Starting phenix.real_space_refine on Wed Feb 4 20:45:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ngi_49385/02_2026/9ngi_49385_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ngi_49385/02_2026/9ngi_49385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ngi_49385/02_2026/9ngi_49385_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ngi_49385/02_2026/9ngi_49385_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ngi_49385/02_2026/9ngi_49385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ngi_49385/02_2026/9ngi_49385.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians S 25 5.16 5 Na 9 4.78 5 C 8305 2.51 5 N 2115 2.21 5 O 2275 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12729 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2540 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain: "B" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2540 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain: "C" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2540 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain: "D" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2540 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain: "E" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2540 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 13 Unusual residues: {' NA': 9, '3CN': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.56, per 1000 atoms: 0.20 Number of scatterers: 12729 At special positions: 0 Unit cell: (92.008, 92.008, 123.256, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 25 16.00 Na 9 11.00 O 2275 8.00 N 2115 7.00 C 8305 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 423.7 milliseconds 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2930 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 20 sheets defined 37.4% alpha, 40.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 62 through 70 Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'A' and resid 176 through 179 Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 208 through 222 Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 227 through 245 removed outlier: 3.912A pdb=" N THR A 234 " --> pdb=" O GLU A 230 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 253 removed outlier: 3.695A pdb=" N ILE A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 287 Processing helix chain 'A' and resid 302 through 320 removed outlier: 3.978A pdb=" N LEU A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 70 Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'B' and resid 176 through 179 Processing helix chain 'B' and resid 201 through 208 Processing helix chain 'B' and resid 208 through 222 Processing helix chain 'B' and resid 223 through 225 No H-bonds generated for 'chain 'B' and resid 223 through 225' Processing helix chain 'B' and resid 227 through 245 removed outlier: 3.912A pdb=" N THR B 234 " --> pdb=" O GLU B 230 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER B 235 " --> pdb=" O ARG B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 253 removed outlier: 3.694A pdb=" N ILE B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 287 Processing helix chain 'B' and resid 302 through 320 removed outlier: 3.978A pdb=" N LEU B 306 " --> pdb=" O LEU B 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 70 Processing helix chain 'C' and resid 118 through 121 Processing helix chain 'C' and resid 176 through 179 Processing helix chain 'C' and resid 201 through 208 Processing helix chain 'C' and resid 208 through 222 Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 227 through 245 removed outlier: 3.912A pdb=" N THR C 234 " --> pdb=" O GLU C 230 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER C 235 " --> pdb=" O ARG C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 253 removed outlier: 3.695A pdb=" N ILE C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 287 Processing helix chain 'C' and resid 302 through 320 removed outlier: 3.978A pdb=" N LEU C 306 " --> pdb=" O LEU C 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 70 Processing helix chain 'D' and resid 118 through 121 Processing helix chain 'D' and resid 176 through 179 Processing helix chain 'D' and resid 201 through 208 Processing helix chain 'D' and resid 208 through 222 Processing helix chain 'D' and resid 223 through 225 No H-bonds generated for 'chain 'D' and resid 223 through 225' Processing helix chain 'D' and resid 227 through 245 removed outlier: 3.912A pdb=" N THR D 234 " --> pdb=" O GLU D 230 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER D 235 " --> pdb=" O ARG D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 253 removed outlier: 3.695A pdb=" N ILE D 252 " --> pdb=" O TYR D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 287 Processing helix chain 'D' and resid 302 through 320 removed outlier: 3.978A pdb=" N LEU D 306 " --> pdb=" O LEU D 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 70 Processing helix chain 'E' and resid 118 through 121 Processing helix chain 'E' and resid 176 through 179 Processing helix chain 'E' and resid 201 through 208 Processing helix chain 'E' and resid 208 through 222 Processing helix chain 'E' and resid 223 through 225 No H-bonds generated for 'chain 'E' and resid 223 through 225' Processing helix chain 'E' and resid 227 through 245 removed outlier: 3.912A pdb=" N THR E 234 " --> pdb=" O GLU E 230 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER E 235 " --> pdb=" O ARG E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 253 removed outlier: 3.696A pdb=" N ILE E 252 " --> pdb=" O TYR E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 287 Processing helix chain 'E' and resid 302 through 320 removed outlier: 3.978A pdb=" N LEU E 306 " --> pdb=" O LEU E 302 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58 removed outlier: 4.775A pdb=" N SER A 109 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 58 removed outlier: 3.809A pdb=" N GLY A 37 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N THR A 32 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLY A 25 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LYS A 34 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ILE A 23 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP A 36 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR A 44 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ASP A 13 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL A 14 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE A 145 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL A 16 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL A 147 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE A 18 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.937A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.937A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 58 removed outlier: 4.775A pdb=" N SER B 109 " --> pdb=" O VAL B 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 56 through 58 removed outlier: 3.810A pdb=" N GLY B 37 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N THR B 32 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLY B 25 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE B 23 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP B 36 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR B 44 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ASP B 13 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL B 14 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE B 145 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL B 16 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL B 147 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE B 18 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.937A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.937A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 56 through 58 removed outlier: 4.775A