Starting phenix.real_space_refine on Thu Aug 6 03:58:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i86_52708/08_2026/9i86_52708.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i86_52708/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9i86_52708/08_2026/9i86_52708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i86_52708/08_2026/9i86_52708.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9i86_52708/08_2026/9i86_52708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i86_52708/08_2026/9i86_52708.map" } 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-2.2rc3-6140/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: 2.49, per 1000 atoms: 0.18 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: 1.14 Conformation dependent library (CDL) restraints added in 402.8 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: 1.91 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: 2.14 Time building geometry restraints manager: 1.55 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: 3.440 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: 0.090 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.890 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:10.380 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.360 ------------------------------------------------------------------------------- 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= 0.405 Angle : 0.693 6.184 9714 Z= 0.566 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 0.69309 / 0.57 ( 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 : 0.283 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: 0.6065 (ttpt) REVERT: A 113 LYS cc_start: 0.8399 (mtpm) cc_final: 0.8005 (mttp) REVERT: B 2 GLU cc_start: 0.7387 (tt0) cc_final: 0.6843 (mp0) REVERT: B 103 LYS cc_start: 0.7209 (mttt) cc_final: 0.6097 (ttpm) 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: 0.6357 (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: 0.6075 (ttpt) REVERT: E 2 GLU cc_start: 0.7460 (tt0) cc_final: 0.6839 (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: 0.6492 (mp0) REVERT: F 103 LYS cc_start: 0.6859 (mttt) cc_final: 0.6266 (ttpt) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 1.2584 time to fit residues: 272.1525 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 : 0.368 ------------------------------------------------------------------------------- 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: 1.9990 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 = 0.4553 r_free = 0.4553 target = 0.222887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.206325 restraints weight = 17706.647| |-----------------------------------------------------------------------------| r_work (start): 0.4384 rms_B_bonded: 1.19 r_work: 0.4258 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.4149 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7070 Z= 0.147 Angle : 0.657 8.913 9714 Z= 0.381 Chirality : 0.055 0.372 1118 Planarity : 0.003 0.026 1120 Dihedral : 19.351 121.500 1238 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.04 % Allowed : 23.11 % 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: 0.31 (0.28), residues: 798 helix: -0.21 (0.41), residues: 186 sheet: 1.53 (0.26), residues: 336 loop : -1.16 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 66 TYR 0.006 0.001 TYR A 108 PHE 0.007 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 0.00282 / 0.15 ( 7070) covalent geometry : angle 0.65685 / 0.38 ( 9714) hydrogen bonds : bond 0.04011 / 2.66 ( 222) hydrogen bonds : angle 7.18768 / 4.94 ( 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 136 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7327 (mm-30) REVERT: A 84 VAL cc_start: 0.6347 (p) cc_final: 0.5883 (m) REVERT: A 103 LYS cc_start: 0.7261 (mttt) cc_final: 0.6857 (mmtm) REVERT: A 113 LYS cc_start: 0.8514 (mtpm) cc_final: 0.8242 (mttm) REVERT: B 17 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7143 (mmtt) REVERT: B 63 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7215 (mt-10) REVERT: B 103 LYS cc_start: 0.7275 (mttt) cc_final: 0.6627 (ttpm) REVERT: C 39 VAL cc_start: 0.7669 (t) cc_final: 0.7418 (m) REVERT: C 103 LYS cc_start: 0.7302 (mttt) cc_final: 0.6528 (ttpt) REVERT: D 1 MET cc_start: 0.7367 (tmm) cc_final: 0.7165 (tmm) REVERT: D 2 GLU cc_start: 0.7281 (tt0) cc_final: 0.6654 (mp0) REVERT: D 103 LYS cc_start: 0.7291 (mttt) cc_final: 0.6723 (ttpt) REVERT: E 63 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7062 (mt-10) REVERT: