Starting phenix.real_space_refine on Sat Aug 23 16:42:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i86_52708/08_2025/9i86_52708.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i86_52708/08_2025/9i86_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_2025/9i86_52708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i86_52708/08_2025/9i86_52708.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9i86_52708/08_2025/9i86_52708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i86_52708/08_2025/9i86_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-2.0-5787/lib/python3.9/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: 2.40, 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: 0.76 Conformation dependent library (CDL) restraints added in 275.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.99 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: 2.63 Time building geometry restraints manager: 1.08 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: 941 0.069 - 0.139: 171 0.139 - 0.208: 0 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: 0.01 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: 2.940 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: 0.070 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.290 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 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 0.051 7070 Z= 0.287 Angle : 0.610 4.636 9714 Z= 0.349 Chirality : 0.051 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 aren 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 covalent geometry : bond 0.00710 ( 7070) covalent geometry : angle 0.61003 ( 9714) hydrogen bonds : bond 0.14601 ( 222) hydrogen bonds : angle 9.30650 ( 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 : 0.213 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: 0.7722 (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: 0.6404 (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: 1.3157 time to fit residues: 283.2057 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 : 0.238 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 105 ASN D 41 GLN D 105 ASN E 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.221276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.202803 restraints weight = 17689.933| |-----------------------------------------------------------------------------| r_work (start): 0.4356 rms_B_bonded: 1.49 r_work: 0.4218 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.4109 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7070 Z= 0.153 Angle : 0.613 4.860 9714 Z= 0.352 Chirality : 0.052 0.358 1118 Planarity : 0.003 0.023 1120 Dihedral : 19.647 138.555 1238 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.42 % Allowed : 23.74 % 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 aren not related in a simple way. whole: 0.47 (0.28), residues: 798 helix: -0.25 (0.40), residues: 186 sheet: 1.78 (0.25), residues: 336 loop : -1.18 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 66 TYR 0.008 0.001 TYR A 108 PHE 0.007 0.001 PHE C 47 TRP 0.005 0.001 TRP E 97 HIS 0.002 0.001 HIS E 19 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 7070) covalent geometry : angle 0.61267 ( 9714) hydrogen bonds : bond 0.03565 ( 222) hydrogen bonds : angle 6.70242 ( 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 123 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7329 (mm-30) REVERT: A 84 VAL cc_start: 0.6216 (p) cc_final: 0.5782 (m) REVERT: A 103 LYS cc_start: 0.7326 (mttt) cc_final: 0.6822 (tttm) REVERT: B 63 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7280 (mt-10) REVERT: B 103 LYS cc_start: 0.7416 (mttt) cc_final: 0.6763 (ttpm) REVERT: C 39 VAL cc_start: 0.7698 (t) cc_final: 0.7469 (m) REVERT: C 103 LYS cc_start: 0.7280 (mttt) cc_final: 0.6525 (ttpt) REVERT: D 1 MET cc_start: 0.7456 (tmm) cc_final: 0.7192 (tmm) REVERT: D 2 GLU cc_start: 0.7410 (tt0) cc_final: 0.6703 (mp0) REVERT: D 103 LYS cc_start: 0.7350 (mttt) cc_final: 0.6781 (ttpt) REVERT: E 63 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7195 (mt-10) REVERT: F 48 ILE cc_start: 0.8299 (mt) cc_final: 0.8055 (mm) REVERT: F 103 LYS cc_start: 0.7456 (mttt) cc_final: 0.7062 (tttt) outliers start: 9 outliers final: 1 residues processed: 117 average time/residue: 1.3440 time to fit residues: 163.6569 Evaluate side-chains 106 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN C 