pdb=" N SER C 109 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 56 through 58 removed outlier: 3.810A pdb=" N GLY C 37 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N THR C 32 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLY C 25 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS C 34 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE C 23 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ASP C 36 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR C 44 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ASP C 13 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL C 14 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE C 145 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL C 16 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL C 147 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE C 18 " --> pdb=" O VAL C 147 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.937A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.937A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 56 through 58 removed outlier: 4.775A pdb=" N SER D 109 " --> pdb=" O VAL D 82 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 56 through 58 removed outlier: 3.808A pdb=" N GLY D 37 " --> pdb=" O PHE D 106 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N THR D 32 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLY D 25 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LYS D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE D 23 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP D 36 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR D 44 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ASP D 13 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL D 14 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE D 145 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL D 16 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL D 147 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE D 18 " --> pdb=" O VAL D 147 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.937A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.937A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 56 through 58 removed outlier: 4.775A pdb=" N SER E 109 " --> pdb=" O VAL E 82 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 56 through 58 removed outlier: 3.809A pdb=" N GLY E 37 " --> pdb=" O PHE E 106 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N THR E 32 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLY E 25 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LYS E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ILE E 23 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP E 36 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR E 44 " --> pdb=" O ASP E 13 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ASP E 13 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL E 14 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE E 145 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL E 16 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL E 147 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE E 18 " --> pdb=" O VAL E 147 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.936A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.936A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) 710 hydrogen bonds defined for protein. 2040 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.80 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4006 1.34 - 1.46: 2999 1.46 - 1.58: 6010 1.58 - 1.69: 5 1.69 - 1.81: 45 Bond restraints: 13065 Sorted by residual: bond pdb=" CA THR D 149 " pdb=" CB THR D 149 " ideal model delta sigma weight residual 1.531 1.625 -0.095 3.28e-02 9.30e+02 8.31e+00 bond pdb=" CA THR E 149 " pdb=" CB THR E 149 " ideal model delta sigma weight residual 1.531 1.625 -0.094 3.28e-02 9.30e+02 8.27e+00 bond pdb=" CA THR A 149 " pdb=" CB THR A 149 " ideal model delta sigma weight residual 1.531 1.625 -0.094 3.28e-02 9.30e+02 8.25e+00 bond pdb=" CA THR B 149 " pdb=" CB THR B 149 " ideal model delta sigma weight residual 1.531 1.625 -0.094 3.28e-02 9.30e+02 8.19e+00 bond pdb=" CA THR C 149 " pdb=" CB THR C 149 " ideal model delta sigma weight residual 1.531 1.624 -0.094 3.28e-02 9.30e+02 8.17e+00 ... (remaining 13060 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 16837 1.79 - 3.57: 782 3.57 - 5.36: 106 5.36 - 7.14: 30 7.14 - 8.93: 25 Bond angle restraints: 17780 Sorted by residual: angle pdb=" CA PRO D 85 " pdb=" N PRO D 85 " pdb=" CD PRO D 85 " ideal model delta sigma weight residual 112.00 106.56 5.44 1.40e+00 5.10e-01 1.51e+01 angle pdb=" CA PRO E 85 " pdb=" N PRO E 85 " pdb=" CD PRO E 85 " ideal model delta sigma weight residual 112.00 106.57 5.43 1.40e+00 5.10e-01 1.50e+01 angle pdb=" C ASN E 60 " pdb=" N THR E 61 " pdb=" CA THR E 61 " ideal model delta sigma weight residual 121.54 128.93 -7.39 1.91e+00 2.74e-01 1.50e+01 angle pdb=" CA PRO B 85 " pdb=" N PRO B 85 " pdb=" CD PRO B 85 " ideal model delta sigma weight residual 112.00 106.58 5.42 1.40e+00 5.10e-01 1.50e+01 angle pdb=" C ASN A 60 " pdb=" N THR A 61 " pdb=" CA THR A 61 " ideal model delta sigma weight residual 121.54 128.93 -7.39 1.91e+00 2.74e-01 1.50e+01 ... (remaining 17775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 6729 16.43 - 32.85: 711 32.85 - 49.28: 125 49.28 - 65.70: 15 65.70 - 82.13: 25 Dihedral angle restraints: 7605 sinusoidal: 3060 harmonic: 4545 Sorted by residual: dihedral pdb=" CA PRO E 201 " pdb=" C PRO E 201 " pdb=" N SER E 202 " pdb=" CA SER E 202 " ideal model delta harmonic sigma weight residual -180.00 -160.16 -19.84 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA PRO A 201 " pdb=" C PRO A 201 " pdb=" N SER A 202 " pdb=" CA SER A 202 " ideal model delta harmonic sigma weight residual -180.00 -160.16 -19.84 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA PRO C 201 " pdb=" C PRO C 201 " pdb=" N SER C 202 " pdb=" CA SER C 202 " ideal model delta harmonic sigma weight residual -180.00 -160.16 -19.84 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 7602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1035 0.037 - 0.075: 581 0.075 - 0.112: 228 0.112 - 0.149: 71 0.149 - 0.187: 40 Chirality restraints: 1955 Sorted by residual: chirality pdb=" CB ILE D 18 " pdb=" CA ILE D 18 " pdb=" CG1 ILE D 18 " pdb=" CG2 ILE D 18 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" CB ILE E 18 " pdb=" CA ILE E 18 " pdb=" CG1 ILE E 18 " pdb=" CG2 ILE E 18 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.67e-01 chirality pdb=" CA PHE B 304 " pdb=" N PHE B 304 " pdb=" C PHE B 304 " pdb=" CB PHE B 304 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.46e-01 ... (remaining 1952 not shown) Planarity restraints: 2265 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 84 " 0.093 5.00e-02 4.00e+02 1.39e-01 3.08e+01 pdb=" N PRO E 85 " -0.240 5.00e-02 4.00e+02 pdb=" CA PRO E 85 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO E 85 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 84 " 0.093 5.00e-02 4.00e+02 1.39e-01 3.08e+01 pdb=" N PRO C 85 " -0.240 5.00e-02 4.00e+02 pdb=" CA PRO C 85 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO C 85 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 84 " 0.093 5.00e-02 4.00e+02 1.39e-01 3.08e+01 pdb=" N PRO A 85 " -0.240 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " 0.072 5.00e-02 4.00e+02 ... (remaining 2262 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3056 2.80 - 3.32: 11939 3.32 - 3.85: 21026 3.85 - 4.37: 23424 4.37 - 4.90: 40635 Nonbonded interactions: 100080 Sorted by model distance: nonbonded pdb=" OD1 ASP A 122 " pdb=" N ARG A 123 " model vdw 2.269 3.120 nonbonded pdb=" OD1 ASP E 122 " pdb=" N ARG E 123 " model vdw 2.269 3.120 nonbonded pdb=" OD1 ASP D 122 " pdb=" N ARG D 123 " model vdw 2.270 3.120 nonbonded pdb=" OD1 ASP B 122 " pdb=" N ARG B 123 " model vdw 2.270 3.120 nonbonded