) REVERT: A 103 LYS cc_start: 0.7410 (mttt) cc_final: 0.6935 (tttm) REVERT: B 63 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7191 (mt-10) REVERT: B 103 LYS cc_start: 0.7664 (mttt) cc_final: 0.6872 (ttpp) REVERT: C 103 LYS cc_start: 0.7608 (mttt) cc_final: 0.6811 (ttpt) REVERT: D 103 LYS cc_start: 0.7550 (mttt) cc_final: 0.6994 (ttpt) REVERT: E 53 GLU cc_start: 0.8129 (pt0) cc_final: 0.7748 (pm20) REVERT: E 63 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7166 (mt-10) REVERT: E 80 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6927 (tt) REVERT: E 103 LYS cc_start: 0.7543 (mttt) cc_final: 0.6793 (ttpt) REVERT: F 78 SER cc_start: 0.8061 (p) cc_final: 0.7836 (m) REVERT: F 128 ARG cc_start: 0.6909 (OUTLIER) cc_final: 0.4691 (mmm160) outliers start: 9 outliers final: 4 residues processed: 106 average time/residue: 1.6283 time to fit residues: 179.1687 Evaluate side-chains 107 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain F residue 128 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 56 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 34 optimal weight: 0.0980 chunk 20 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.217265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.199797 restraints weight = 17766.920| |-----------------------------------------------------------------------------| r_work (start): 0.4336 rms_B_bonded: 1.11 r_work: 0.4211 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.4103 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7070 Z= 0.157 Angle : 0.612 7.834 9714 Z= 0.355 Chirality : 0.052 0.352 1118 Planarity : 0.003 0.025 1120 Dihedral : 19.678 128.407 1238 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.04 % Allowed : 25.47 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.27), residues: 798 helix: 0.91 (0.39), residues: 186 sheet: 1.11 (0.26), residues: 336 loop : -1.09 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 35 TYR 0.006 0.001 TYR D 108 PHE 0.008 0.001 PHE A 54 TRP 0.008 0.001 TRP B 97 HIS 0.002 0.001 HIS F 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 ( 7070) covalent geometry : angle 0.61171 / 0.35 ( 9714) hydrogen bonds : bond 0.03209 / 2.11 ( 222) hydrogen bonds : angle 5.29825 / 3.57 ( 648) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6944 (mm-30) REVERT: A 103 LYS cc_start: 0.7447 (mttt) cc_final: 0.6956 (tttm) REVERT: B 63 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7208 (mt-10) REVERT: B 103 LYS cc_start: 0.7737 (mttt) cc_final: 0.6922 (ttpp) REVERT: C 103 LYS cc_start: 0.7679 (mttt) cc_final: 0.6870 (ttpt) REVERT: D 103 LYS cc_start: 0.7559 (mttt) cc_final: 0.7018 (ttpt) REVERT: E 53 GLU cc_start: 0.8139 (pt0) cc_final: 0.7749 (pm20) REVERT: E 63 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7197 (mt-10) REVERT: E 80 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7069 (tt) REVERT: E 103 LYS cc_start: 0.7585 (mttt) cc_final: 0.6833 (ttpt) REVERT: F 63 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6477 (mt-10) REVERT: F 128 ARG cc_start: 0.6993 (OUTLIER) cc_final: 0.4623 (mmm160) outliers start: 13 outliers final: 7 residues processed: 105 average time/residue: 1.8536 time to fit residues: 201.5460 Evaluate side-chains 109 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 128 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.221938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.205257 restraints weight = 17758.954| |-----------------------------------------------------------------------------| r_work (start): 0.4398 rms_B_bonded: 1.05 r_work: 0.4266 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.4162 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7070 Z= 0.132 Angle : 0.585 7.252 9714 Z= 0.341 Chirality : 0.052 0.350 1118 Planarity : 0.003 0.023 1120 Dihedral : 19.668 131.969 1238 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.89 % Allowed : 25.47 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.28), residues: 798 helix: 1.04 (0.39), residues: 186 sheet: 1.15 (0.26), residues: 336 loop : -1.01 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 35 TYR 0.009 0.001 TYR E 31 PHE 0.007 0.001 PHE A 54 TRP 0.007 0.001 TRP C 97 HIS 0.002 0.001 HIS C 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 ( 7070) covalent geometry : angle 0.58476 / 0.34 ( 9714) hydrogen bonds : bond 0.02996 / 1.97 ( 222) hydrogen bonds : angle 5.19251 / 3.49 ( 648) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5426.03 seconds wall clock time: 92 minutes 23.04 seconds (5543.04 seconds total)