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.212260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.192976 restraints weight = 17794.657| |-----------------------------------------------------------------------------| r_work (start): 0.4266 rms_B_bonded: 1.20 r_work: 0.4139 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.4033 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7070 Z= 0.198 Angle : 0.655 5.625 9714 Z= 0.374 Chirality : 0.053 0.352 1118 Planarity : 0.004 0.026 1120 Dihedral : 20.033 135.379 1238 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.30 % Allowed : 21.70 % 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 aren not related in a simple way. whole: 0.43 (0.28), residues: 798 helix: -0.10 (0.40), residues: 186 sheet: 1.65 (0.26), residues: 336 loop : -1.18 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 35 TYR 0.012 0.002 TYR C 31 PHE 0.008 0.001 PHE C 47 TRP 0.008 0.001 TRP C 97 HIS 0.002 0.001 HIS D 19 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 7070) covalent geometry : angle 0.65487 ( 9714) hydrogen bonds : bond 0.03648 ( 222) hydrogen bonds : angle 6.12390 ( 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 144 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7276 (mm-30) REVERT: A 103 LYS cc_start: 0.7461 (mttt) cc_final: 0.6954 (tttm) REVERT: B 63 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7242 (mt-10) REVERT: B 103 LYS cc_start: 0.7614 (mttt) cc_final: 0.6900 (ttpm) REVERT: C 39 VAL cc_start: 0.7787 (t) cc_final: 0.7557 (m) REVERT: C 53 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7270 (tt0) REVERT: C 103 LYS cc_start: 0.7644 (mttt) cc_final: 0.6879 (ttpt) REVERT: D 1 MET cc_start: 0.7668 (tmm) cc_final: 0.7278 (tmm) REVERT: D 63 GLU cc_start: 0.7410 (mm-30) cc_final: 0.7187 (mt-10) REVERT: D 103 LYS cc_start: 0.7559 (mttt) cc_final: 0.6971 (ttpt) REVERT: E 63 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7230 (mt-10) REVERT: E 80 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6895 (tt) REVERT: F 48 ILE cc_start: 0.8417 (mt) cc_final: 0.8194 (mm) REVERT: F 63 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7092 (mm-30) outliers start: 21 outliers final: 2 residues processed: 129 average time/residue: 1.5788 time to fit residues: 210.7780 Evaluate side-chains 112 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain E residue 74 LYS Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain F residue 63 GLU 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: 2.9990 chunk 5 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 25 optimal weight: 0.1980 chunk 80 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.219519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.201933 restraints weight = 17626.761| |-----------------------------------------------------------------------------| r_work (start): 0.4357 rms_B_bonded: 1.10 r_work: 0.4224 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.4119 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4685 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= 0.133 Angle : 0.578 4.578 9714 Z= 0.332 Chirality : 0.051 0.353 1118 Planarity : 0.003 0.024 1120 Dihedral : 19.886 144.895 1238 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.89 % Allowed : 25.00 % 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 aren not related in a simple way. whole: 0.60 (0.28), residues: 798 helix: 0.31 (0.39), residues: 186 sheet: 1.64 (0.26), residues: 336 loop : -1.14 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 33 TYR 0.007 0.001 TYR E 31 PHE 0.007 0.001 PHE A 54 TRP 0.006 0.001 TRP C 97 HIS 0.002 0.001 HIS A 19 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 7070) covalent geometry : angle 0.57762 ( 9714) hydrogen bonds : bond 0.03037 ( 222) hydrogen bonds : angle 5.61193 ( 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 118 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.254 Fit side-chains REVERT: A 103 LYS cc_start: 0.7414 (mttt) cc_final: 0.6952 (tttm) REVERT: B 63 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7198 (mt-10) REVERT: B 103 LYS cc_start: 0.7650 (mttt) cc_final: 0.6920 (ttpm) REVERT: C 39 VAL cc_start: 0.7822 (t) cc_final: 0.7621 (m) REVERT: C 53 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7404 (tt0) REVERT: C 103 LYS cc_start: 0.7541 (mttt) cc_final: 0.6768 (ttpt) REVERT: D 1 MET cc_start: 0.7693 (tmm) cc_final: 0.7268 (tmm) REVERT: D 103 LYS cc_start: 0.7527 (mttt) cc_final: 0.6967 (ttpt) REVERT: E 63 