pdb=" OD1 ASP C 122 " pdb=" N ARG C 123 " model vdw 2.270 3.120 ... (remaining 100075 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 11 through 401) selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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 group one per residue 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: 0.960 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.200 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 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 : 0.006 0.095 13065 Z= 0.239 Angle : 0.917 8.931 17780 Z= 0.501 Chirality : 0.057 0.187 1955 Planarity : 0.010 0.139 2265 Dihedral : 14.494 82.126 4675 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.20), residues: 1540 helix: -0.30 (0.21), residues: 515 sheet: 0.17 (0.24), residues: 475 loop : -2.17 (0.23), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 163 TYR 0.023 0.002 TYR D 248 PHE 0.028 0.002 PHE E 78 TRP 0.063 0.004 TRP E 220 HIS 0.004 0.001 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00551 (13065) covalent geometry : angle 0.91683 (17780) hydrogen bonds : bond 0.19528 ( 620) hydrogen bonds : angle 8.37200 ( 2040) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 434 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8431 (pm20) REVERT: A 115 ASP cc_start: 0.7529 (t70) cc_final: 0.6654 (m-30) REVERT: A 131 GLU cc_start: 0.8781 (mt-10) cc_final: 0.7746 (mt-10) REVERT: A 247 PHE cc_start: 0.7977 (m-10) cc_final: 0.7520 (m-10) REVERT: B 19 PHE cc_start: 0.7868 (t80) cc_final: 0.7253 (t80) REVERT: B 64 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8471 (pm20) REVERT: B 102 TYR cc_start: 0.8276 (t80) cc_final: 0.7884 (t80) REVERT: B 107 LEU cc_start: 0.7434 (tt) cc_final: 0.7205 (tt) REVERT: B 115 ASP cc_start: 0.7616 (t70) cc_final: 0.6813 (m-30) REVERT: B 131 GLU cc_start: 0.8703 (mt-10) cc_final: 0.7648 (mt-10) REVERT: B 192 THR cc_start: 0.8444 (m) cc_final: 0.8144 (m) REVERT: B 223 PHE cc_start: 0.8634 (m-10) cc_final: 0.8074 (m-10) REVERT: B 247 PHE cc_start: 0.7971 (m-10) cc_final: 0.7455 (m-10) REVERT: C 64 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8485 (pm20) REVERT: C 115 ASP cc_start: 0.7517 (t70) cc_final: 0.6679 (m-30) REVERT: C 131 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8043 (mt-10) REVERT: C 150 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7545 (tm-30) REVERT: C 159 GLU cc_start: 0.8508 (pm20) cc_final: 0.7628 (tt0) REVERT: C 192 THR cc_start: 0.8364 (m) cc_final: 0.7737 (p) REVERT: C 223 PHE cc_start: 0.8615 (m-10) cc_final: 0.8279 (m-10) REVERT: C 247 PHE cc_start: 0.7907 (m-10) cc_final: 0.7559 (m-10) REVERT: C 266 ILE cc_start: 0.8624 (tp) cc_final: 0.7777 (tp) REVERT: D 64 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8416 (pm20) REVERT: D 102 TYR cc_start: 0.8198 (t80) cc_final: 0.7770 (t80) REVERT: D 115 ASP cc_start: 0.7510 (t70) cc_final: 0.6715 (m-30) REVERT: D 131 GLU cc_start: 0.8639 (mt-10) cc_final: 0.7565 (mt-10) REVERT: D 150 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7527 (tm-30) REVERT: D 199 ARG cc_start: 0.8342 (ttm-80) cc_final: 0.7469 (ttm-80) REVERT: D 223 PHE cc_start: 0.8692 (m-10) cc_final: 0.8414 (m-10) REVERT: D 247 PHE cc_start: 0.8022 (m-10) cc_final: 0.7607 (m-10) REVERT: D 266 ILE cc_start: 0.8535 (tp) cc_final: 0.8330 (tp) REVERT: E 115 ASP cc_start: 0.7574 (t70) cc_final: 0.6709 (m-30) REVERT: E 131 GLU cc_start: 0.8769 (mt-10) cc_final: 0.7688 (mt-10) REVERT: E 192 THR cc_start: 0.8445 (m) cc_final: 0.8058 (m) REVERT: E 199 ARG cc_start: 0.8229 (ttm-80) cc_final: 0.7512 (ttm-80) REVERT: E 214 LEU cc_start: 0.8555 (mp) cc_final: 0.8308 (mp) REVERT: E 252 ILE cc_start: 0.8896 (mp) cc_final: 0.8671 (mp) outliers start: 0 outliers final: 0 residues processed: 434 average time/residue: 0.0925 time to fit residues: 58.9504 Evaluate side-chains 346 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN B 139 GLN C 139 GLN D 139 GLN E 139 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.123847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.094856 restraints weight = 30613.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.097915 restraints weight = 18951.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.099887 restraints weight = 13538.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.101747 restraints weight = 10637.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.102652 restraints weight = 8841.278| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13065 Z= 0.246 Angle : 0.665 7.075 17780 Z= 0.353 Chirality : 0.048 0.151 1955 Planarity : 0.006 0.084 2265 Dihedral : 5.636 22.415 1715 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.21), residues: 1540 helix: 0.85 (0.22), residues: 530 sheet: 0.11 (0.25), residues: 450 loop : -2.28 (0.22), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 91 TYR 0.018 0.002 TYR D 204 PHE 0.013 0.002 PHE B 247 TRP 0.020 0.002 TRP E 220 HIS 0.004 0.001 HIS C 285 Details of bonding type rmsd covalent geometry : bond 0.00541 (13065) covalent geometry : angle 0.66499 (17780) hydrogen bonds : bond 0.04333 ( 620) hydrogen bonds : angle 5.77137 ( 2040) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 0.401 Fit side-chains REVERT: A 93 MET cc_start: 0.9020 (tpp) cc_final: 0.8631 (tpp) REVERT: A 102 TYR cc_start: 0.8244 (t80) cc_final: 0.7884 (t80) REVERT: A 107 LEU cc_start: 0.8107 (tt) cc_final: 0.7730 (tt) REVERT: A 140 LEU cc_start: 0.9236 (tt) cc_final: 0.9024 (tt) REVERT: A 191 ILE cc_start: 0.8747 (mt) cc_final: 0.8533 (mt) REVERT: A 198 VAL cc_start: 0.8946 (p) cc_final: 0.8742 (m) REVERT: A 265 MET cc_start: 0.8920 (ttt) cc_final: 0.8712 (ttt) REVERT: B 19 PHE cc_start: 0.7959 (t80) cc_final: 0.7623 (t80) REVERT: B 93 MET cc_start: 0.8990 (tpp) cc_final: 0.8595 (tpp) REVERT: B 102 TYR cc_start: 0.8346 (t80) cc_final: 0.7972 (t80) REVERT: B 107 LEU cc_start: 0.7916 (tt) cc_final: 0.7595 (tt) REVERT: B 131 GLU cc_start: 0.8869 (mt-10) cc_final: 0.7702 (mt-10) REVERT: B 198 VAL cc_start: 0.8985 (p) cc_final: 0.8676 (m) REVERT: B 199 ARG cc_start: 0.8372 (ttm-80) cc_final: 0.7955 (ttm-80) REVERT: B 301 ARG cc_start: 0.7534 (ptp90) cc_final: 0.7147 (ptp-110) REVERT: C 64 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8491 (pm20) REVERT: C 102 TYR cc_start: 0.8250 (t80) cc_final: 0.7948 (t80) REVERT: C 107 LEU cc_start: 0.7918 (tp) cc_final: 0.7708 (tp) REVERT: C 131 GLU cc_start: 0.8889 (mt-10) cc_final: 0.7982 (mt-10) REVERT: C 148 TYR cc_start: 0.7960 (m-80) cc_final: 0.7742 (m-80) REVERT: C 156 GLU cc_start: 0.8509 (pp20) cc_final: 0.8301 (pp20) REVERT: C 199 ARG cc_start: 0.8532 (ttm-80) cc_final: 0.8090 (ttm-80) REVERT: C 212 LEU cc_start: 0.9218 (tp) cc_final: 0.8948 (tp) REVERT: C 265 MET cc_start: 0.8814 (ttt) cc_final: 0.8602 (ttt) REVERT: C 266 ILE cc_start: 0.8616 (tp) cc_final: 0.7914 (tp) REVERT: D 77 GLU cc_start: 0.7615 (pm20) cc_final: 0.7265 (pm20) REVERT: D 102 TYR cc_start: 0.8264 (t80) cc_final: 0.7891 (t80) REVERT: D 131 GLU cc_start: 0.8573 (mt-10) cc_final: 0.7994 (mt-10) REVERT: D 198 VAL cc_start: 0.9029 (p) cc_final: 0.8824 (m) REVERT: D 199 ARG cc_start: 0.8483 (ttm-80) cc_final: 0.8080 (ttm-80) REVERT: D 212 LEU cc_start: 0.9110 (tp) cc_final: 0.8788 (tp) REVERT: D 223 PHE cc_start: 0.8668 (m-80) cc_final: 0.8180 (m-10) REVERT: E 77 GLU cc_start: 0.7640 (pm20) cc_final: 0.6915 (pm20) REVERT: E 93 MET cc_start: 0.9073 (tpp) cc_final: 0.8653 (tpp) REVERT: E 102 TYR cc_start: 0.8252 (t80) cc_final: 0.7829 (t80) REVERT: E 131 GLU cc_start: 0.8531 (mt-10) cc_final: 0.7055 (mt-10) REVERT: E 199 ARG cc_start: 0.8519 (ttm-80) cc_final: 0.8227 (ttm-80) REVERT: E 203 TYR cc_start: 0.8394 (t80) cc_final: 0.7986 (t80) REVERT: E 301 ARG cc_start: 0.7215 (mtt180) cc_final: 0.7014 (ptp-110) outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 0.0880 time to fit residues: 48.4566 Evaluate side-chains 291 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 93 optimal weight: 0.0170 chunk 124 optimal weight: 0.0970 chunk 91 optimal weight: 20.0000 chunk 116 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 113 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 chunk 90 optimal weight: 8.9990 chunk 152 optimal weight: 5.9990 overall best weight: 1.0220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN B 139 GLN B 285 HIS C 139 GLN D 69 ASN D 139 GLN D 285 HIS E 139 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.129910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.100172 restraints weight = 30270.