Starting phenix.real_space_refine on Thu Jun 12 00:57:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i86_52708/06_2025/9i86_52708.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i86_52708/06_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_52708/06_2025/9i86_52708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i86_52708/06_2025/9i86_52708.map" model { file = "/net/cci-nas-00/data/ceres_data/9i86_52708/06_2025/9i86_52708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i86_52708/06_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-5710/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: 7.79, per 1000 atoms: 0.57 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: 3.25 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 5.60 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: 4.71 Time building geometry restraints manager: 4.04 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: 3.760 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: 0.250 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 36.860 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.370 ------------------------------------------------------------------------------- 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 : 1.419 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: 3.0803 time to fit residues: 663.7462 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 : 0.930 ------------------------------------------------------------------------------- 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: 0.6980 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4524 r_free = 0.4524 target = 0.219895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.202423 restraints weight = 17413.542| |-----------------------------------------------------------------------------| r_work (start): 0.4355 rms_B_bonded: 1.10 r_work: 0.4223 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.4118 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7070 Z= 0.159 Angle : 0.629 5.071 9714 Z= 0.360 Chirality : 0.053 0.359 1118 Planarity : 0.004 0.024 1120 Dihedral : 19.707 137.644 1238 Min Nonbonded Distance : 2.339 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: -0.31 (0.39), residues: 186 sheet: 1.80 (0.25), residues: 336 loop : -1.19 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 97 HIS 0.002 0.001 HIS E 19 PHE 0.007 0.001 PHE B 54 TYR 0.011 0.002 TYR C 31 ARG 0.003 0.000 ARG F 66 Details of bonding type rmsd hydrogen bonds : bond 0.03510 ( 222) hydrogen bonds : angle 6.65374 ( 648) covalent geometry : bond 0.00354 ( 7070) covalent geometry : angle 0.62871 ( 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 : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7305 (mm-30) REVERT: A 84 VAL cc_start: 0.6247 (p) cc_final: 0.5811 (m) REVERT: A 103 LYS cc_start: 0.7344 (mttt) cc_final: 0.6841 (tttm) REVERT: B 63 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7263 (mt-10) REVERT: B 103 LYS cc_start: 0.7439 (mttt) cc_final: 0.6789 (ttpm) REVERT: C 31 TYR cc_start: 0.8418 (p90) cc_final: 0.8092 (p90) REVERT: C 39 VAL cc_start: 0.7658 (t) cc_final: 0.7432 (m) REVERT: C 103 LYS cc_start: 0.7343 (mttt) cc_final: 0.6610 (ttpt) REVERT: D 1 MET cc_start: 0.7466 (tmm) cc_final: 0.7180 (tmm) REVERT: D 63 GLU cc_start: 0.7353 (mm-30) cc_final: 0.7125 (mt-10) REVERT: D 78 SER cc_start: 0.7901 (p) cc_final: 0.7669 (m) REVERT: D 103 LYS cc_start: 0.7345 (mttt) cc_final: 0.6784 (ttpt) REVERT: E 63 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7172 (mt-10) REVERT: F 48 ILE cc_start: 0.8367 (mt) cc_final: 0.8123 (mm) REVERT: F 103 LYS cc_start: 0.7471 (mttt) cc_final: 0.7083 (tttt) outliers start: 11 outliers final: 1 residues processed: 121 average time/residue: 3.3494 time to fit residues: 421.4468 Evaluate side-chains 107 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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: 0.3980 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.4489 r_free = 0.4489 target = 0.215901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.197128 restraints weight = 17743.708| |-----------------------------------------------------------------------------| r_work (start): 0.4307 rms_B_bonded: 1.18 r_work: 0.4183 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.4075 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3987 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= 0.153 Angle : 0.597 4.731 9714 Z= 0.342 Chirality : 0.052 0.351 1118 Planarity : 0.004 0.024 1120 Dihedral : 19.762 143.452 1238 