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7311 (mt-10) REVERT: E 80 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.6995 (tt) REVERT: F 23 GLU cc_start: 0.8104 (pm20) cc_final: 0.7874 (pm20) REVERT: F 63 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.7058 (mm-30) outliers start: 12 outliers final: 4 residues processed: 112 average time/residue: 1.5844 time to fit residues: 183.5124 Evaluate side-chains 111 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 74 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 72 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.218132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.200520 restraints weight = 17908.324| |-----------------------------------------------------------------------------| r_work (start): 0.4345 rms_B_bonded: 1.11 r_work: 0.4211 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.4110 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4941 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= 0.141 Angle : 0.584 4.693 9714 Z= 0.335 Chirality : 0.051 0.351 1118 Planarity : 0.003 0.026 1120 Dihedral : 19.812 144.474 1238 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.67 % Allowed : 24.69 % 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 aren not related in a simple way. whole: 0.62 (0.28), residues: 798 helix: 0.62 (0.39), residues: 186 sheet: 1.46 (0.25), residues: 336 loop : -1.08 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 33 TYR 0.005 0.001 TYR F 108 PHE 0.006 0.001 PHE B 54 TRP 0.008 0.001 TRP C 97 HIS 0.002 0.001 HIS A 19 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 7070) covalent geometry : angle 0.58440 ( 9714) hydrogen bonds : bond 0.03049 ( 222) hydrogen bonds : angle 5.33778 ( 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 124 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6940 (mm-30) REVERT: A 103 LYS cc_start: 0.7420 (mttt) cc_final: 0.6936 (tttm) REVERT: B 63 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7229 (mt-10) REVERT: B 103 LYS cc_start: 0.7681 (mttt) cc_final: 0.6945 (ttpm) REVERT: B 109 GLU cc_start: 0.8328 (tt0) cc_final: 0.8010 (tt0) REVERT: C 39 VAL cc_start: 0.7858 (t) cc_final: 0.7658 (m) REVERT: C 103 LYS cc_start: 0.7626 (mttt) cc_final: 0.6817 (ttpt) REVERT: D 63 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6572 (mt-10) REVERT: D 103 LYS cc_start: 0.7595 (mttt) cc_final: 0.7027 (ttpt) REVERT: E 80 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7069 (tt) REVERT: E 103 LYS cc_start: 0.7572 (mttt) cc_final: 0.6776 (ttpt) REVERT: F 23 GLU cc_start: 0.8108 (pm20) cc_final: 0.7884 (pm20) REVERT: F 63 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7045 (mm-30) outliers start: 17 outliers final: 4 residues processed: 111 average time/residue: 1.6630 time to fit residues: 190.7998 Evaluate side-chains 105 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 46 ASP Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain D residue 63 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: 0.4980 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 31 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.220396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.204489 restraints weight = 17430.789| |-----------------------------------------------------------------------------| r_work (start): 0.4324 rms_B_bonded: 1.00 r_work: 0.4176 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.4072 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7070 Z= 0.149 Angle : 0.587 4.890 9714 Z= 0.336 Chirality : 0.051 0.351 1118 Planarity : 0.003 0.023 1120 Dihedral : 19.866 142.726 1238 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.67 % Allowed : 24.21 % 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 aren not related in a simple way. whole: 0.56 (0.28), residues: 798 helix: 0.73 (0.39), residues: 186 sheet: 1.30 (0.25), residues: 336 loop : -1.05 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 35 TYR 0.005 0.001 TYR F 108 PHE 0.008 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 covalent geometry : bond 0.00341 ( 7070) covalent geometry : angle 0.58734 ( 9714) hydrogen bonds : bond 0.03071 ( 222) hydrogen bonds : angle 5.27077 ( 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 120 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6911 (mm-30) REVERT: A 103 LYS cc_start: 0.7455 (mttt) cc_final: 0.6996 (tttm) REVERT: B 63 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7206 (mt-10) REVERT: B 103 LYS cc_start: 0.7710 (mttt) cc_final: 0.6977 (tttm) REVERT: B 109 GLU cc_start: 0.8347 (tt0) cc_final: 0.8086 (tt0) REVERT: C 39 VAL cc_start: 0.7948 (t) cc_final: 0.7734 (m) REVERT: C 103 LYS cc_start: 0.7593 (mttt) cc_final: 0.6790 (ttpt) REVERT: D 63 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6562 (mt-10) REVERT: D 103 LYS cc_start: 0.7529 (mttt) cc_final: 0.7003 (ttpt) REVERT: E 80 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7111 (tt) REVERT: E 103 LYS cc_start: 0.7591 (mttt) cc_final: 0.6809 (ttpt) REVERT: F 23 GLU cc_start: 0.8070 (pm20) cc_final: 0.7834 (pm20) REVERT: F 63 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7068 (mm-30) REVERT: F 128 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.4542 (mmm160) outliers start: 17 outliers final: 5 residues processed: 110 average time/residue: 1.6042 time to fit residues: 182.8289 Evaluate side-chains 109 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain D residue 63 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: 2.9990 chunk 80 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.220086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.204894 restraints weight = 17350.274| |-----------------------------------------------------------------------------| r_work (start): 0.4375 rms_B_bonded: 0.99 r_work: 0.4199 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.4092 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.5262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7070 Z= 0.151 Angle : 0.589 4.916 9714 Z= 0.338 Chirality : 0.051 0.350 1118 Planarity : 0.003 0.024 1120 Dihedral : 19.858 142.917 1238 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.67 % Allowed : 24.69 % 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 aren not related in a simple way. whole: 0.58 (0.28), residues: 798 helix: 0.90 (0.39), residues: 186 sheet: 1.23 (0.26), residues: 336 loop : -1.05 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 35 TYR 0.007 0.001 TYR E 31 PHE 0.008 0.001 PHE A 54 TRP 0.006 0.001 TRP C 97 HIS 0.002 0.001 HIS C 19 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 7070) covalent geometry : angle 0.58880 ( 9714) hydrogen bonds : bond 0.03092 ( 222) hydrogen bonds : angle 5.20273 ( 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 115 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6916 (mm-30) REVERT: A 103 LYS cc_start: 0.7482 (mttt) cc_final: 0.6984 (tttm) REVERT: B 55 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7982 (tt0) REVERT: B 63 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7230 (mt-10) REVERT: B 103 LYS cc_start: 0.7780 (mttt) cc_final: 0.7024 (ttpm) REVERT: B 109 GLU cc_start: 0.8297 (tt0) cc_final: 0.8004 (tt0) REVERT: C 103 LYS cc_start: 0.7709 (mttt) cc_final: 0.6838 (ttpt) REVERT: D 63 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6560 (mt-10) REVERT: D 103 LYS cc_start: 0.7490 (mttt) cc_final: 0.6969 (ttpt) REVERT: E 53 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7801 (pm20) REVERT: E 80 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7145 (tt) REVERT: E 103 LYS cc_start: 0.7582 (mttt) cc_final: 0.6785 (ttpt) REVERT: F 23 GLU cc_start: 0.8086 (pm20) cc_final: 0.7836 (pm20) REVERT: F 63 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7067 (mm-30) REVERT: F 128 ARG cc_start: 0.7079 (OUTLIER) cc_final: 0.4546 (mmm160) outliers start: 17 outliers final: 6 residues processed: 106 average time/residue: 1.6787 time to fit residues: 184.0616 Evaluate side-chains 107 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 55 GLU 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 53 GLU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 124 LEU 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: 0.5980 chunk 52 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.220764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.205167 restraints weight = 17549.022| |-----------------------------------------------------------------------------| r_work (start): 0.4333 rms_B_bonded: 1.01 r_work: 0.4192 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.4080 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.5376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7070 Z= 0.134 Angle : 0.569 4.470 9714 Z= 0.327 Chirality : 0.051 0.349 1118 Planarity : 0.003 0.022 1120 Dihedral : 19.774 146.176 1238 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.20 % Allowed : 25.47 % 