F 2 GLU cc_start: 0.7499 (tt0) cc_final: 0.6921 (mp0) outliers start: 13 outliers final: 3 residues processed: 124 average time/residue: 1.2289 time to fit residues: 159.6315 Evaluate side-chains 116 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 LYS Chi-restraints excluded: chain B residue 25 THR 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: 1.9990 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.4474 r_free = 0.4474 target = 0.214307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.195965 restraints weight = 17784.247| |-----------------------------------------------------------------------------| r_work (start): 0.4296 rms_B_bonded: 1.15 r_work: 0.4162 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.4050 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7070 Z= 0.189 Angle : 0.671 9.363 9714 Z= 0.386 Chirality : 0.055 0.356 1118 Planarity : 0.004 0.030 1120 Dihedral : 19.927 122.475 1238 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.83 % Allowed : 22.33 % 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: 1.60 (0.26), residues: 336 loop : -1.17 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 33 TYR 0.013 0.002 TYR C 31 PHE 0.009 0.001 PHE C 47 TRP 0.007 0.001 TRP B 97 HIS 0.002 0.001 HIS E 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.19 ( 7070) covalent geometry : angle 0.67071 / 0.39 ( 9714) hydrogen bonds : bond 0.03752 / 2.47 ( 222) hydrogen bonds : angle 6.42726 / 4.39 ( 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 132 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7308 (mm-30) REVERT: A 103 LYS cc_start: 0.7471 (mttt) cc_final: 0.6937 (tttm) REVERT: A 113 LYS cc_start: 0.8576 (mtpm) cc_final: 0.8356 (mttm) REVERT: B 63 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7281 (mt-10) REVERT: B 103 LYS cc_start: 0.7401 (mttt) cc_final: 0.6741 (ttpm) REVERT: C 31 TYR cc_start: 0.8472 (p90) cc_final: 0.8111 (p90) REVERT: C 39 VAL cc_start: 0.7752 (t) cc_final: 0.7507 (m) REVERT: C 53 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7462 (mm-30) REVERT: C 103 LYS cc_start: 0.7636 (mttt) cc_final: 0.6869 (ttpt) REVERT: D 1 MET cc_start: 0.7586 (tmm) cc_final: 0.7221 (tmm) REVERT: D 63 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7193 (mt-10) REVERT: D 78 SER cc_start: 0.7959 (p) cc_final: 0.7757 (m) REVERT: D 103 LYS cc_start: 0.7486 (mttt) cc_final: 0.6904 (ttpt) REVERT: E 63 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7174 (mt-10) REVERT: E 80 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7098 (tt) REVERT: F 48 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8141 (mm) REVERT: F 78 SER cc_start: 0.8061 (p) cc_final: 0.7807 (m) outliers start: 18 outliers final: 4 residues processed: 120 average time/residue: 1.4988 time to fit residues: 186.8488 Evaluate side-chains 110 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU 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: 1.9990 chunk 64 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 46 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4486 r_free = 0.4486 target = 0.215543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.198374 restraints weight = 17706.866| |-----------------------------------------------------------------------------| r_work (start): 0.4322 rms_B_bonded: 1.06 r_work: 0.4193 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.4089 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4083 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= 0.139 Angle : 0.609 7.966 9714 Z= 0.353 Chirality : 0.053 0.354 1118 Planarity : 0.003 0.027 1120 Dihedral : 19.868 130.276 1238 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.36 % Allowed : 23.27 % 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: 0.45 (0.28), residues: 798 helix: 0.19 (0.40), residues: 186 sheet: 1.50 (0.26), residues: 336 loop : -1.15 (0.32), 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 0.002 0.001 HIS A 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 ( 7070) covalent geometry : angle 0.60905 / 0.35 ( 9714) hydrogen bonds : bond 0.03294 / 2.18 ( 222) hydrogen bonds : angle 5.99443 / 4.08 ( 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 126 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7307 (mm-30) REVERT: A 103 LYS cc_start: 0.7449 (mttt) cc_final: 0.6938 (tttm) REVERT: A 113 LYS cc_start: 0.8611 (mtpm) cc_final: 0.8387 (mttm) REVERT: B 63 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7273 (mt-10) REVERT: B 103 LYS cc_start: 0.7541 (mttt) cc_final: 0.6937 (ttpm) REVERT: C 31 TYR cc_start: 0.8275 (p90) cc_final: 0.7946 (p90) REVERT: C 39 VAL cc_start: 0.7806 (t) cc_final: 0.7575 (m) REVERT: C 53 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7224 (tt0) REVERT: C 103 LYS cc_start: 0.7556 (mttt) cc_final: 0.6781 (ttpt) REVERT: D 1 MET cc_start: 0.7620 (tmm) cc_final: 0.7232 (tmm) REVERT: D 63 GLU cc_start: 0.7348 (mm-30) cc_final: 0.7134 (mt-10) REVERT: D 103 LYS cc_start: 0.7515 (mttt) cc_final: 0.6916 (ttpt) REVERT: E 63 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7218 (mt-10) REVERT: E 80 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6912 (tt) REVERT: F 63 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6423 (mt-10) REVERT: F 78 SER cc_start: 0.8026 (p) cc_final: 0.7766 (m) outliers start: 15 outliers final: 5 residues processed: 114 average time/residue: 1.6121 time to fit residues: 191.0517 Evaluate side-chains 116 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 109 GLU 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: 2.9990 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4481 r_free = 0.4481 target = 0.214999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.196649 restraints weight = 18052.365| |-----------------------------------------------------------------------------| r_work (start): 0.4303 rms_B_bonded: 1.35 r_work: 0.4169 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.4061 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4367 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= 0.138 Angle : 0.603 8.059 9714 Z= 0.349 Chirality : 0.052 0.353 1118 Planarity : 0.003 0.025 1120 Dihedral : 19.850 130.721 1238 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.83 % Allowed : 23.27 % Favored : 73.90 % 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: 0.46 (0.28), residues: 798 helix: 0.39 (0.39), residues: 186 sheet: 1.40 (0.26), residues: 336 loop : -1.14 (0.31), 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 0.007 0.001 PHE B 54 TRP 0.007 0.001 TRP C 97 HIS 0.002 0.001 HIS A 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 ( 7070) covalent geometry : angle 0.60287 / 0.35 ( 9714) hydrogen bonds : bond 0.03202 / 2.11 ( 222) hydrogen bonds : angle 5.75477 / 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 125 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7299 (mm-30) REVERT: A 103 LYS cc_start: 0.7433 (mttt) cc_final: 0.6902 (tttm) REVERT: A 113 LYS cc_start: 0.8632 (mtpm) cc_final: 0.8383 (mttm) REVERT: B 63 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7289 (mt-10) REVERT: B 103 LYS cc_start: 0.7582 (mttt) cc_final: 0.6928 (ttpm) REVERT: C 31 TYR cc_start: 0.8320 (p90) cc_final: 0.8025 (p90) REVERT: C 39 VAL cc_start: 0.7803 (t) cc_final: 0.7577 (m) REVERT: C 53 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7325 (tt0) REVERT: C 103 LYS cc_start: 0.7536 (mttt) cc_final: 0.6783 (ttpt) REVERT: D 1 MET cc_start: 0.7649 (tmm) cc_final: 0.7209 (tmm) REVERT: D 63 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7134 (mt-10) REVERT: D 103 LYS cc_start: 0.7522 (mttt) cc_final: 0.6929 (ttpt) REVERT: E 63 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7207 (mt-10) REVERT: E 80 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6826 (tt) REVERT: F 63 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6529 (mt-10) REVERT: F 78 SER cc_start: 0.8030 (p) cc_final: 0.7760 (m) outliers start: 18 outliers final: 7 residues processed: 111 average time/residue: 1.7058 time to fit residues: 196.3068 Evaluate side-chains 115 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 E residue 109 GLU 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: 0.9990 chunk 1 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.0070 chunk 61 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.6602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 130 GLN D 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.220283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.203102 restraints weight = 17760.983| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 1.11 r_work: 0.4164 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.4055 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7070 Z= 0.123 Angle : 0.581 7.281 9714 Z= 0.338 Chirality : 0.052 0.352 1118 Planarity : 0.003 0.027 1120 Dihedral : 19.774 136.034 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 : 1.89 % Allowed : 24.69 % Favored : 73.43 % 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: 