Starting phenix.real_space_refine on Thu May 15 17:02:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i86_52708/05_2025/9i86_52708.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i86_52708/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9i86_52708/05_2025/9i86_52708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i86_52708/05_2025/9i86_52708.map" model { file = "/net/cci-nas-00/data/ceres_data/9i86_52708/05_2025/9i86_52708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i86_52708/05_2025/9i86_52708.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 6.97, per 1000 atoms: 0.51 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: 3.28 Conformation dependent library (CDL) restraints added in 952.0 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: 5.95 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: 4.33 Time building geometry restraints manager: 3.96 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: 0.06 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: 2.880 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: 0.230 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 34.300 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 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:14.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.990 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (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 TRP 0.004 0.001 TRP F 97 HIS 0.000 0.000 HIS A 19 PHE 0.004 0.001 PHE D 44 TYR 0.005 0.001 TYR A 108 ARG 0.001 0.000 ARG A 128 Details of bonding type rmsd hydrogen bonds : bond 0.14601 ( 222) hydrogen bonds : angle 9.30650 ( 648) covalent geometry : bond 0.00710 ( 7070) covalent geometry : angle 0.61003 ( 9714) *********************** 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 : 0.937 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: 0.6046 (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: 0.6354 (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: 0.6841 (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: 0.6275 (ttpt) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 3.0303 time to fit residues: 653.2509 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 : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 ASN D 24 ASN D 41 GLN E 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.220146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.202655 restraints weight = 17420.879| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 1.11 r_work: 0.4226 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.4125 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7070 Z= 0.156 Angle : 0.625 5.064 9714 Z= 0.358 Chirality : 0.052 0.360 1118 Planarity : 0.004 0.024 1120 Dihedral : 19.694 137.649 1238 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.73 % Allowed : 23.58 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.28), residues: 798 helix: -0.28 (0.40), residues: 186 sheet: 1.79 (0.25), residues: 336 loop : -1.19 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 97 HIS 0.002 0.001 HIS E 19 PHE 0.007 0.001 PHE B 54 TYR 0.012 0.002 TYR C 31 ARG 0.003 0.001 ARG F 66 Details of bonding type rmsd hydrogen bonds : bond 0.03523 ( 222) hydrogen bonds : angle 6.65543 ( 648) covalent geometry : bond 0.00348 ( 7070) covalent geometry : angle 0.62462 ( 9714) *********************** 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 128 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7308 (mm-30) REVERT: A 84 VAL cc_start: 0.6252 (p) cc_final: 0.5817 (m) REVERT: A 103 LYS cc_start: 0.7344 (mttt) cc_final: 0.6839 (tttm) REVERT: B 63 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7251 (mt-10) REVERT: B 103 LYS cc_start: 0.7415 (mttt) cc_final: 0.6778 (ttpm) REVERT: C 31 TYR cc_start: 0.8417 (p90) cc_final: 0.8121 (p90) REVERT: C 39 VAL cc_start: 0.7656 (t) cc_final: 0.7429 (m) REVERT: C 103 LYS cc_start: 0.7307 (mttt) cc_final: 0.6571 (ttpt) REVERT: D 1 MET cc_start: 0.7456 (tmm) cc_final: 0.7172 (tmm) REVERT: D 63 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7125 (mt-10) REVERT: D 78 SER cc_start: 0.7922 (p) cc_final: 0.7690 (m) REVERT: D 103 LYS cc_start: 0.7341 (mttt) cc_final: 0.6787 (ttpt) REVERT: E 63 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7158 (mt-10) REVERT: F 48 ILE cc_start: 0.8311 (mt) cc_final: 0.8073 (mm) REVERT: F 103 LYS cc_start: 0.7468 (mttt) cc_final: 