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.83 % Allowed : 22.48 % 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: 0.59 (0.28), residues: 798 helix: 0.01 (0.39), residues: 186 sheet: 1.83 (0.26), residues: 336 loop : -1.20 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 97 HIS 0.002 0.001 HIS A 19 PHE 0.008 0.001 PHE C 47 TYR 0.006 0.001 TYR F 108 ARG 0.002 0.000 ARG F 33 Details of bonding type rmsd hydrogen bonds : bond 0.03255 ( 222) hydrogen bonds : angle 5.91853 ( 648) covalent geometry : bond 0.00348 ( 7070) covalent geometry : angle 0.59663 ( 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 134 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7269 (mm-30) REVERT: A 103 LYS cc_start: 0.7398 (mttt) cc_final: 0.6893 (tttm) REVERT: B 63 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7254 (mt-10) REVERT: B 103 LYS cc_start: 0.7595 (mttt) cc_final: 0.6888 (ttpm) REVERT: C 39 VAL cc_start: 0.7770 (t) cc_final: 0.7545 (m) REVERT: C 53 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7248 (tt0) REVERT: C 103 LYS cc_start: 0.7586 (mttt) cc_final: 0.6822 (ttpt) REVERT: D 1 MET cc_start: 0.7583 (tmm) cc_final: 0.7215 (tmm) REVERT: D 103 LYS cc_start: 0.7466 (mttt) cc_final: 0.6888 (ttpt) REVERT: E 63 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7222 (mt-10) REVERT: F 38 LYS cc_start: 0.7631 (mtmt) cc_final: 0.6984 (pttp) REVERT: F 48 ILE cc_start: 0.8372 (mt) cc_final: 0.8132 (mm) REVERT: F 51 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7646 (mp0) REVERT: F 63 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.7053 (mm-30) REVERT: F 78 SER cc_start: 0.7954 (p) cc_final: 0.7717 (m) outliers start: 18 outliers final: 2 residues processed: 119 average time/residue: 4.3122 time to fit residues: 536.2882 Evaluate side-chains 113 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain F residue 51 GLU 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: 3.9990 chunk 80 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.4507 r_free = 0.4507 target = 0.217102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.199303 restraints weight = 17521.488| |-----------------------------------------------------------------------------| r_work (start): 0.4334 rms_B_bonded: 1.10 r_work: 0.4200 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.4095 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7070 Z= 0.168 Angle : 0.613 5.227 9714 Z= 0.350 Chirality : 0.052 0.354 1118 Planarity : 0.004 0.028 1120 Dihedral : 19.918 139.366 1238 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.14 % Allowed : 22.80 % Favored : 74.06 % 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: 0.26 (0.38), residues: 186 sheet: 1.65 (0.26), residues: 336 loop : -1.19 (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 0.007 0.001 PHE C 54 TYR 0.005 0.001 TYR F 108 ARG 0.002 0.000 ARG E 33 Details of bonding type rmsd hydrogen bonds : bond 0.03273 ( 222) hydrogen bonds : angle 5.72199 ( 648) covalent geometry : bond 0.00381 ( 7070) covalent geometry : angle 0.61326 ( 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 135 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.7599 (mpp-170) cc_final: 0.7379 (mpp-170) REVERT: A 63 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7322 (mm-30) REVERT: A 103 LYS cc_start: 0.7474 (mttt) cc_final: 0.6991 (tttm) REVERT: B 63 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7236 (mt-10) REVERT: B 103 LYS cc_start: 0.7634 (mttt) cc_final: 0.6875 (ttpm) REVERT: C 39 VAL cc_start: 0.7769 (t) cc_final: 0.7561 (m) REVERT: C 53 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7519 (tt0) REVERT: C 55 GLU cc_start: 0.8214 (tt0) cc_final: 0.7943 (tt0) REVERT: C 103 LYS cc_start: 0.7619 (mttt) cc_final: 0.6824 (ttpt) REVERT: C 124 LEU cc_start: 0.6342 (OUTLIER) cc_final: 0.6057 (mt) REVERT: D 63 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6703 (mt-10) REVERT: D 103 LYS cc_start: 0.7500 (mttt) cc_final: 0.6967 (ttpt) REVERT: E 63 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7193 (mt-10) REVERT: E 80 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.6962 (tt) REVERT: F 63 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7079 (mm-30) REVERT: F 78 SER cc_start: 0.8046 (p) cc_final: 0.7827 (m) outliers start: 20 outliers final: 6 residues processed: 122 average time/residue: 4.2681 time to fit residues: 540.7532 Evaluate side-chains 113 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain F residue 63 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 76 optimal