0.61 (0.28), residues: 798 helix: 0.68 (0.40), residues: 186 sheet: 1.41 (0.26), residues: 336 loop : -1.07 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 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 0.00238 / 0.12 ( 7070) covalent geometry : angle 0.58082 / 0.34 ( 9714) hydrogen bonds : bond 0.02984 / 1.97 ( 222) hydrogen bonds : angle 5.45820 / 3.70 ( 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 119 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7294 (mm-30) REVERT: A 103 LYS cc_start: 0.7430 (mttt) cc_final: 0.6911 (tttm) REVERT: A 113 LYS cc_start: 0.8622 (mtpm) cc_final: 0.8417 (mttm) REVERT: B 63 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7207 (mt-10) REVERT: B 103 LYS cc_start: 0.7614 (mttt) cc_final: 0.6884 (ttpm) REVERT: C 39 VAL cc_start: 0.7841 (t) cc_final: 0.7628 (m) REVERT: C 53 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7370 (tt0) REVERT: C 103 LYS cc_start: 0.7450 (mttt) cc_final: 0.6708 (ttpt) REVERT: D 1 MET cc_start: 0.7700 (tmm) cc_final: 0.7297 (tmm) REVERT: D 63 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7121 (mt-10) REVERT: D 103 LYS cc_start: 0.7473 (mttt) cc_final: 0.6916 (ttpt) REVERT: E 63 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7255 (mt-10) REVERT: E 80 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6813 (tt) REVERT: F 63 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6503 (mt-10) REVERT: F 78 SER cc_start: 0.8074 (p) cc_final: 0.7822 (m) REVERT: F 128 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.4713 (mmm160) outliers start: 12 outliers final: 5 residues processed: 112 average time/residue: 1.6082 time to fit residues: 186.9681 Evaluate side-chains 112 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 109 GLU 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=2.50 ------------------------------------------------------------------------------- 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: 2.9990 chunk 79 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.4486 r_free = 0.4486 target = 0.214850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.197138 restraints weight = 17604.840| |-----------------------------------------------------------------------------| r_work (start): 0.4315 rms_B_bonded: 1.12 r_work: 0.4183 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.4081 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4775 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= 0.193 Angle : 0.659 9.214 9714 Z= 0.378 Chirality : 0.054 0.355 1118 Planarity : 0.004 0.029 1120 Dihedral : 19.847 124.368 1238 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.14 % Allowed : 24.06 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.28), residues: 798 helix: 0.58 (0.39), residues: 186 sheet: 1.20 (0.26), residues: 336 loop : -1.17 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 33 TYR 0.008 0.002 TYR E 31 PHE 0.008 0.002 PHE A 54 TRP 0.009 0.002 TRP C 97 HIS 0.003 0.001 HIS A 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 ( 7070) covalent geometry : angle 0.65900 / 0.38 ( 9714) hydrogen bonds : bond 0.03566 / 2.34 ( 222) hydrogen bonds : angle 5.59571 / 3.80 ( 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 121 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7285 (mm-30) REVERT: A 103 LYS cc_start: 0.7493 (mttt) cc_final: 0.7006 (tttm) REVERT: B 63 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7199 (mt-10) REVERT: B 103 LYS cc_start: 0.7655 (mttt) cc_final: 0.6948 (ttpm) REVERT: C 53 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7447 (tt0) REVERT: C 103 LYS cc_start: 0.7727 (mttt) cc_final: 0.6940 (ttpt) REVERT: D 103 LYS cc_start: 0.7553 (mttt) cc_final: 0.7000 (ttpt) REVERT: E 63 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7209 (mt-10) REVERT: E 80 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7015 (tt) REVERT: F 23 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7928 (pm20) REVERT: F 63 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6412 (mt-10) REVERT: F 78 SER cc_start: 0.8145 (p) cc_final: 0.7894 (m) REVERT: F 128 ARG cc_start: 0.6924 (OUTLIER) cc_final: 0.4670 (mmm160) outliers start: 20 outliers final: 7 residues processed: 110 average time/residue: 1.6942 time to fit residues: 193.3215 Evaluate side-chains 107 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 109 GLU Chi-restraints excluded: chain B residue 128 ARG 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 23 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: 