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.103564 restraints weight = 18214.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.105771 restraints weight = 12731.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.107176 restraints weight = 9874.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.107285 restraints weight = 8310.416| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13065 Z= 0.112 Angle : 0.558 6.057 17780 Z= 0.296 Chirality : 0.047 0.167 1955 Planarity : 0.005 0.060 2265 Dihedral : 4.986 20.452 1715 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.14 % Allowed : 2.82 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.22), residues: 1540 helix: 1.33 (0.23), residues: 500 sheet: 0.50 (0.23), residues: 520 loop : -1.79 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 117 TYR 0.027 0.001 TYR E 148 PHE 0.008 0.001 PHE A 119 TRP 0.009 0.001 TRP C 206 HIS 0.008 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00254 (13065) covalent geometry : angle 0.55819 (17780) hydrogen bonds : bond 0.03591 ( 620) hydrogen bonds : angle 5.02598 ( 2040) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 399 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.9136 (mt-10) cc_final: 0.8510 (pm20) REVERT: A 102 TYR cc_start: 0.8164 (t80) cc_final: 0.7917 (t80) REVERT: A 107 LEU cc_start: 0.7605 (tt) cc_final: 0.7062 (tt) REVERT: A 115 ASP cc_start: 0.7727 (t70) cc_final: 0.6590 (m-30) REVERT: A 198 VAL cc_start: 0.8930 (p) cc_final: 0.8668 (m) REVERT: A 212 LEU cc_start: 0.9100 (tp) cc_final: 0.8864 (tp) REVERT: A 265 MET cc_start: 0.8838 (ttt) cc_final: 0.8535 (ttt) REVERT: B 64 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8508 (pm20) REVERT: B 79 ILE cc_start: 0.9223 (mm) cc_final: 0.8849 (mm) REVERT: B 102 TYR cc_start: 0.8215 (t80) cc_final: 0.7873 (t80) REVERT: B 115 ASP cc_start: 0.7650 (t70) cc_final: 0.6535 (m-30) REVERT: B 198 VAL cc_start: 0.9003 (p) cc_final: 0.8721 (m) REVERT: B 223 PHE cc_start: 0.8690 (m-10) cc_final: 0.8388 (m-10) REVERT: C 64 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8471 (pm20) REVERT: C 93 MET cc_start: 0.8884 (tpp) cc_final: 0.8616 (tpp) REVERT: C 107 LEU cc_start: 0.7763 (tp) cc_final: 0.7512 (tp) REVERT: C 131 GLU cc_start: 0.8466 (mt-10) cc_final: 0.7235 (mt-10) REVERT: C 212 LEU cc_start: 0.9119 (tp) cc_final: 0.8743 (tp) REVERT: C 265 MET cc_start: 0.8747 (ttt) cc_final: 0.8476 (ttt) REVERT: C 266 ILE cc_start: 0.8560 (tp) cc_final: 0.7710 (tp) REVERT: D 64 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8396 (pm20) REVERT: D 102 TYR cc_start: 0.8185 (t80) cc_final: 0.7887 (t80) REVERT: D 115 ASP cc_start: 0.7584 (t70) cc_final: 0.6629 (m-30) REVERT: D 131 GLU cc_start: 0.8656 (mt-10) cc_final: 0.6942 (mt-10) REVERT: D 198 VAL cc_start: 0.8944 (p) cc_final: 0.8696 (m) REVERT: D 212 LEU cc_start: 0.9053 (tp) cc_final: 0.8804 (tp) REVERT: D 265 MET cc_start: 0.8740 (ttt) cc_final: 0.8491 (ttt) REVERT: E 102 TYR cc_start: 0.8151 (t80) cc_final: 0.7899 (t80) REVERT: E 107 LEU cc_start: 0.7651 (tt) cc_final: 0.7093 (tt) REVERT: E 131 GLU cc_start: 0.8684 (mt-10) cc_final: 0.6999 (mt-10) outliers start: 2 outliers final: 0 residues processed: 399 average time/residue: 0.0875 time to fit residues: 53.3691 Evaluate side-chains 326 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 126 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 81 optimal weight: 0.4980 chunk 92 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 28 optimal weight: 0.0170 overall best weight: 2.7024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 GLN B 69 ASN B 139 GLN B 285 HIS C 69 ASN C 139 GLN D 139 GLN D 285 HIS E 69 ASN E 139 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.125617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.097141 restraints weight = 30629.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.100267 restraints weight = 18730.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.101965 restraints weight = 13196.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.104028 restraints weight = 10678.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.105105 restraints weight = 8815.554| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13065 Z= 0.163 Angle : 0.588 5.728 17780 Z= 0.310 Chirality : 0.047 0.193 1955 Planarity : 0.005 0.056 2265 Dihedral : 5.057 22.441 1715 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.07 % Allowed : 5.34 % Favored : 94.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.22), residues: 1540 helix: 1.44 (0.23), residues: 505 sheet: 0.13 (0.25), residues: 450 loop : -1.90 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 91 TYR 0.018 0.001 TYR C 203 PHE 0.016 0.001 PHE B 228 TRP 0.013 0.001 TRP C 206 HIS 0.004 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00364 (13065) covalent geometry : angle 0.58801 (17780) hydrogen bonds : bond 0.03630 ( 620) hydrogen bonds : angle 5.11978 ( 2040) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 378 time to evaluate : 0.407 Fit side-chains REVERT: A 39 ILE cc_start: 0.8972 (tp) cc_final: 0.8588 (pt) REVERT: A 64 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8530 (pm20) REVERT: A 77 GLU cc_start: 0.7670 (pp20) cc_final: 0.7449 (pp20) REVERT: A 102 TYR cc_start: 0.8266 (t80) cc_final: 0.8007 (t80) REVERT: A 107 LEU cc_start: 0.7963 (tt) cc_final: 0.7651 (tt) REVERT: A 198 VAL cc_start: 0.8902 (p) cc_final: 0.8670 (m) REVERT: A 212 LEU cc_start: 0.9093 (tp) cc_final: 0.8800 (tp) REVERT: A 239 MET cc_start: 0.8985 (ttp) cc_final: 0.8639 (ttt) REVERT: A 265 MET cc_start: 0.8842 (ttt) cc_final: 0.8522 (ttt) REVERT: B 64 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8538 (pm20) REVERT: B 102 TYR cc_start: 0.8277 (t80) cc_final: 0.8024 (t80) REVERT: B 107 LEU cc_start: 0.7756 (tt) cc_final: 0.7493 (tp) REVERT: B 198 VAL cc_start: 0.8990 (p) cc_final: 0.8643 (m) REVERT: B 212 LEU cc_start: 0.9053 (tp) cc_final: 0.8850 (tp) REVERT: B 301 ARG cc_start: 0.7570 (ptp90) cc_final: 0.7198 (ptp-110) REVERT: C 19 PHE cc_start: 0.8145 (t80) cc_final: 0.7931 (t80) REVERT: C 39 ILE cc_start: 0.9034 (tp) cc_final: 0.8609 (pt) REVERT: C 64 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8497 (pm20) REVERT: C 93 MET cc_start: 0.8920 (tpp) cc_final: 0.8644 (tpp) REVERT: C 102 TYR cc_start: 0.8597 (t80) cc_final: 0.8134 (t80) REVERT: C 107 LEU cc_start: 0.7928 (tp) cc_final: 0.7708 (tp) REVERT: C 199 ARG cc_start: 0.7855 (ttp-170) cc_final: 0.7495 (ttm170) REVERT: C 212 LEU cc_start: 0.9049 (tp) cc_final: 0.8631 (tp) REVERT: C 265 MET cc_start: 0.8727 (ttt) cc_final: 0.8454 (ttt) REVERT: C 266 ILE cc_start: 0.8576 (tp) cc_final: 0.7776 (tp) REVERT: D 39 ILE cc_start: 0.8995 (tp) cc_final: 0.8566 (pt) REVERT: D 64 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8504 (pm20) REVERT: D 102 TYR cc_start: 0.8289 (t80) cc_final: 0.7957 (t80) REVERT: D 131 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8079 (mt-10) REVERT: D 140 LEU cc_start: 0.9143 (tt) cc_final: 0.8926 (tt) REVERT: D 198 VAL cc_start: 0.8943 (p) cc_final: 0.8628 (m) REVERT: D 212 LEU cc_start: 0.9048 (tp) cc_final: 0.8755 (tp) REVERT: D 265 MET cc_start: 0.8744 (ttt) cc_final: 0.8493 (ttt) REVERT: D 285 HIS cc_start: 0.7579 (OUTLIER) cc_final: 0.7361 (t70) REVERT: D 301 ARG cc_start: 0.7020 (ptp90) cc_final: 0.6506 (ptp-110) REVERT: E 64 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8674 (pm20) REVERT: E 102 TYR cc_start: 0.8238 (t80) cc_final: 0.7898 (t80) REVERT: E 140 LEU cc_start: 0.9066 (tt) cc_final: 0.8840 (tt) REVERT: E 199 ARG cc_start: 0.8126 (ttm170) cc_final: 0.7799 (ttm170) outliers start: 1 outliers final: 0 residues processed: 378 average time/residue: 0.0818 time to fit residues: 47.5960 Evaluate side-chains 310 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 309 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 113 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 70 optimal weight: 0.0170 chunk 152 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 64 optimal weight: 8.9990 chunk 131 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 overall best weight: 4.