0.7080 (tttt) outliers start: 11 outliers final: 1 residues processed: 121 average time/residue: 3.2358 time to fit residues: 407.6314 Evaluate side-chains 109 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 73 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.4443 r_free = 0.4443 target = 0.210895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.191825 restraints weight = 17763.458| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 1.17 r_work: 0.4134 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.4025 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7070 Z= 0.211 Angle : 0.671 5.961 9714 Z= 0.382 Chirality : 0.054 0.353 1118 Planarity : 0.004 0.027 1120 Dihedral : 20.148 133.755 1238 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.46 % Allowed : 21.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.28), residues: 798 helix: -0.19 (0.39), residues: 186 sheet: 1.60 (0.26), residues: 336 loop : -1.21 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 97 HIS 0.003 0.001 HIS C 19 PHE 0.008 0.002 PHE C 47 TYR 0.008 0.002 TYR C 31 ARG 0.002 0.000 ARG E 128 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 222) hydrogen bonds : angle 6.15470 ( 648) covalent geometry : bond 0.00488 ( 7070) covalent geometry : angle 0.67106 ( 9714) *********************** 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: 22 poor density : 122 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7296 (mm-30) REVERT: A 103 LYS cc_start: 0.7479 (mttt) cc_final: 0.6969 (tttm) REVERT: B 63 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7227 (mt-10) REVERT: B 103 LYS cc_start: 0.7618 (mttt) cc_final: 0.6896 (ttpm) REVERT: C 53 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7403 (tt0) REVERT: C 103 LYS cc_start: 0.7629 (mttt) cc_final: 0.6916 (ttpt) REVERT: D 1 MET cc_start: 0.7664 (tmm) cc_final: 0.7301 (tmm) REVERT: D 103 LYS cc_start: 0.7518 (mttt) cc_final: 0.6933 (ttpt) REVERT: E 63 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7251 (mt-10) REVERT: E 80 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6931 (tt) REVERT: F 48 ILE cc_start: 0.8429 (mt) cc_final: 0.8199 (mm) REVERT: F 63 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6979 (mm-30) outliers start: 22 outliers final: 2 residues processed: 127 average time/residue: 3.6462 time to fit residues: 481.6822 Evaluate side-chains 115 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain 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 71 optimal weight: 2.9990 chunk 80 optimal weight: 0.3980 chunk 78 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 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 = 0.4518 r_free = 0.4518 target = 0.218362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.200737 restraints weight = 17544.668| |-----------------------------------------------------------------------------| r_work (start): 0.4347 rms_B_bonded: 1.12 r_work: 0.4214 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.4111 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4710 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= 0.139 Angle : 0.587 4.679 9714 Z= 0.337 Chirality : 0.051 0.352 1118 Planarity : 0.003 0.025 1120 Dihedral : 19.952 142.925 1238 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.42 % Allowed : 25.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.28), residues: 798 helix: 0.22 (0.39), residues: 186 sheet: 1.59 (0.26), residues: 336 loop : -1.18 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 97 HIS 0.002 0.001 HIS C 19 PHE 0.008 0.001 PHE B 92 TYR 0.005 0.001 TYR F 108 ARG 0.002 0.000 ARG E 33 Details of bonding type rmsd hydrogen bonds : bond 0.03080 ( 222) hydrogen bonds : angle 5.62374 ( 648) covalent geometry : bond 0.00311 ( 7070) covalent geometry : angle 0.58710 ( 9714) *********************** 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 116 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: A 103 LYS cc_start: 0.7478 (mttt) cc_final: 0.6999 (tttm) REVERT: B 63 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7212 (mt-10) REVERT: B 103 LYS cc_start: 0.7661 (mttt) cc_final: 0.6931 (ttpm) REVERT: C 39 VAL cc_start: 0.7770 (t) cc_final: 0.7532 (m) REVERT: C 53 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7465 (tt0) REVERT: C 103 LYS cc_start: 0.7571 (mttt) cc_final: 0.6775 (ttpt) REVERT: D 63 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6661 (mt-10) REVERT: D 103 LYS cc_start: 0.7500 (mttt) cc_final: 0.6952 (ttpt) REVERT: E 63 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7306 (mt-10) REVERT: F 23 GLU cc_start: 0.8119 (pm20) cc_final: 0.7872 (pm20) REVERT: F 63 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.7014 (mm-30) outliers start: 9 outliers final: 4 residues processed: 109 average time/residue: 3.7702 time to fit residues: 425.2095 Evaluate side-chains 108 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 D residue 63 GLU Chi-restraints excluded: chain E residue 53 GLU 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 76 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 43 optimal weight: 0.0170 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- 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 = 0.4521 r_free = 0.4521 target = 0.218670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.201110 restraints weight = 17715.134| |-----------------------------------------------------------------------------| r_work (start): 0.4349 rms_B_bonded: 1.12 r_work: 0.4221 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.4111 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4922 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= 0.134 Angle : 0.576 4.524 9714 Z= 0.331 Chirality : 0.051 0.351 1118 Planarity : 0.003 0.024 1120 Dihedral : 19.838 146.169 1238 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.20 % Allowed : 24.84 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.28), residues: 798 helix: 0.58 (0.39), residues: 186 sheet: 1.43 (0.26), residues: 336 loop : -1.13 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 97 HIS 0.001 0.001 HIS C 19 PHE 0.009 0.001 PHE C 54 TYR 0.005 0.001 TYR C 110 ARG 0.003 0.000 ARG C 66 Details of bonding type rmsd hydrogen bonds : bond 0.02954 ( 222) hydrogen bonds : angle 5.26790 ( 648) covalent geometry : bond 0.00305 ( 7070) covalent geometry : angle 0.57582 ( 9714) *********************** 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 114 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6974 (mm-30) REVERT: A 103 LYS cc_start: 0.7433 (mttt) cc_final: 0.6943 (tttm) REVERT: B 63 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7234 (mt-10) REVERT: B 103 LYS cc_start: 0.7674 (mttt) cc_final: 0.6910 (ttpm) REVERT: B 109 GLU cc_start: 0.8314 (tt0) cc_final: 0.7997 (tt0) REVERT: C 39 VAL cc_start: 0.7761 (t) cc_final: 0.7533 (m) REVERT: C 103 LYS cc_start: 0.7634 (mttt) cc_final: 0.6805 (ttpt) REVERT: D 63 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6631 (mt-10) REVERT: D 103 LYS cc_start: 0.7551 (mttt) cc_final: 0.6997 (ttpt) REVERT: E 80 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.6957 (tt) REVERT: E 103 LYS cc_start: 0.7564 (mttt) cc_final: 0.6773 (ttpt) REVERT: F 63 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.7004 (mm-30) outliers start: 14 outliers final: 3 residues processed: 106 average time/residue: 3.8259 time to fit residues: 419.6625 Evaluate side-chains 103 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain 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 4 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 47 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 = 0.4471 r_free = 0.4471 target = 0.213343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.195469 restraints weight = 17791.087| |-----------------------------------------------------------------------------| r_work (start): 0.4298 rms_B_bonded: 1.09 r_work: 0.4166 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.4060 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7070 Z= 0.212 Angle : 0.647 6.136 9714 Z= 0.369 Chirality : 0.053 0.352 1118 Planarity : 0.004 0.028 1120 Dihedral : 20.105 134.292 1238 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.83 % Allowed : 23.58 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.28), residues: 798 helix: 0.52 (0.39), residues: 186 sheet: 1.22 (0.26), residues: 336 loop : -1.13 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 97 HIS 0.004 0.002 HIS A 19 PHE 0.007 0.002 PHE B 54 TYR 0.012 0.002 TYR C 31 ARG 0.002 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.03534 ( 222) hydrogen bonds : angle 5.45736 ( 648) covalent geometry : bond 0.00497 ( 7070) covalent geometry : angle 0.64747 ( 9714) *********************** 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 122 