0.0040 chunk 52 optimal weight: 0.0970 chunk 5 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- 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 = 0.4533 r_free = 0.4533 target = 0.219730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.202772 restraints weight = 17782.122| |-----------------------------------------------------------------------------| r_work (start): 0.4366 rms_B_bonded: 1.06 r_work: 0.4236 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.4131 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7070 Z= 0.117 Angle : 0.580 7.007 9714 Z= 0.337 Chirality : 0.052 0.351 1118 Planarity : 0.003 0.025 1120 Dihedral : 19.825 136.723 1238 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.73 % Allowed : 25.79 % 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: 0.59 (0.28), residues: 798 helix: 0.83 (0.40), residues: 186 sheet: 1.27 (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 E 33 TYR 0.004 0.001 TYR F 108 PHE 0.005 0.001 PHE B 92 TRP 0.005 0.001 TRP B 97 HIS 0.001 0.001 HIS C 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.12 ( 7070) covalent geometry : angle 0.58026 / 0.34 ( 9714) hydrogen bonds : bond 0.02890 / 1.89 ( 222) hydrogen bonds : angle 5.27038 / 3.55 ( 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 110 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7274 (mt-10) REVERT: A 103 LYS cc_start: 0.7434 (mttt) cc_final: 0.6935 (tttm) REVERT: B 63 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7206 (mt-10) REVERT: B 103 LYS cc_start: 0.7614 (mttt) cc_final: 0.6845 (ttpt) REVERT: C 39 VAL cc_start: 0.7860 (t) cc_final: 0.7623 (m) REVERT: C 103 LYS cc_start: 0.7588 (mttt) cc_final: 0.6772 (ttpt) REVERT: D 103 LYS cc_start: 0.7520 (mttt) cc_final: 0.6949 (ttpt) REVERT: E 63 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7275 (mt-10) REVERT: E 80 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.6903 (tt) REVERT: F 23 GLU cc_start: 0.8109 (pm20) cc_final: 0.7876 (pm20) REVERT: F 63 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6459 (mt-10) REVERT: F 78 SER cc_start: 0.8062 (p) cc_final: 0.7853 (m) REVERT: F 128 ARG cc_start: 0.6903 (OUTLIER) cc_final: 0.4700 (mmm160) outliers start: 11 outliers final: 6 residues processed: 101 average time/residue: 1.5331 time to fit residues: 160.7947 Evaluate side-chains 105 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 128 ARG 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 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: 1.9990 chunk 64 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 43 optimal weight: 0.0050 chunk 40 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 overall best weight: 1.0198 ------------------------------------------------------------------------------- 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 = 0.217573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.200317 restraints weight = 17778.723| |-----------------------------------------------------------------------------| r_work (start): 0.4343 rms_B_bonded: 1.08 r_work: 0.4210 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.4103 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7070 Z= 0.146 Angle : 0.599 8.072 9714 Z= 0.347 Chirality : 0.052 0.352 1118 Planarity : 0.003 0.026 1120 Dihedral : 19.815 131.219 1238 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.57 % Allowed : 26.10 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.28), residues: 798 helix: 0.85 (0.39), residues: 186 sheet: 1.19 (0.26), residues: 336 loop : -1.04 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 33 TYR 0.006 0.001 TYR D 108 PHE 0.007 0.001 PHE B 54 TRP 0.007 0.001 TRP C 97 HIS 0.002 0.001 HIS A 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.15 ( 7070) covalent geometry : angle 0.59905 / 0.35 ( 9714) hydrogen bonds : bond 0.03102 / 2.05 ( 222) hydrogen bonds : angle 5.24774 / 3.54 ( 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 106 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7300 (mt-10) REVERT: A 103 LYS cc_start: 0.7466 (mttt) cc_final: 0.6950 (tttm) REVERT: B 63 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7236 (mt-10) REVERT: B 103 LYS cc_start: 0.7640 (mttt) cc_final: 0.6889 (ttpm) REVERT: C 53 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7399 (tt0) REVERT: C 103 LYS cc_start: 0.7642 (mttt) cc_final: 0.6840 (ttpt) REVERT: D 103 LYS cc_start: 0.7584 (mttt) cc_final: 0.7013 (ttpt) REVERT: E 63 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7252 (mt-10) REVERT: E 80 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.6978 (tt) REVERT: E 103 LYS cc_start: 0.7559 (mttt) cc_final: 0.6797 (ttpt) REVERT: F 23 GLU cc_start: 0.8122 (pm20) cc_final: 0.7891 (pm20) REVERT: F 63 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6421 (mt-10) REVERT: F 78 SER cc_start: 0.8097 (p) cc_final: 0.7892 (m) REVERT: F 128 ARG cc_start: 0.6968 (OUTLIER) cc_final: 0.4630 (mmm160) outliers start: 10 outliers final: 4 residues processed: 100 average time/residue: 1.6963 time to fit residues: 175.9916 Evaluate side-chains 100 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 128 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 56 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4551 r_free = 0.4551 target = 0.220727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.205594 restraints weight = 17489.318| |-----------------------------------------------------------------------------| r_work (start): 0.4383 rms_B_bonded: 0.98 r_work: 0.4205 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.4107 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7070 Z= 0.143 Angle : 0.604 7.985 9714 Z= 0.349 Chirality : 0.052 0.351 1118 Planarity : 0.003 0.028 1120 Dihedral : 19.828 131.888 1238 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.42 % Allowed : 26.26 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.28), residues: 798 helix: 0.97 (0.39), residues: 186 sheet: 1.15 (0.26), residues: 336 loop : -1.05 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 128 TYR 0.006 0.001 TYR F 108 PHE 0.006 0.001 PHE F 54 TRP 0.007 0.001 TRP B 97 HIS 0.002 0.001 HIS F 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 7070) covalent geometry : angle 0.60422 / 0.35 ( 9714) hydrogen bonds : bond 0.03085 / 2.04 ( 222) hydrogen bonds : angle 5.23270 / 3.53 ( 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 101 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7290 (mt-10) REVERT: A 103 LYS cc_start: 0.7460 (mttt) cc_final: 0.6947 (tttm) REVERT: B 63 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7202 (mt-10) REVERT: B 103 LYS cc_start: 0.7709 (mttt) cc_final: 0.6949 (ttpm) REVERT: C 53 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7350 (tt0) REVERT: C 103 LYS cc_start: 0.7686 (mttt) cc_final: 0.6865 (ttpt) REVERT: D 103 LYS cc_start: 0.7568 (mttt) cc_final: 0.7010 (ttpt) REVERT: E 63 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7233 (mt-10) REVERT: E 80 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7065 (tt) REVERT: E 103 LYS cc_start: 0.7581 (mttt) cc_final: 0.6814 (ttpt) REVERT: F 23 GLU cc_start: 0.8125 (pm20) cc_final: 0.7894 (pm20) REVERT: F 63 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6370 (mt-10) REVERT: F 128 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.4583 (mmm160) outliers start: 9 outliers final: 5 residues processed: 96 average time/residue: 1.6905 time to fit residues: 168.2877 Evaluate side-chains 99 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 109 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 F residue 63 GLU 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: 0.2980 chunk 81 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.4536 r_free = 0.4536 target = 0.219354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.203845 restraints weight = 17527.293| |-----------------------------------------------------------------------------| r_work (start): 0.4370 rms_B_bonded: 0.95 r_work: 0.4195 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.4092 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.5173 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= 0.159 Angle : 0.615 8.190 9714 Z= 0.355 Chirality : 0.053 0.351 1118 Planarity : 0.003 0.027 1120 Dihedral : 19.869 130.061 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 : 1.73 % Allowed : 26.10 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.27), residues: 798 helix: 0.99 (0.39), residues: 186 sheet: 1.13 (0.26), residues: 336 loop : -1.04 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 35 TYR 0.007 0.001 TYR C 31 PHE 0.009 0.001 PHE C 54 TRP 0.008 0.001 TRP C 97 HIS 0.002 0.001 HIS E 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 ( 7070) covalent geometry : angle 0.61517 / 0.35 ( 9714) hydrogen bonds : bond 0.03213 / 2.12 ( 222) hydrogen bonds : angle 5.23959 / 3.53 ( 648) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5366.18 seconds wall clock time: 91 minutes 15.46 seconds (5475.46 seconds total)