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 aren not related in a simple way. whole: 0.54 (0.28), residues: 798 helix: 1.07 (0.39), residues: 186 sheet: 0.71 (0.25), residues: 366 loop : -0.60 (0.34), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 35 TYR 0.004 0.001 TYR F 108 PHE 0.007 0.001 PHE B 54 TRP 0.006 0.001 TRP C 97 HIS 0.002 0.001 HIS A 19 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 7070) covalent geometry : angle 0.56946 ( 9714) hydrogen bonds : bond 0.02874 ( 222) hydrogen bonds : angle 5.05404 ( 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: 14 poor density : 96 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6857 (mm-30) REVERT: A 103 LYS cc_start: 0.7481 (mttt) cc_final: 0.7011 (tttm) REVERT: B 55 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.8022 (tt0) REVERT: B 63 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7219 (mt-10) REVERT: B 103 LYS cc_start: 0.7814 (mttt) cc_final: 0.7075 (tttm) REVERT: B 109 GLU cc_start: 0.8301 (tt0) cc_final: 0.7995 (tt0) REVERT: C 103 LYS cc_start: 0.7704 (mttt) cc_final: 0.6845 (ttpt) REVERT: D 63 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6567 (mt-10) REVERT: D 103 LYS cc_start: 0.7482 (mttt) cc_final: 0.6968 (ttpt) REVERT: E 103 LYS cc_start: 0.7546 (mttt) cc_final: 0.6761 (ttpt) REVERT: F 23 GLU cc_start: 0.8058 (pm20) cc_final: 0.7790 (pm20) REVERT: F 63 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7018 (mm-30) REVERT: F 128 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.4509 (mmm160) outliers start: 14 outliers final: 5 residues processed: 103 average time/residue: 1.6223 time to fit residues: 172.9842 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 : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 124 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: 1.9990 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4546 r_free = 0.4546 target = 0.220595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.204018 restraints weight = 17739.201| |-----------------------------------------------------------------------------| r_work (start): 0.4379 rms_B_bonded: 1.07 r_work: 0.4246 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.4137 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7070 Z= 0.138 Angle : 0.575 4.677 9714 Z= 0.330 Chirality : 0.051 0.349 1118 Planarity : 0.003 0.023 1120 Dihedral : 19.764 144.745 1238 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 1.73 % Allowed : 25.63 % 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 aren not related in a simple way. whole: 0.55 (0.28), residues: 798 helix: 1.18 (0.39), residues: 186 sheet: 0.65 (0.25), residues: 366 loop : -0.58 (0.34), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 35 TYR 0.005 0.001 TYR E 31 PHE 0.010 0.001 PHE D 54 TRP 0.006 0.001 TRP C 97 HIS 0.002 0.001 HIS A 19 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 7070) covalent geometry : angle 0.57512 ( 9714) hydrogen bonds : bond 0.02943 ( 222) hydrogen bonds : angle 5.02383 ( 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: 11 poor density : 95 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6900 (mm-30) REVERT: A 103 LYS cc_start: 0.7473 (mttt) cc_final: 0.7013 (tttm) REVERT: B 55 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.8033 (tt0) REVERT: B 63 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7250 (mt-10) REVERT: B 103 LYS cc_start: 0.7829 (mttt) cc_final: 0.7066 (tttm) REVERT: B 109 GLU cc_start: 0.8306 (tt0) cc_final: 0.8000 (tt0) REVERT: C 53 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7444 (tt0) REVERT: C 103 LYS cc_start: 0.7748 (mttt) cc_final: 0.6846 (ttpt) REVERT: D 63 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6550 (mt-10) REVERT: D 103 LYS cc_start: 0.7499 (mttt) cc_final: 0.6985 (ttpt) REVERT: E 80 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7182 (tt) REVERT: E 103 LYS cc_start: 0.7560 (mttt) cc_final: 0.6767 (ttpt) REVERT: F 23 GLU cc_start: 0.8038 (pm20) cc_final: 0.7822 (pm20) REVERT: F 63 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7043 (mm-30) REVERT: F 128 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.4568 (mmm160) outliers start: 11 outliers final: 4 residues processed: 101 average time/residue: 1.6389 time to fit residues: 171.3474 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 : 0.208 ------------------------------------------------------------------------------- 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 55 