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 1.000 Fit side-chains REVERT: A 63 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6977 (mm-30) REVERT: A 103 LYS cc_start: 0.7529 (mttt) cc_final: 0.7032 (tttm) REVERT: B 63 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7240 (mt-10) REVERT: B 103 LYS cc_start: 0.7804 (mttt) cc_final: 0.7021 (tttm) REVERT: C 53 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7552 (tt0) REVERT: C 63 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.7084 (mt-10) REVERT: C 103 LYS cc_start: 0.7695 (mttt) cc_final: 0.6855 (ttpt) REVERT: C 109 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7826 (tt0) REVERT: D 63 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6740 (mt-10) REVERT: D 103 LYS cc_start: 0.7551 (mttt) cc_final: 0.7009 (ttpt) REVERT: E 80 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7150 (tt) REVERT: E 103 LYS cc_start: 0.7631 (mttt) cc_final: 0.6834 (ttpt) REVERT: F 23 GLU cc_start: 0.8124 (pm20) cc_final: 0.7878 (pm20) REVERT: F 63 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7028 (mm-30) outliers start: 18 outliers final: 8 residues processed: 113 average time/residue: 3.7394 time to fit residues: 437.7604 Evaluate side-chains 114 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 B residue 53 GLU Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain D residue 38 LYS 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 18 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.220349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.205573 restraints weight = 17415.048| |-----------------------------------------------------------------------------| r_work (start): 0.4379 rms_B_bonded: 0.93 r_work: 0.4206 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.4097 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7070 Z= 0.145 Angle : 0.588 4.796 9714 Z= 0.338 Chirality : 0.051 0.351 1118 Planarity : 0.003 0.026 1120 Dihedral : 19.922 142.358 1238 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.28), residues: 798 helix: 0.72 (0.39), residues: 186 sheet: 1.22 (0.26), residues: 336 loop : -1.11 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 97 HIS 0.002 0.001 HIS C 19 PHE 0.009 0.001 PHE E 92 TYR 0.005 0.001 TYR F 108 ARG 0.002 0.000 ARG E 33 Details of bonding type rmsd hydrogen bonds : bond 0.03045 ( 222) hydrogen bonds : angle 5.23578 ( 648) covalent geometry : bond 0.00328 ( 7070) covalent geometry : angle 0.58808 ( 9714) *********************** 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: 17 poor density : 104 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6912 (mm-30) REVERT: A 103 LYS cc_start: 0.7516 (mttt) cc_final: 0.7023 (tttm) REVERT: B 63 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7231 (mt-10) REVERT: B 103 LYS cc_start: 0.7821 (mttt) cc_final: 0.7035 (tttm) REVERT: B 109 GLU cc_start: 0.8294 (tt0) cc_final: 0.8034 (tt0) REVERT: C 53 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7513 (tt0) REVERT: C 103 LYS cc_start: 0.7653 (mttt) cc_final: 0.6835 (ttpt) REVERT: C 109 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7865 (tt0) REVERT: D 63 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6723 (mt-10) REVERT: D 103 LYS cc_start: 0.7494 (mttt) cc_final: 0.6964 (ttpt) REVERT: E 80 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7139 (tt) REVERT: E 103 LYS cc_start: 0.7576 (mttt) cc_final: 0.6792 (ttpt) REVERT: F 23 GLU cc_start: 0.8111 (pm20) cc_final: 0.7853 (pm20) REVERT: F 63 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6970 (mm-30) REVERT: F 128 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.4535 (mmm160) outliers start: 17 outliers final: 5 residues processed: 111 average time/residue: 3.8408 time to fit residues: 441.1099 Evaluate side-chains 112 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain C residue 109 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 34 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 43 optimal weight: 0.0980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.220145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.203521 restraints weight = 17731.378| |-----------------------------------------------------------------------------| r_work (start): 0.4374 rms_B_bonded: 1.06 r_work: 0.4241 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.4147 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5370 