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 GLN B 139 GLN B 285 HIS ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 GLN E 139 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.121307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.093411 restraints weight = 31388.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.096244 restraints weight = 18876.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.098676 restraints weight = 13063.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.100505 restraints weight = 10099.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.101432 restraints weight = 8183.449| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13065 Z= 0.225 Angle : 0.641 5.643 17780 Z= 0.338 Chirality : 0.048 0.148 1955 Planarity : 0.005 0.057 2265 Dihedral : 5.422 24.174 1715 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.22), residues: 1540 helix: 1.01 (0.23), residues: 540 sheet: -0.21 (0.24), residues: 480 loop : -1.85 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 91 TYR 0.019 0.002 TYR D 203 PHE 0.009 0.001 PHE B 247 TRP 0.014 0.002 TRP D 206 HIS 0.004 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00497 (13065) covalent geometry : angle 0.64131 (17780) hydrogen bonds : bond 0.03840 ( 620) hydrogen bonds : angle 5.28181 ( 2040) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 360 time to evaluate : 0.499 Fit side-chains REVERT: A 35 VAL cc_start: 0.9008 (t) cc_final: 0.8805 (t) REVERT: A 39 ILE cc_start: 0.9059 (tp) cc_final: 0.8566 (pt) REVERT: A 64 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8718 (pm20) REVERT: A 77 GLU cc_start: 0.7894 (pp20) cc_final: 0.7503 (pp20) REVERT: A 90 LYS cc_start: 0.8362 (pttt) cc_final: 0.7872 (mttp) REVERT: A 102 TYR cc_start: 0.8367 (t80) cc_final: 0.7870 (t80) REVERT: A 107 LEU cc_start: 0.8074 (tt) cc_final: 0.7821 (tp) REVERT: A 161 TRP cc_start: 0.7151 (m-10) cc_final: 0.6685 (m-10) REVERT: A 198 VAL cc_start: 0.8859 (p) cc_final: 0.8579 (m) REVERT: A 203 TYR cc_start: 0.8536 (t80) cc_final: 0.8298 (t80) REVERT: A 212 LEU cc_start: 0.9064 (tp) cc_final: 0.8720 (tp) REVERT: A 265 MET cc_start: 0.8823 (ttt) cc_final: 0.8444 (ttt) REVERT: B 64 GLU cc_start: 0.9158 (mt-10) cc_final: 0.8728 (pm20) REVERT: B 77 GLU cc_start: 0.7733 (pp20) cc_final: 0.7362 (pp20) REVERT: B 102 TYR cc_start: 0.8412 (t80) cc_final: 0.8082 (t80) REVERT: B 107 LEU cc_start: 0.8028 (tt) cc_final: 0.7674 (tt) REVERT: B 198 VAL cc_start: 0.9004 (p) cc_final: 0.8646 (m) REVERT: B 223 PHE cc_start: 0.8591 (m-10) cc_final: 0.8220 (m-10) REVERT: B 265 MET cc_start: 0.8907 (ttt) cc_final: 0.8692 (ttt) REVERT: C 39 ILE cc_start: 0.9128 (tp) cc_final: 0.8595 (pt) REVERT: C 64 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8664 (pm20) REVERT: C 93 MET cc_start: 0.8999 (tpp) cc_final: 0.8694 (tpp) REVERT: C 102 TYR cc_start: 0.8637 (t80) cc_final: 0.8148 (t80) REVERT: C 115 ASP cc_start: 0.7831 (t0) cc_final: 0.7610 (t0) REVERT: C 131 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8484 (mt-10) REVERT: C 148 TYR cc_start: 0.8071 (m-80) cc_final: 0.7852 (m-80) REVERT: C 199 ARG cc_start: 0.8117 (ttp-170) cc_final: 0.7881 (ttp-170) REVERT: C 212 LEU cc_start: 0.9030 (tp) cc_final: 0.8568 (tp) REVERT: C 266 ILE cc_start: 0.8605 (tp) cc_final: 0.7965 (tp) REVERT: D 39 ILE cc_start: 0.9069 (tp) cc_final: 0.8583 (pt) REVERT: D 64 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8629 (pm20) REVERT: D 102 TYR cc_start: 0.8427 (t80) cc_final: 0.8034 (t80) REVERT: D 131 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8108 (mt-10) REVERT: D 198 VAL cc_start: 0.8976 (p) cc_final: 0.8727 (m) REVERT: D 199 ARG cc_start: 0.8205 (ttp-170) cc_final: 0.7930 (ttm-80) REVERT: D 203 TYR cc_start: 0.8563 (t80) cc_final: 0.8351 (t80) REVERT: D 212 LEU cc_start: 0.9028 (tp) cc_final: 0.8701 (tp) REVERT: D 265 MET cc_start: 0.8773 (ttt) cc_final: 0.8509 (ttt) REVERT: E 64 GLU cc_start: 0.9171 (mt-10) cc_final: 0.8674 (pm20) REVERT: E 102 TYR cc_start: 0.8352 (t80) cc_final: 0.7946 (t80) REVERT: E 131 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8482 (mt-10) REVERT: E 140 LEU cc_start: 0.9143 (tt) cc_final: 0.8886 (tt) REVERT: E 199 ARG cc_start: 0.8045 (ttm170) cc_final: 0.7743 (ttp80) REVERT: E 203 TYR cc_start: 0.8419 (t80) cc_final: 0.8082 (t80) outliers start: 0 outliers final: 0 residues processed: 360 average time/residue: 0.0907 time to fit residues: 49.5916 Evaluate side-chains 301 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 109 optimal weight: 10.0000 chunk 87 optimal weight: 0.0070 chunk 20 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 28 optimal weight: 0.5980 chunk 93 optimal weight: 9.9990 overall best weight: 0.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 GLN B 139 GLN C 139 GLN ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 GLN E 139 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.127266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.098678 restraints weight = 30035.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.101836 restraints weight = 17613.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.103489 restraints weight = 12383.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.105992 restraints weight = 10015.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.107156 restraints weight = 8007.936| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13065 Z= 0.112 Angle : 0.561 5.499 17780 Z= 0.296 Chirality : 0.047 0.170 1955 Planarity : 0.004 0.049 2265 Dihedral : 4.981 29.925 1715 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.22), residues: 1540 helix: 1.18 (0.23), residues: 540 sheet: -0.04 (0.25), residues: 450 loop : -1.82 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 199 TYR 0.020 0.001 TYR C 203 PHE 0.014 0.001 PHE E 274 TRP 0.020 0.001 TRP B 220 HIS 0.003 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00255 (13065) covalent geometry : angle 0.56141 (17780) hydrogen bonds : bond 0.03284 ( 620) hydrogen bonds : angle 4.79673 ( 2040) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 383 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.8559 (mttp) cc_final: 0.8299 (mptt) REVERT: A 39 ILE cc_start: 0.9011 (tp) cc_final: 0.8655 (pt) REVERT: A 64 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8677 (pm20) REVERT: A 102 TYR cc_start: 0.8324 (t80) cc_final: 0.8080 (t80) REVERT: A 198 VAL cc_start: 0.8853 (p) cc_final: 0.8642 (m) REVERT: A 212 LEU cc_start: 0.9051 (tp) cc_final: 0.8633 (tp) REVERT: A 265 MET cc_start: 0.8744 (ttt) cc_final: 0.8315 (ttt) REVERT: A 301 ARG cc_start: 0.6318 (ptp90) cc_final: 0.6048 (ptp90) REVERT: B 64 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8660 (pm20) REVERT: B 77 GLU cc_start: 0.7828 (pp20) cc_final: 0.7605 (pp20) REVERT: B 102 TYR cc_start: 0.8346 (t80) cc_final: 0.8089 (t80) REVERT: B 115 ASP cc_start: 0.7698 (t70) cc_final: 0.6595 (m-30) REVERT: B 148 TYR cc_start: 0.7849 (m-80) cc_final: 0.7607 (m-80) REVERT: B 191 ILE cc_start: 0.8737 (mt) cc_final: 0.8524 (mt) REVERT: B 198 VAL cc_start: 0.8979 (p) cc_final: 0.8646 (m) REVERT: B 199 ARG cc_start: 0.8292 (ttm-80) cc_final: 0.7918 (ttm-80) REVERT: B 221 SER cc_start: 0.8618 (m) cc_final: 0.8390 (p) REVERT: B 265 MET cc_start: 0.8916 (ttt) cc_final: 0.8697 (ttt) REVERT: B 301 ARG cc_start: 0.7389 (ptp90) cc_final: 0.7053 (ptp90) REVERT: C 39 ILE cc_start: 0.9076 (tp) cc_final: 0.8637 (pt) REVERT: C 64 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8608 (pm20) REVERT: C 93 MET cc_start: 0.8897 (tpp) cc_final: 0.8515 (tpp) REVERT: C 102 TYR cc_start: 0.8593 (t80) cc_final: 0.8073 (t80) REVERT: C 107 LEU cc_start: 0.7855 (tp) cc_final: 0.7564 (tp) REVERT: C 140 LEU cc_start: 0.9131 (tt) cc_final: 0.8916 (tt) REVERT: C 199 ARG cc_start: 0.7894 (ttp-170) cc_final: 0.7625 (ttp-170) REVERT: C 210 LEU cc_start: 0.9018 (tt) cc_final: 0.8798 (tp) REVERT: C 212 LEU cc_start: 0.9040 (tp) cc_final: 0.8775 (tp) REVERT: C 221 SER cc_start: 0.8636 (m) cc_final: 0.8325 (p) REVERT: C 265 MET cc_start: 0.8740 (ttt) cc_final: 0.8446 (ttt) REVERT: C 266 ILE cc_start: 0.8491 (tp) cc_final: 0.8185 (mt) REVERT: D 39 ILE cc_start: 0.9067 (tp) cc_final: 0.8641 (pt) REVERT: D 64 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8596 (pm20) REVERT: D 102 TYR cc_start: 0.8377 (t80) cc_final: 0.8022 (t80) REVERT: D 107 LEU cc_start: 0.7709 (tp) cc_final: 0.6452 (mp) REVERT: D 140 LEU cc_start: 0.9175 (tt) cc_final: 0.8950 (tt) REVERT: D 198 VAL cc_start: 0.8955 (p) cc_final: 0.8662 (m) REVERT: D 199 ARG cc_start: 0.8016 (ttp-170) cc_final: 0.7503 (ttp-170) REVERT: D 212 LEU cc_start: 0.8976 (tp) cc_final: 0.8665 (tp) REVERT: D 239 MET cc_start: 0.9082 (ttp) cc_final: 0.8753 (ttt) REVERT: D 265 MET cc_start: 0.8675 (ttt) cc_final: 0.8412 (ttt) REVERT: E 34 LYS cc_start: 0.8679 (mtpp) cc_final: 0.8443 (mptt) REVERT: E 56 LEU cc_start: 0.9307 (tp) cc_final: 0.9091 (tp) REVERT: E 102 TYR cc_start: 0.8286 (t80) cc_final: 0.7890 (t80) REVERT: E 107 LEU cc_start: 0.7683 (tt) cc_final: 0.7109 (tt) REVERT: E 114 MET cc_start: 0.7553 (mtm) cc_final: 0.7170 (ttm) REVERT: E 115 ASP cc_start: 0.7920 (t70) cc_final: 0.6755 (m-30) REVERT: E 131 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8461 (mt-10) REVERT: E 140 LEU cc_start: 0.9084 (tt) cc_final: 0.8841 (tt) REVERT: E 212 LEU cc_start: 0.8909 (tp) cc_final: 0.8678 (tp) REVERT: E 265 MET cc_start: 0.8761 (ttt) cc_final: 0.8496 (ttt) outliers start: 0 outliers final: 0 residues processed: 383 average time/residue: 0.0900 time to fit residues: 53.1212 Evaluate side-chains 315 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 64 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 126 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 110 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 chunk 48 optimal weight: 20.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 GLN E 285 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.120503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.092944 restraints weight = 31313.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.096186 restraints weight = 19108.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.098057 restraints weight = 13254.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.099689 restraints weight = 10282.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.100665 restraints weight = 8525.740| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 13065 Z= 0.264 Angle : 0.693 7.396 17780 Z= 0.368 Chirality : 0.049 0.157 1955 Planarity : 0.005 0.064 2265 Dihedral : 5.647 23.570 1715 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.22), residues: 1540 helix: 0.94 (0.23), residues: 540 sheet: -0.46 (0.25), residues: 450 loop : -1.96 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 199 TYR 0.026 0.003 TYR E 204 PHE 0.018 0.002 PHE A 228 TRP 0.017 0.002 TRP C 206 HIS 0.004 0.002 HIS A 284 Details of bonding type rmsd covalent geometry : bond 0.00580 (13065) covalent geometry : angle 0.69333 (17780) hydrogen bonds : bond 0.04008 ( 620) hydrogen bonds : angle 5.42495 ( 2040) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 0.398 Fit side-chains REVERT: A 39 ILE cc_start: 0.9028 (tp) cc_final: 0.8538 (pt) REVERT: A 64 GLU cc_start: 0.9234 (mt-10) cc_final: 0.8731 (pm20) REVERT: A 77 GLU cc_start: 0.7770 (pp20) cc_final: 0.7444 (pp20) REVERT: A 90 LYS cc_start: 0.8490 (pttt) cc_final: 0.7963 (mttp) REVERT: A 102 TYR cc_start: 0.8323 (t80) cc_final: 0.7775 (t80) REVERT: A 107 LEU cc_start: 0.7997 (tt) cc_final: 0.7502 (tt) REVERT: A 161 TRP cc_start: 0.7127 (m-10) cc_final: 0.6803 (m-10) REVERT: A 198 VAL cc_start: 0.8932 (p) cc_final: 0.8631 (m) REVERT: A 203 TYR cc_start: 0.8584 (t80) cc_final: 0.8112 (t80) REVERT: A 212 LEU cc_start: 0.9185 (tp) cc_final: 0.8856 (tp) REVERT: A 265 MET cc_start: 0.8790 (ttt) cc_final: 0.8408 (ttt) REVERT: A 301 ARG cc_start: 0.6958 (ptp90) cc_final: 0.6642 (ptp90) REVERT: B 64 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8657 (pm20) REVERT: B 102 TYR cc_start: 0.8430 (t80) cc_final: 0.8041 (t80) REVERT: B 115 ASP cc_start: 0.7631 (t70) cc_final: 0.7411 (t0) REVERT: B 198 VAL cc_start: 0.9002 (p) cc_final: 0.8654 (m) REVERT: B 199 ARG cc_start: 0.8294 (ttm-80) cc_final: 0.7958 (ttm-80) REVERT: C 39 ILE cc_start: 0.9075 (tp) cc_final: 0.8483 (pt) REVERT: C 64 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8700 (pm20) REVERT: C 93 MET cc_start: 0.9015 (tpp) cc_final: 0.8668 (tpp) REVERT: C 102 TYR cc_start: 0.8577 (t80) cc_final: 0.8043 (t80) REVERT: C 107 LEU cc_start: 0.8070 (tp) cc_final: 0.7815 (tp) REVERT: C 140 LEU cc_start: 0.9166 (tt) cc_final: 0.8916 (tt) REVERT: C 148 TYR cc_start: 0.7964 (m-80) cc_final: 0.7734 (m-80) REVERT: C 150 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7220 (tm-30) REVERT: C 212 LEU cc_start: 0.9189 (tp) cc_final: 0.8912 (tp) REVERT: C 265 MET cc_start: 0.8706 (ttt) cc_final: 0.8387 (ttt) REVERT: C 266 ILE cc_start: 0.8617 (tp) cc_final: 0.7831 (tp) REVERT: C 301 ARG cc_start: 0.7434 (ptp90) cc_final: 0.7122 (ptp90) REVERT: D 39 ILE cc_start: 0.9057 (tp) cc_final: 0.8584 (pt) REVERT: D 64 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8668 (pm20) REVERT: D 77 GLU cc_start: 0.7607 (pp20) cc_final: 0.7115 (pp20) REVERT: D 102 TYR cc_start: 0.8411 (t80) cc_final: 0.7977 (t80) REVERT: D 107 LEU cc_start: 0.7896 (tp) cc_final: 0.7584 (tt) REVERT: D 150 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7285 (tm-30) REVERT: D 198 VAL cc_start: 0.9004 (p) cc_final: 0.8794 (m) REVERT: D 199 ARG cc_start: 0.8128 (ttp-170) cc_final: 0.7824 (ttm-80) REVERT: D 203 TYR cc_start: 0.8638 (t80) cc_final: 0.8195 (t80) REVERT: D 212 LEU cc_start: 0.9005 (tp) cc_final: 0.8668 (tp) REVERT: D 265 MET cc_start: 0.8707 (ttt) cc_final: 0.8456 (ttt) REVERT: D 266 ILE cc_start: 0.8692 (tp) cc_final: 0.8456 (tp) REVERT: E 39 ILE cc_start: 0.9030 (tp) cc_final: 0.8617 (pt) REVERT: E 64 GLU cc_start: 0.9188 (mt-10) cc_final: 0.8706 (pm20) REVERT: E 102 TYR cc_start: 0.8365 (t80) cc_final: 0.7927 (t80) REVERT: E 107 LEU cc_start: 0.8088 (tt) cc_final: 0.7805 (tt) REVERT: E 114 MET cc_start: 0.7605 (mtm) cc_final: 0.7246 (ttm) REVERT: E 131 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8341 (mt-10) REVERT: E 140 LEU cc_start: 0.9114 (tt) cc_final: 0.8845 (tt) REVERT: E 152 ILE cc_start: 0.8281 (pt) cc_final: 0.7967 (pt) REVERT: E 199 ARG cc_start: 0.8007 (ttm170) cc_final: 0.7553 (ttp80) REVERT: E 203 TYR cc_start: 0.8414 (t80) cc_final: 0.8031 (t80) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.0881 time to fit residues: 49.3985 Evaluate side-chains 310 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 11 optimal weight: 0.8980 chunk 122 optimal weight: 8.9990 chunk 136 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 154 optimal weight: 0.0870 chunk 106 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 142 optimal weight: 5.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 GLN C 139 GLN ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 GLN E 139 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.126099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.097854 restraints weight = 30483.