weight: 2.9990 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: 2.9990 chunk 43 optimal weight: 0.0980 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.4490 r_free = 0.4490 target = 0.215439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.197736 restraints weight = 17662.938| |-----------------------------------------------------------------------------| r_work (start): 0.4322 rms_B_bonded: 1.10 r_work: 0.4188 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.4083 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7070 Z= 0.169 Angle : 0.609 5.274 9714 Z= 0.349 Chirality : 0.052 0.352 1118 Planarity : 0.004 0.027 1120 Dihedral : 20.019 139.563 1238 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.52 % Allowed : 24.84 % 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 (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: 0.50 (0.28), residues: 798 helix: 0.50 (0.39), residues: 186 sheet: 1.41 (0.26), residues: 336 loop : -1.16 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 97 HIS 0.002 0.001 HIS C 19 PHE 0.007 0.001 PHE B 54 TYR 0.005 0.001 TYR F 108 ARG 0.002 0.000 ARG A 128 Details of bonding type rmsd hydrogen bonds : bond 0.03338 ( 222) hydrogen bonds : angle 5.49068 ( 648) covalent geometry : bond 0.00387 ( 7070) covalent geometry : angle 0.60910 ( 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 120 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.913 Fit side-chains REVERT: A 63 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7336 (mm-30) REVERT: A 103 LYS cc_start: 0.7460 (mttt) cc_final: 0.6966 (tttm) REVERT: B 63 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7216 (mt-10) REVERT: B 103 LYS cc_start: 0.7778 (mttt) cc_final: 0.6998 (ttpm) REVERT: C 53 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7531 (tt0) REVERT: C 55 GLU cc_start: 0.8288 (tt0) cc_final: 0.8076 (tt0) REVERT: C 63 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.7081 (mt-10) REVERT: C 103 LYS cc_start: 0.7693 (mttt) cc_final: 0.6853 (ttpt) REVERT: D 63 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6661 (mt-10) REVERT: D 103 LYS cc_start: 0.7530 (mttt) cc_final: 0.6996 (ttpt) REVERT: E 80 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7095 (tt) REVERT: E 103 LYS cc_start: 0.7626 (mttt) cc_final: 0.6834 (ttpt) REVERT: F 63 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7078 (mm-30) outliers start: 16 outliers final: 5 residues processed: 109 average time/residue: 3.7502 time to fit residues: 423.0804 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 : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 63 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 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: 2.9990 chunk 78 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 21 optimal weight: 0.0040 chunk 41 optimal weight: 2.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- 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 = 0.4511 r_free = 0.4511 target = 0.216824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.200923 restraints weight = 17552.776| |-----------------------------------------------------------------------------| r_work (start): 0.4354 rms_B_bonded: 1.15 r_work: 0.4224 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.4121 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.5225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7070 Z= 0.191 Angle : 0.635 5.485 9714 Z= 0.363 Chirality : 0.053 0.353 1118 Planarity : 0.004 0.029 1120 Dihedral : 20.124 136.488 1238 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.83 % Allowed : 24.53 % 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 (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: 0.41 (0.28), residues: 798 helix: 0.56 (0.39), residues: 186 sheet: 1.24 (0.26), residues: 336 loop : -1.15 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 97 HIS 0.002 0.001 HIS A 19 PHE 0.010 0.001 PHE E 92 TYR 0.008 0.002 TYR E 31 ARG 0.002 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.03498 ( 222) hydrogen bonds : angle 5.54281 ( 648) covalent geometry : bond 0.00441 ( 7070) covalent geometry : angle 0.63492 ( 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 123 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 1.013 Fit side-chains REVERT: A 35 ARG cc_start: 0.7742 (mpp-170) cc_final: 0.7492 (mpp-170) REVERT: A 63 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7383 (mt-10) REVERT: A 103 LYS cc_start: 0.7509 (mttt) cc_final: 0.7035 (tttm) REVERT: B 63 