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= 0.139 Angle : 0.580 4.687 9714 Z= 0.333 Chirality : 0.051 0.350 1118 Planarity : 0.003 0.026 1120 Dihedral : 19.801 145.019 1238 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.52 % Allowed : 24.21 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.28), residues: 798 helix: 0.92 (0.39), residues: 186 sheet: 0.62 (0.25), residues: 366 loop : -0.65 (0.34), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 97 HIS 0.001 0.001 HIS A 19 PHE 0.007 0.001 PHE B 54 TYR 0.005 0.001 TYR F 108 ARG 0.003 0.000 ARG C 33 Details of bonding type rmsd hydrogen bonds : bond 0.02930 ( 222) hydrogen bonds : angle 5.06700 ( 648) covalent geometry : bond 0.00318 ( 7070) covalent geometry : angle 0.57999 ( 9714) *********************** 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 117 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.7639 (mpp-170) cc_final: 0.7350 (mpp-170) REVERT: A 63 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6873 (mm-30) REVERT: A 103 LYS cc_start: 0.7478 (mttt) cc_final: 0.7023 (tttm) REVERT: B 63 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7225 (mt-10) REVERT: B 103 LYS cc_start: 0.7850 (mttt) cc_final: 0.7089 (tttm) REVERT: B 109 GLU cc_start: 0.8260 (tt0) cc_final: 0.7963 (tt0) REVERT: C 103 LYS cc_start: 0.7706 (mttt) cc_final: 0.6856 (ttpt) REVERT: D 63 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6658 (mt-10) REVERT: D 103 LYS cc_start: 0.7481 (mttt) cc_final: 0.6964 (ttpt) REVERT: E 80 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7134 (tt) REVERT: E 103 LYS cc_start: 0.7539 (mttt) cc_final: 0.6753 (ttpt) REVERT: F 23 GLU cc_start: 0.8061 (pm20) cc_final: 0.7860 (pm20) REVERT: F 63 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6999 (mm-30) REVERT: F 128 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.4555 (mmm160) outliers start: 16 outliers final: 4 residues processed: 110 average time/residue: 3.9452 time to fit residues: 449.0252 Evaluate side-chains 110 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain B residue 25 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 68 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.4507 r_free = 0.4507 target = 0.216165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.200741 restraints weight = 17395.034| |-----------------------------------------------------------------------------| r_work (start): 0.4361 rms_B_bonded: 0.96 r_work: 0.4229 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.4125 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.5469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7070 Z= 0.203 Angle : 0.640 5.860 9714 Z= 0.365 Chirality : 0.053 0.351 1118 Planarity : 0.004 0.028 1120 Dihedral : 20.073 135.402 1238 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.04 % Allowed : 24.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.28), residues: 798 helix: 0.85 (0.38), residues: 186 sheet: 0.53 (0.25), residues: 366 loop : -0.68 (0.33), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 97 HIS 0.004 0.002 HIS A 19 PHE 0.010 0.001 PHE D 54 TYR 0.007 0.002 TYR D 108 ARG 0.003 0.001 ARG A 35 Details of bonding type rmsd hydrogen bonds : bond 0.03474 ( 222) hydrogen bonds : angle 5.26737 ( 648) covalent geometry : bond 0.00473 ( 7070) covalent geometry : angle 0.64017 ( 9714) *********************** 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 123 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 1.028 Fit side-chains REVERT: A 63 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6912 (mm-30) REVERT: A 103 LYS cc_start: 0.7505 (mttt) cc_final: 0.7064 (tttm) REVERT: B 63 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7203 (mt-10) REVERT: B 103 LYS cc_start: 0.7827 (mttt) cc_final: 0.7078 (tttm) REVERT: C 7 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8054 (tp) REVERT: C 53 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7503 (tt0) REVERT: C 103 LYS cc_start: 0.7815 (mttt) cc_final: 0.6904 (ttpt) REVERT: D 63 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6643 (mt-10) REVERT: D 103 LYS cc_start: 0.7497 (mttt) cc_final: 0.6991 (ttpt) REVERT: E 80 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7228 (tt) REVERT: E 103 LYS cc_start: 0.7560 (mttt) cc_final: 0.6821 (ttpt) REVERT: F 23 GLU cc_start: 0.8052 (pm20) cc_final: 0.7813 (pm20) REVERT: F 63 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6997 (mm-30) REVERT: F 128 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.4573 (mmm160) outliers start: 13 outliers final: 7 residues processed: 118 average time/residue: 3.5660 time to fit residues: 435.9419 Evaluate side-chains 121 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 53 GLU Chi-restraints excluded: chain C residue 7 LEU 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 112 VAL Chi-restraints excluded: chain F residue 128 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 55 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 71 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4543 r_free = 0.4543 target = 0.220820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.204304 restraints weight = 17677.864| |-----------------------------------------------------------------------------| r_work (start): 0.4384 rms_B_bonded: 1.06 r_work: 0.4247 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.4155 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.5595 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= 0.129 Angle : 0.576 4.473 9714 Z= 0.330 Chirality : 0.051 0.349 1118 Planarity : 0.003 0.025 1120 Dihedral : 19.877 146.498 1238 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.57 % Allowed : 25.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.28), residues: 798 helix: 1.12 (0.38), residues: 186 sheet: 0.59 (0.25), residues: 366 loop : -0.60 (0.34), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 97 HIS 0.001 0.001 HIS D 19 PHE 0.007 0.001 PHE B 54 TYR 0.004 0.001 TYR C 110 ARG 0.004 0.000 ARG A 35 Details of bonding type rmsd hydrogen bonds : bond 0.02823 ( 222) hydrogen bonds : angle 4.99341 ( 648) covalent geometry : bond 0.00295 ( 7070) covalent geometry : angle 0.57579 ( 9714) ********************** 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: 10 poor density : 106 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6791 (mm-30) REVERT: A 103 LYS cc_start: 0.7449 (mttt) cc_final: 0.6988 (tttm) REVERT: B 63 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7250 (mt-10) REVERT: B 103 LYS cc_start: 0.7810 (mttt) cc_final: 0.7052 (tttm) REVERT: B 109 GLU cc_start: 0.8256 (tt0) cc_final: 0.7956 (tt0) REVERT: C 7 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7987 (tp) REVERT: C 53 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7445 (tt0) REVERT: C 103 LYS cc_start: 0.7758 (mttt) cc_final: 0.6872 (ttpt) REVERT: D 103 LYS cc_start: 0.7474 (mttt) cc_final: 0.6954 (ttpt) REVERT: E 80 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7118 (tt) REVERT: E 103 LYS cc_start: 0.7521 (mttt) cc_final: 0.6725 (ttpt) REVERT: F 23 GLU cc_start: 0.8051 (pm20) cc_final: 0.7839 (pm20) REVERT: F 63 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7005 (mm-30) REVERT: F 128 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.4536 (mmm160) outliers start: 10 outliers final: 3 residues processed: 113 average time/residue: 3.7196 time to fit residues: 437.9321 Evaluate side-chains 112 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain C residue 7 LEU 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 3 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.4531 r_free = 0.4531 target = 0.219335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.202689 restraints weight = 17707.922| |-----------------------------------------------------------------------------| r_work (start): 0.4371 rms_B_bonded: 1.06 r_work: 0.4240 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.4135 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.5620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7070 Z= 0.144 Angle : 0.591 4.777 9714 Z= 0.338 Chirality : 0.051 0.349 1118 Planarity : 0.003 0.026 1120 Dihedral : 19.857 143.566 1238 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.28), residues: 798 helix: 1.19 (0.38), residues: 186 sheet: 0.51 (0.25), residues: 366 loop : -0.59 (0.33), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 97 HIS 0.001 0.001 HIS E 19 PHE 0.007 0.001 PHE B 54 TYR 0.005 0.001 TYR D 108 ARG 0.004 0.000 ARG A 35 Details of bonding type rmsd hydrogen bonds : bond 0.02996 ( 222) hydrogen bonds : angle 4.97080 ( 648) covalent geometry : bond 0.00331 ( 7070) covalent geometry : angle 0.59093 ( 9714) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11202.06 seconds wall clock time: 191 minutes 43.31 seconds (11503.31 seconds total)