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.101074 restraints weight = 18560.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.103195 restraints weight = 13026.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.104511 restraints weight = 10131.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.104874 restraints weight = 8560.993| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13065 Z= 0.123 Angle : 0.591 6.048 17780 Z= 0.313 Chirality : 0.048 0.146 1955 Planarity : 0.004 0.053 2265 Dihedral : 5.163 21.481 1715 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.22), residues: 1540 helix: 1.29 (0.23), residues: 540 sheet: -0.33 (0.25), residues: 450 loop : -1.90 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 199 TYR 0.020 0.001 TYR C 203 PHE 0.016 0.001 PHE D 228 TRP 0.027 0.001 TRP D 220 HIS 0.006 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00294 (13065) covalent geometry : angle 0.59096 (17780) hydrogen bonds : bond 0.03406 ( 620) hydrogen bonds : angle 4.98799 ( 2040) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 0.426 Fit side-chains REVERT: A 59 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7978 (mm-30) REVERT: A 64 GLU cc_start: 0.9158 (mt-10) cc_final: 0.8733 (pm20) REVERT: A 102 TYR cc_start: 0.8284 (t80) cc_final: 0.7875 (t80) REVERT: A 140 LEU cc_start: 0.9225 (tt) cc_final: 0.9020 (tt) REVERT: A 198 VAL cc_start: 0.8846 (p) cc_final: 0.8602 (m) REVERT: A 209 ILE cc_start: 0.8737 (pt) cc_final: 0.8530 (pt) REVERT: A 212 LEU cc_start: 0.9138 (tp) cc_final: 0.8792 (tp) REVERT: A 265 MET cc_start: 0.8666 (ttt) cc_final: 0.8261 (ttt) REVERT: A 301 ARG cc_start: 0.6770 (ptp90) cc_final: 0.6418 (ptp90) REVERT: B 64 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8664 (pm20) REVERT: B 79 ILE cc_start: 0.9071 (mm) cc_final: 0.8767 (mm) REVERT: B 102 TYR cc_start: 0.8331 (t80) cc_final: 0.8001 (t80) REVERT: B 115 ASP cc_start: 0.7618 (t70) cc_final: 0.6401 (m-30) REVERT: B 129 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7226 (mt-10) REVERT: B 131 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8242 (mt-10) REVERT: B 198 VAL cc_start: 0.8976 (p) cc_final: 0.8676 (m) REVERT: B 199 ARG cc_start: 0.8253 (ttm-80) cc_final: 0.7914 (ttm-80) REVERT: B 212 LEU cc_start: 0.9127 (tp) cc_final: 0.8890 (tp) REVERT: B 301 ARG cc_start: 0.7456 (ptp90) cc_final: 0.7212 (ptp90) REVERT: C 64 GLU cc_start: 0.9113 (mt-10) cc_final: 0.8636 (pm20) REVERT: C 102 TYR cc_start: 0.8507 (t80) cc_final: 0.8071 (t80) REVERT: C 107 LEU cc_start: 0.7954 (tp) cc_final: 0.7599 (tp) REVERT: C 115 ASP cc_start: 0.7664 (t70) cc_final: 0.6536 (m-30) REVERT: C 131 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8301 (mt-10) REVERT: C 140 LEU cc_start: 0.9113 (tt) cc_final: 0.8882 (tt) REVERT: C 150 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7337 (tm-30) REVERT: C 191 ILE cc_start: 0.8837 (mt) cc_final: 0.8601 (mt) REVERT: C 212 LEU cc_start: 0.9107 (tp) cc_final: 0.8797 (tp) REVERT: C 265 MET cc_start: 0.8644 (ttt) cc_final: 0.8309 (ttt) REVERT: C 266 ILE cc_start: 0.8604 (tp) cc_final: 0.7776 (tp) REVERT: C 301 ARG cc_start: 0.7714 (ptp-170) cc_final: 0.6937 (ttp-170) REVERT: D 39 ILE cc_start: 0.9057 (tp) cc_final: 0.8596 (pt) REVERT: D 64 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8595 (pm20) REVERT: D 102 TYR cc_start: 0.8376 (t80) cc_final: 0.7895 (t80) REVERT: D 107 LEU cc_start: 0.7820 (tp) cc_final: 0.7208 (tt) REVERT: D 198 VAL cc_start: 0.8986 (p) cc_final: 0.8755 (m) REVERT: D 199 ARG cc_start: 0.8089 (ttp-170) cc_final: 0.7761 (ttm-80) REVERT: D 212 LEU cc_start: 0.9144 (tp) cc_final: 0.8860 (tp) REVERT: D 265 MET cc_start: 0.8594 (ttt) cc_final: 0.8346 (ttt) REVERT: D 301 ARG cc_start: 0.6554 (ptp90) cc_final: 0.6293 (ttp-170) REVERT: E 34 LYS cc_start: 0.8456 (mttp) cc_final: 0.8251 (mmtm) REVERT: E 77 GLU cc_start: 0.7818 (pp20) cc_final: 0.7488 (pp20) REVERT: E 102 TYR cc_start: 0.8310 (t80) cc_final: 0.7909 (t80) REVERT: E 107 LEU cc_start: 0.7777 (tt) cc_final: 0.7354 (tt) REVERT: E 114 MET cc_start: 0.7630 (mtm) cc_final: 0.7267 (ttm) REVERT: E 115 ASP cc_start: 0.7900 (t70) cc_final: 0.6689 (m-30) REVERT: E 131 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8357 (mt-10) REVERT: E 265 MET cc_start: 0.8708 (ttt) cc_final: 0.8479 (ttt) REVERT: E 301 ARG cc_start: 0.6740 (ptp90) cc_final: 0.6394 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 377 average time/residue: 0.0827 time to fit residues: 47.6873 Evaluate side-chains 312 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 136 optimal weight: 8.9990 chunk 68 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 69 optimal weight: 0.0870 chunk 28 optimal weight: 0.0570 chunk 14 optimal weight: 8.9990 chunk 74 optimal weight: 0.6980 overall best weight: 2.1680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 GLN B 139 GLN C 139 GLN ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 GLN E 139 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.123624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.095578 restraints weight = 30749.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.098897 restraints weight = 18178.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.101163 restraints weight = 12579.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.102578 restraints weight = 9639.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.103047 restraints weight = 8037.282| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13065 Z= 0.144 Angle : 0.598 5.897 17780 Z= 0.313 Chirality : 0.048 0.216 1955 Planarity : 0.004 0.051 2265 Dihedral : 5.083 20.990 1715 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.22), residues: 1540 helix: 1.23 (0.23), residues: 540 sheet: -0.40 (0.25), residues: 450 loop : -1.89 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 199 TYR 0.019 0.002 TYR A 203 PHE 0.016 0.001 PHE B 228 TRP 0.016 0.001 TRP B 206 HIS 0.004 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00335 (13065) covalent geometry : angle 0.59800 (17780) hydrogen bonds : bond 0.03471 ( 620) hydrogen bonds : angle 5.02314 ( 2040) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.9198 (mt-10) cc_final: 0.8706 (pm20) REVERT: A 102 TYR cc_start: 0.8317 (t80) cc_final: 0.7913 (t80) REVERT: A 140 LEU cc_start: 0.9267 (tt) cc_final: 0.9052 (tt) REVERT: A 198 VAL cc_start: 0.8841 (p) cc_final: 0.8592 (m) REVERT: A 199 ARG cc_start: 0.8297 (ttm-80) cc_final: 0.8030 (ttm-80) REVERT: A 212 LEU cc_start: 0.9112 (tp) cc_final: 0.8746 (tp) REVERT: A 265 MET cc_start: 0.8766 (ttt) cc_final: 0.8380 (ttt) REVERT: A 301 ARG cc_start: 0.6884 (ptp90) cc_final: 0.6659 (ptp90) REVERT: B 64 GLU cc_start: 0.9135 (mt-10) cc_final: 0.8691 (pm20) REVERT: B 102 TYR cc_start: 0.8361 (t80) cc_final: 0.7935 (t80) REVERT: B 107 LEU cc_start: 0.7712 (tt) cc_final: 0.7492 (tp) REVERT: B 114 MET cc_start: 0.7876 (mtt) cc_final: 0.7626 (ttm) REVERT: B 115 ASP cc_start: 0.7668 (t70) cc_final: 0.6578 (m-30) REVERT: B 131 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8182 (mt-10) REVERT: B 198 VAL cc_start: 0.8963 (p) cc_final: 0.8620 (m) REVERT: B 199 ARG cc_start: 0.8334 (ttm-80) cc_final: 0.7960 (ttm-80) REVERT: B 212 LEU cc_start: 0.9130 (tp) cc_final: 0.8909 (tp) REVERT: B 301 ARG cc_start: 0.7390 (ptp90) cc_final: 0.7120 (ptp90) REVERT: C 39 ILE cc_start: 0.9174 (tp) cc_final: 0.8695 (pt) REVERT: C 64 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8648 (pm20) REVERT: C 102 TYR cc_start: 0.8604 (t80) cc_final: 0.8192 (t80) REVERT: C 107 LEU cc_start: 0.7910 (tp) cc_final: 0.7633 (tp) REVERT: C 131 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8262 (mt-10) REVERT: C 140 LEU cc_start: 0.9186 (tt) cc_final: 0.8966 (tt) REVERT: C 150 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7352 (tm-30) REVERT: C 212 LEU cc_start: 0.9103 (tp) cc_final: 