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7214 (mt-10) REVERT: B 103 LYS cc_start: 0.7801 (mttt) cc_final: 0.7027 (tttm) REVERT: C 53 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7516 (tt0) REVERT: C 63 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.7014 (mt-10) REVERT: C 103 LYS cc_start: 0.7727 (mttt) cc_final: 0.6875 (ttpt) REVERT: D 63 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6685 (mt-10) REVERT: D 103 LYS cc_start: 0.7572 (mttt) cc_final: 0.7029 (ttpt) REVERT: E 80 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7144 (tt) REVERT: E 103 LYS cc_start: 0.7613 (mttt) cc_final: 0.6838 (ttpt) REVERT: F 23 GLU cc_start: 0.8154 (pm20) cc_final: 0.7898 (pm20) REVERT: F 63 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7033 (mm-30) REVERT: F 128 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.4575 (mmm160) outliers start: 18 outliers final: 7 residues processed: 114 average time/residue: 3.7469 time to fit residues: 442.5543 Evaluate side-chains 112 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 18 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 25 optimal weight: 0.0970 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.0020 overall best weight: 0.6190 ------------------------------------------------------------------------------- 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 = 0.4546 r_free = 0.4546 target = 0.220794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.205631 restraints weight = 17514.600| |-----------------------------------------------------------------------------| r_work (start): 0.4398 rms_B_bonded: 1.00 r_work: 0.4258 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.4159 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.5344 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 : 0.573 4.455 9714 Z= 0.330 Chirality : 0.051 0.349 1118 Planarity : 0.003 0.025 1120 Dihedral : 19.869 146.023 1238 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.04 % Allowed : 25.94 % Favored : 72.01 % 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: 0.54 (0.28), residues: 798 helix: 0.84 (0.39), residues: 186 sheet: 1.21 (0.26), residues: 336 loop : -1.06 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 97 HIS 0.002 0.001 HIS A 19 PHE 0.010 0.001 PHE B 92 TYR 0.006 0.001 TYR E 31 ARG 0.002 0.000 ARG E 33 Details of bonding type rmsd hydrogen bonds : bond 0.02935 ( 222) hydrogen bonds : angle 5.25503 ( 648) covalent geometry : bond 0.00291 ( 7070) covalent geometry : angle 0.57302 ( 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 119 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: A 35 ARG cc_start: 0.7699 (mpp-170) cc_final: 0.7443 (mpp-170) REVERT: A 103 LYS cc_start: 0.7522 (mttt) cc_final: 0.7055 (tttm) REVERT: B 63 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7213 (mt-10) REVERT: B 103 LYS cc_start: 0.7829 (mttt) cc_final: 0.7068 (ttpm) REVERT: C 53 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7450 (tt0) REVERT: C 103 LYS cc_start: 0.7712 (mttt) cc_final: 0.6872 (ttpt) REVERT: D 63 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6671 (mt-10) REVERT: D 103 LYS cc_start: 0.7487 (mttt) cc_final: 0.6974 (ttpt) REVERT: E 53 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7796 (pm20) REVERT: E 80 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7191 (tt) REVERT: E 103 LYS cc_start: 0.7546 (mttt) cc_final: 0.6773 (ttpt) REVERT: F 23 GLU cc_start: 0.8095 (pm20) cc_final: 0.7831 (pm20) REVERT: F 63 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7008 (mm-30) REVERT: F 128 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.4598 (mmm160) outliers start: 13 outliers final: 3 residues processed: 111 average time/residue: 3.8930 time to fit residues: 447.5773 Evaluate side-chains 107 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 112 VAL Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 128 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 34 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 21 optimal weight: 0.1980 chunk 2 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 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 D 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.219574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.204138 restraints weight = 17513.826| |-----------------------------------------------------------------------------| r_work (start): 0.4368 rms_B_bonded: 0.99 r_work: 0.4191 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.4085 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.5409 