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 E residue 124 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 56 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 0.0000 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 0.2980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.221783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.205577 restraints weight = 17767.500| |-----------------------------------------------------------------------------| r_work (start): 0.4393 rms_B_bonded: 1.03 r_work: 0.4257 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.4154 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.5507 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= 0.127 Angle : 0.564 4.453 9714 Z= 0.323 Chirality : 0.051 0.349 1118 Planarity : 0.003 0.022 1120 Dihedral : 19.719 147.630 1238 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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 aren not related in a simple way. whole: 0.63 (0.28), residues: 798 helix: 1.31 (0.39), residues: 186 sheet: 0.66 (0.25), residues: 366 loop : -0.52 (0.34), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 35 TYR 0.005 0.001 TYR E 31 PHE 0.007 0.001 PHE B 54 TRP 0.006 0.001 TRP C 97 HIS 0.002 0.001 HIS A 19 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 7070) covalent geometry : angle 0.56409 ( 9714) hydrogen bonds : bond 0.02774 ( 222) hydrogen bonds : angle 4.94591 ( 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 116 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6845 (mm-30) REVERT: A 103 LYS cc_start: 0.7462 (mttt) cc_final: 0.6986 (tttm) REVERT: B 55 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.8010 (tt0) REVERT: B 63 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7230 (mt-10) REVERT: B 103 LYS cc_start: 0.7823 (mttt) cc_final: 0.7066 (tttm) REVERT: B 109 GLU cc_start: 0.8279 (tt0) cc_final: 0.7970 (tt0) REVERT: C 39 VAL cc_start: 0.7926 (t) cc_final: 0.7654 (m) REVERT: C 103 LYS cc_start: 0.7773 (mttt) cc_final: 0.6872 (ttpt) REVERT: D 63 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6540 (mt-10) REVERT: D 103 LYS cc_start: 0.7487 (mttt) cc_final: 0.6966 (ttpt) REVERT: E 53 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7790 (pm20) REVERT: E 80 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7145 (tt) REVERT: E 103 LYS cc_start: 0.7534 (mttt) cc_final: 0.6749 (ttpt) REVERT: F 23 GLU cc_start: 0.8037 (pm20) cc_final: 0.7817 (pm20) REVERT: F 63 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7042 (mm-30) REVERT: F 128 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.4572 (mmm160) outliers start: 13 outliers final: 3 residues processed: 110 average time/residue: 1.6219 time to fit residues: 184.5805 Evaluate side-chains 109 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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 55 GLU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 112 VAL 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 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: 0.0980 chunk 81 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 52 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.219131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.202381 restraints weight = 17628.298| |-----------------------------------------------------------------------------| r_work (start): 0.4367 rms_B_bonded: 1.09 r_work: 0.4234 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.4128 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.5542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7070 Z= 0.158 Angle : 0.594 5.070 9714 Z= 0.340 Chirality : 0.052 0.353 1118 Planarity : 0.003 0.024 1120 Dihedral : 19.806 141.564 1238 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 1.73 % Allowed : 25.16 % 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 aren not related in a simple way. whole: 0.56 (0.28), residues: 798 helix: 1.31 (0.38), residues: 186 sheet: 0.58 (0.25), residues: 366 loop : -0.56 (0.34), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 35 TYR 0.006 0.001 TYR D 108 PHE 0.008 0.001 PHE F 54 TRP 0.006 0.001 TRP C 97 HIS 0.002 0.001 HIS C 19 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 7070) covalent geometry : angle 0.59417 ( 9714) hydrogen bonds : bond 0.03088 ( 222) hydrogen bonds : angle 5.07147 ( 648) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5009.63 seconds wall clock time: 85 minutes 7.65 seconds (5107.65 seconds total)