0.8798 (tp) REVERT: C 265 MET cc_start: 0.8703 (ttt) cc_final: 0.8374 (ttt) REVERT: C 266 ILE cc_start: 0.8611 (tp) cc_final: 0.7883 (tp) REVERT: C 294 ASP cc_start: 0.7613 (m-30) cc_final: 0.6967 (m-30) REVERT: D 39 ILE cc_start: 0.9115 (tp) cc_final: 0.8666 (pt) REVERT: D 64 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8637 (pm20) REVERT: D 102 TYR cc_start: 0.8467 (t80) cc_final: 0.8007 (t80) REVERT: D 107 LEU cc_start: 0.7767 (tp) cc_final: 0.7477 (tt) REVERT: D 198 VAL cc_start: 0.8989 (p) cc_final: 0.8746 (m) REVERT: D 199 ARG cc_start: 0.8148 (ttp-170) cc_final: 0.7815 (ttm-80) REVERT: D 212 LEU cc_start: 0.9084 (tp) cc_final: 0.8769 (tp) REVERT: D 265 MET cc_start: 0.8706 (ttt) cc_final: 0.8421 (ttt) REVERT: D 266 ILE cc_start: 0.8450 (tp) cc_final: 0.8215 (tp) REVERT: D 301 ARG cc_start: 0.6632 (ptp90) cc_final: 0.6394 (ttp-170) REVERT: E 64 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8679 (pm20) REVERT: E 102 TYR cc_start: 0.8424 (t80) cc_final: 0.7921 (t80) REVERT: E 107 LEU cc_start: 0.7857 (tt) cc_final: 0.7325 (tt) REVERT: E 131 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8266 (mt-10) REVERT: E 212 LEU cc_start: 0.9028 (tp) cc_final: 0.8798 (tp) REVERT: E 265 MET cc_start: 0.8802 (ttt) cc_final: 0.8580 (ttt) REVERT: E 301 ARG cc_start: 0.6703 (ptp90) cc_final: 0.6352 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 0.0882 time to fit residues: 50.6485 Evaluate side-chains 314 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 79 optimal weight: 0.3980 chunk 152 optimal weight: 0.0000 chunk 100 optimal weight: 0.1980 chunk 147 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 51 optimal weight: 0.4980 chunk 8 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 GLN B 139 GLN C 139 GLN ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 GLN E 139 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.128966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.100382 restraints weight = 30380.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.103821 restraints weight = 17958.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.106186 restraints weight = 12440.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.107915 restraints weight = 9519.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.109092 restraints weight = 7818.960| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13065 Z= 0.113 Angle : 0.583 6.496 17780 Z= 0.301 Chirality : 0.047 0.163 1955 Planarity : 0.004 0.050 2265 Dihedral : 4.743 17.558 1715 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.22), residues: 1540 helix: 1.29 (0.23), residues: 540 sheet: -0.09 (0.25), residues: 485 loop : -1.66 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 91 TYR 0.020 0.001 TYR C 203 PHE 0.023 0.001 PHE C 274 TRP 0.017 0.002 TRP D 220 HIS 0.003 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00269 (13065) covalent geometry : angle 0.58268 (17780) hydrogen bonds : bond 0.03220 ( 620) hydrogen bonds : angle 4.75699 ( 2040) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8776 (pm20) REVERT: A 102 TYR cc_start: 0.8281 (t80) cc_final: 0.7991 (t80) REVERT: A 198 VAL cc_start: 0.8802 (p) cc_final: 0.8540 (m) REVERT: A 199 ARG cc_start: 0.8208 (ttm-80) cc_final: 0.7337 (ttp-170) REVERT: A 210 LEU cc_start: 0.8983 (tp) cc_final: 0.8762 (tt) REVERT: A 212 LEU cc_start: 0.9060 (tp) cc_final: 0.8807 (tp) REVERT: A 214 LEU cc_start: 0.8409 (mp) cc_final: 0.8151 (mp) REVERT: A 265 MET cc_start: 0.8686 (ttt) cc_final: 0.8471 (ttt) REVERT: A 301 ARG cc_start: 0.6655 (ptp90) cc_final: 0.6335 (ptp90) REVERT: B 64 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8614 (pm20) REVERT: B 102 TYR cc_start: 0.8237 (t80) cc_final: 0.7896 (t80) REVERT: B 114 MET cc_start: 0.7857 (mtt) cc_final: 0.7626 (ttm) REVERT: B 115 ASP cc_start: 0.7694 (t70) cc_final: 0.6711 (m-30) REVERT: B 148 TYR cc_start: 0.7712 (m-80) cc_final: 0.7261 (m-80) REVERT: B 198 VAL cc_start: 0.8930 (p) cc_final: 0.8605 (m) REVERT: B 199 ARG cc_start: 0.8329 (ttm-80) cc_final: 0.7955 (ttm-80) REVERT: B 212 LEU cc_start: 0.9112 (tp) cc_final: 0.8846 (tp) REVERT: C 34 LYS cc_start: 0.8617 (mttp) cc_final: 0.8365 (mptt) REVERT: C 64 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8573 (pm20) REVERT: C 77 GLU cc_start: 0.7784 (pp20) cc_final: 0.7369 (pp20) REVERT: C 102 TYR cc_start: 0.8517 (t80) cc_final: 0.8048 (t80) REVERT: C 115 ASP cc_start: 0.7793 (t0) cc_final: 0.6576 (m-30) REVERT: C 131 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8235 (mt-10) REVERT: C 150 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7314 (tm-30) REVERT: C 191 ILE cc_start: 0.8851 (mt) cc_final: 0.8643 (mt) REVERT: C 212 LEU cc_start: 0.9061 (tp) cc_final: 0.8770 (tp) REVERT: C 221 SER cc_start: 0.8656 (m) cc_final: 0.8334 (p) REVERT: C 265 MET cc_start: 0.8616 (ttt) cc_final: 0.8330 (ttt) REVERT: C 294 ASP cc_start: 0.7551 (m-30) cc_final: 0.6916 (m-30) REVERT: C 301 ARG cc_start: 0.7582 (ptp-170) cc_final: 0.6825 (ttp-170) REVERT: D 64 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8578 (pm20) REVERT: D 102 TYR cc_start: 0.8308 (t80) cc_final: 0.7915 (t80) REVERT: D 107 LEU cc_start: 0.7643 (tp) cc_final: 0.7381 (tt) REVERT: D 198 VAL cc_start: 0.8939 (p) cc_final: 0.8652 (m) REVERT: D 199 ARG cc_start: 0.8036 (ttp-170) cc_final: 0.7496 (ttp-170) REVERT: D 212 LEU cc_start: 0.9041 (tp) cc_final: 0.8772 (tp) REVERT: D 265 MET cc_start: 0.8574 (ttt) cc_final: 0.8308 (ttt) REVERT: D 266 ILE cc_start: 0.8529 (tp) cc_final: 0.8043 (tp) REVERT: D 294 ASP cc_start: 0.7692 (m-30) cc_final: 0.7469 (m-30) REVERT: D 301 ARG cc_start: 0.6259 (ptp90) cc_final: 0.6013 (ttp-170) REVERT: E 102 TYR cc_start: 0.8322 (t80) cc_final: 0.7949 (t80) REVERT: E 107 LEU cc_start: 0.7543 (tt) cc_final: 0.7267 (tt) REVERT: E 115 ASP cc_start: 0.8022 (t0) cc_final: 0.6705 (m-30) REVERT: E 131 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8409 (mt-10) REVERT: E 212 LEU cc_start: 0.9011 (tp) cc_final: 0.8773 (tp) REVERT: E 265 MET cc_start: 0.8728 (ttt) cc_final: 0.8485 (ttt) REVERT: E 301 ARG cc_start: 0.6545 (ptp90) cc_final: 0.6304 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 403 average time/residue: 0.0792 time to fit residues: 49.2364 Evaluate side-chains 303 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 111 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 chunk 141 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 chunk 14 optimal weight: 0.0060 chunk 51 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 GLN A 139 GLN B 139 GLN C 139 GLN ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 GLN E 139 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.128057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.100354 restraints weight = 30393.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.103584 restraints weight = 18519.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.105164 restraints weight = 12982.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.107281 restraints weight = 10578.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.108338 restraints weight = 8658.163| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13065 Z= 0.120 Angle : 0.581 6.540 17780 Z= 0.301 Chirality : 0.047 0.196 1955 Planarity : 0.004 0.057 2265 Dihedral : 4.719 16.799 1715 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.22), residues: 1540 helix: 1.21 (0.22), residues: 540 sheet: -0.03 (0.25), residues: 460 loop : -1.64 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 199 TYR 0.019 0.001 TYR C 203 PHE 0.017 0.001 PHE D 274 TRP 0.015 0.002 TRP D 206 HIS 0.003 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00286 (13065) covalent geometry : angle 0.58104 (17780) hydrogen bonds : bond 0.03164 ( 620) hydrogen bonds : angle 4.75894 ( 2040) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2171.04 seconds wall clock time: 38 minutes 4.49 seconds (2284.49 seconds total)