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= 0.140 Angle : 0.583 4.675 9714 Z= 0.335 Chirality : 0.051 0.350 1118 Planarity : 0.003 0.026 1120 Dihedral : 19.793 144.745 1238 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.04 % Allowed : 25.31 % 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 (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: 0.97 (0.39), residues: 186 sheet: 0.65 (0.25), residues: 366 loop : -0.65 (0.33), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 97 HIS 0.002 0.001 HIS A 19 PHE 0.006 0.001 PHE B 54 TYR 0.005 0.001 TYR D 108 ARG 0.002 0.000 ARG C 33 Details of bonding type rmsd hydrogen bonds : bond 0.02974 ( 222) hydrogen bonds : angle 5.17553 ( 648) covalent geometry : bond 0.00320 ( 7070) covalent geometry : angle 0.58319 ( 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 112 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.7712 (mpp-170) cc_final: 0.7448 (mpp-170) REVERT: A 103 LYS cc_start: 0.7528 (mttt) cc_final: 0.7011 (tttm) REVERT: B 63 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7231 (mt-10) REVERT: B 103 LYS cc_start: 0.7872 (mttt) cc_final: 0.7047 (ttpm) REVERT: C 7 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.8020 (tp) REVERT: C 103 LYS cc_start: 0.7765 (mttt) cc_final: 0.6879 (ttpt) REVERT: D 63 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6686 (mt-10) REVERT: D 103 LYS cc_start: 0.7496 (mttt) cc_final: 0.6954 (ttpt) REVERT: E 53 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7860 (pm20) REVERT: E 80 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7078 (tt) REVERT: E 103 LYS cc_start: 0.7574 (mttt) cc_final: 0.6762 (ttpt) REVERT: F 23 GLU cc_start: 0.8103 (pm20) cc_final: 0.7869 (pm20) REVERT: F 63 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.7017 (mm-30) REVERT: F 128 ARG cc_start: 0.7127 (OUTLIER) cc_final: 0.4437 (mmm160) outliers start: 13 outliers final: 1 residues processed: 105 average time/residue: 3.8402 time to fit residues: 417.5304 Evaluate side-chains 107 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 128 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.4484 r_free = 0.4484 target = 0.213128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.198127 restraints weight = 17330.485| |-----------------------------------------------------------------------------| r_work (start): 0.4338 rms_B_bonded: 0.90 r_work: 0.4202 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.4094 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.5488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 7070 Z= 0.280 Angle : 0.725 6.593 9714 Z= 0.409 Chirality : 0.056 0.354 1118 Planarity : 0.004 0.035 1120 Dihedral : 20.429 127.549 1238 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.30 % Allowed : 24.21 % 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 (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: 0.17 (0.28), residues: 798 helix: 0.70 (0.38), residues: 186 sheet: 0.47 (0.25), residues: 366 loop : -0.74 (0.33), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 97 HIS 0.005 0.003 HIS C 19 PHE 0.008 0.002 PHE D 54 TYR 0.010 0.002 TYR D 108 ARG 0.003 0.001 ARG F 128 Details of bonding type rmsd hydrogen bonds : bond 0.04077 ( 222) hydrogen bonds : angle 5.59700 ( 648) covalent geometry : bond 0.00656 ( 7070) covalent geometry : angle 0.72465 ( 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 124 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 1.053 Fit side-chains REVERT: A 63 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6523 (mt-10) REVERT: A 103 LYS cc_start: 0.7587 (mttt) cc_final: 0.7116 (tttm) REVERT: B 63 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7181 (mt-10) REVERT: B 103 LYS cc_start: 0.7826 (mttt) cc_final: 0.7077 (tttm) REVERT: C 7 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8045 (tp) REVERT: C 53 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7573 (tt0) REVERT: C 103 LYS cc_start: 0.7880 (mttt) cc_final: 0.6994 (ttpt) REVERT: D 63 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6655 (mt-10) REVERT: D 103 LYS cc_start: 0.7597 (mttt) cc_final: 0.7066 (ttpt) REVERT: E 53 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7854 (pm20) REVERT: E 80 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7300 (tt) REVERT: E 103 LYS cc_start: 0.7621 (mttt) cc_final: 0.6895 (ttpt) REVERT: F 23 GLU cc_start: 0.8115 (pm20) cc_final: 0.7866 (pm20) REVERT: F 63 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6998 (mm-30) REVERT: F 128 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.4459 (mmm160) outliers start: 21 outliers final: 6 residues processed: 115 average time/residue: 4.0120 time to fit residues: 478.5954 Evaluate side-chains 114 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU 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 109 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 53 GLU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 128 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 55 optimal weight: 0.0270 chunk 73 optimal weight: 0.0170 chunk 57 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 41 optimal weight: 0.2980 chunk 65 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 overall best weight: 0.3076 ------------------------------------------------------------------------------- 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 = 0.222052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.205929 restraints weight = 17691.683| |-----------------------------------------------------------------------------| r_work (start): 0.4401 rms_B_bonded: 1.06 r_work: 0.4265 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.4166 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.5607 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= 0.120 Angle : 0.572 4.428 9714 Z= 0.328 Chirality : 0.051 0.348 1118 Planarity : 0.003 0.023 1120 Dihedral : 20.020 147.604 1238 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.57 % Allowed : 26.10 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.10 (0.38), residues: 186 sheet: 0.55 (0.25), residues: 366 loop : -0.59 (0.34), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 97 HIS 0.002 0.001 HIS B 19 PHE 0.006 0.001 PHE B 54 TYR 0.004 0.001 TYR C 31 ARG 0.002 0.000 ARG C 33 Details of bonding type rmsd hydrogen bonds : bond 0.02747 ( 222) hydrogen bonds : angle 5.06576 ( 648) covalent geometry : bond 0.00280 ( 7070) covalent geometry : angle 0.57227 ( 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 120 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 LYS cc_start: 0.7469 (mttt) cc_final: 0.7000 (tttm) REVERT: B 63 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7215 (mt-10) REVERT: B 103 LYS cc_start: 0.7791 (mttt) cc_final: 0.7007 (ttpm) REVERT: C 7 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7987 (tp) REVERT: C 53 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7435 (tt0) REVERT: C 103 LYS cc_start: 0.7751 (mttt) cc_final: 0.6832 (ttpt) REVERT: D 103 LYS cc_start: 0.7478 (mttt) cc_final: 0.6954 (ttpt) REVERT: E 53 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7795 (pm20) REVERT: E 103 LYS cc_start: 0.7554 (mttt) cc_final: 0.6731 (ttpt) REVERT: F 23 GLU cc_start: 0.8082 (pm20) cc_final: 0.7858 (pm20) REVERT: F 63 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6987 (mm-30) REVERT: F 128 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.4543 (mmm160) outliers start: 10 outliers final: 3 residues processed: 115 average time/residue: 4.9124 time to fit residues: 597.5367 Evaluate side-chains 117 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 53 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 3 optimal weight: 3.9990 chunk 33 optimal weight: 0.0770 chunk 68 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.220351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.203893 restraints weight = 17720.312| |-----------------------------------------------------------------------------| r_work (start): 0.4382 rms_B_bonded: 1.08 r_work: 0.4249 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.4149 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.5654 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 4.455 9714 Z= 0.330 Chirality : 0.051 0.349 1118 Planarity : 0.003 0.025 1120 Dihedral : 19.847 146.699 1238 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 0.94 % Allowed : 26.42 % 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 (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: 0.49 (0.28), residues: 798 helix: 1.25 (0.38), residues: 186 sheet: 0.51 (0.25), residues: 366 loop : -0.53 (0.34), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 97 HIS 0.001 0.001 HIS D 19 PHE 0.006 0.001 PHE B 54 TYR 0.004 0.001 TYR D 108 ARG 0.001 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.02846 ( 222) hydrogen bonds : angle 4.96175 ( 648) covalent geometry : bond 0.00297 ( 7070) covalent geometry : angle 0.57579 ( 9714) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13987.11 seconds wall clock time: 247 minutes 44.67 seconds (14864.67 seconds total)