Starting phenix.real_space_refine on Fri Jun 5 12:56:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dav_46699/06_2026/9dav_46699_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dav_46699/06_2026/9dav_46699.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dav_46699/06_2026/9dav_46699.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dav_46699/06_2026/9dav_46699.map" model { file = "/net/cci-nas-00/data/ceres_data/9dav_46699/06_2026/9dav_46699_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dav_46699/06_2026/9dav_46699_trim.cif" } resolution = 2.8 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 52 5.16 5 C 6482 2.51 5 N 1786 2.21 5 O 1820 1.98 5 H 10060 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20204 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 5013 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 17, 'TRANS': 300} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 5013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 5013 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 17, 'TRANS': 300} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 5013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 5013 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 17, 'TRANS': 300} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 5013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 5013 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 17, 'TRANS': 300} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'Y6H': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'1SY': 1, 'Y6H': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.61, per 1000 atoms: 0.18 Number of scatterers: 20204 At special positions: 0 Unit cell: (89.832, 96.924, 104.016, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 52 16.00 P 4 15.00 O 1820 8.00 N 1786 7.00 C 6482 6.00 H 10060 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 523.8 milliseconds 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2368 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 8 sheets defined 64.5% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 16 through 37 Processing helix chain 'A' and resid 39 through 70 removed outlier: 3.556A pdb=" N THR A 43 " --> pdb=" O PRO A 39 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU A 68 " --> pdb=" O CYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 80 through 90 Processing helix chain 'A' and resid 91 through 108 Processing helix chain 'A' and resid 117 through 134 Processing helix chain 'A' and resid 140 through 152 Processing helix chain 'A' and resid 154 through 167 removed outlier: 3.794A pdb=" N GLY A 158 " --> pdb=" O ASN A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 removed outlier: 5.159A pdb=" N LEU A 172 " --> pdb=" O ARG A 169 " (cutoff:3.500A) Proline residue: A 173 - end of helix Processing helix chain 'A' and resid 174 through 185 removed outlier: 3.772A pdb=" N ARG A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 272 removed outlier: 3.545A pdb=" N THR A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 278 removed outlier: 6.404A pdb=" N GLN A 276 " --> pdb=" O GLN A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 302 removed outlier: 3.597A pdb=" N ASP A 301 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 335 removed outlier: 3.524A pdb=" N GLN A 335 " --> pdb=" O ARG A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 37 Processing helix chain 'B' and resid 39 through 70 removed outlier: 3.607A pdb=" N THR B 43 " --> pdb=" O PRO B 39 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU B 68 " --> pdb=" O CYS B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 78 removed outlier: 3.522A pdb=" N ARG B 78 " --> pdb=" O HIS B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 90 Processing helix chain 'B' and resid 91 through 109 Processing helix chain 'B' and resid 117 through 134 Processing helix chain 'B' and resid 140 through 152 Processing helix chain 'B' and resid 154 through 167 removed outlier: 3.841A pdb=" N GLY B 158 " --> pdb=" O ASN B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 185 Proline residue: B 173 - end of helix removed outlier: 4.511A pdb=" N GLN B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ALA B 177 " --> pdb=" O PRO B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 215 Processing helix chain 'B' and resid 262 through 274 removed outlier: 3.784A pdb=" N GLN B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 301 removed outlier: 3.812A pdb=" N ASP B 301 " --> pdb=" O ASP B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 335 Processing helix chain 'C' and resid 16 through 37 Processing helix chain 'C' and resid 39 through 70 removed outlier: 3.556A pdb=" N THR C 43 " --> pdb=" O PRO C 39 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU C 68 " --> pdb=" O CYS C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 77 Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 91 through 108 Processing helix chain 'C' and resid 117 through 134 Processing helix chain 'C' and resid 140 through 152 Processing helix chain 'C' and resid 154 through 167 removed outlier: 3.795A pdb=" N GLY C 158 " --> pdb=" O ASN C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 173 removed outlier: 5.159A pdb=" N LEU C 172 " --> pdb=" O ARG C 169 " (cutoff:3.500A) Proline residue: C 173 - end of helix Processing helix chain 'C' and resid 174 through 185 removed outlier: 3.772A pdb=" N ARG C 178 " --> pdb=" O GLU C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 272 removed outlier: 3.544A pdb=" N THR C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 278 removed outlier: 6.403A pdb=" N GLN C 276 " --> pdb=" O GLN C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 302 removed outlier: 3.597A pdb=" N ASP C 301 " --> pdb=" O ASP C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 335 removed outlier: 3.523A pdb=" N GLN C 335 " --> pdb=" O ARG C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 37 Processing helix chain 'D' and resid 39 through 70 removed outlier: 3.608A pdb=" N THR D 43 " --> pdb=" O PRO D 39 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU D 68 " --> pdb=" O CYS D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 78 removed outlier: 3.522A pdb=" N ARG D 78 " --> pdb=" O HIS D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 90 Processing helix chain 'D' and resid 91 through 109 Processing helix chain 'D' and resid 117 through 134 Processing helix chain 'D' and resid 140 through 152 Processing helix chain 'D' and resid 154 through 167 removed outlier: 3.841A pdb=" N GLY D 158 " --> pdb=" O ASN D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 185 Proline residue: D 173 - end of helix removed outlier: 4.512A pdb=" N GLN D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ALA D 177 " --> pdb=" O PRO D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 215 Processing helix chain 'D' and resid 262 through 274 removed outlier: 3.784A pdb=" N GLN D 266 " --> pdb=" O ALA D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 301 removed outlier: 3.812A pdb=" N ASP D 301 " --> pdb=" O ASP D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 335 Processing sheet with id=AA1, first strand: chain 'A' and resid 219 through 224 removed outlier: 4.856A pdb=" N ILE A 244 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N SER A 243 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N VAL A 258 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N TYR A 245 " --> pdb=" O THR A 256 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N THR A 256 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU A 247 " --> pdb=" O ALA A 254 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N VAL A 258 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ARG A 197 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N GLU A 260 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N TYR A 199 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ARG A 310 " --> pdb=" O GLN A 196 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU A 198 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ILE A 312 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE A 200 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N TYR A 314 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU A 202 " --> pdb=" O TYR A 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 228 through 232 removed outlier: 6.602A pdb=" N ARG A 232 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LYS A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 219 through 223 removed outlier: 6.897A pdb=" N ILE B 244 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLU B 249 " --> pdb=" O ARG B 253 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ARG B 253 " --> pdb=" O GLU B 249 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 228 through 232 removed outlier: 6.763A pdb=" N ARG B 232 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LYS B 236 " --> pdb=" O ARG B 232 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 219 through 224 removed outlier: 4.856A pdb=" N ILE C 244 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N SER C 243 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N VAL C 258 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N TYR C 245 " --> pdb=" O THR C 256 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N THR C 256 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU C 247 " --> pdb=" O ALA C 254 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N VAL C 258 " --> pdb=" O SER C 195 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ARG C 197 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N GLU C 260 " --> pdb=" O ARG C 197 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N TYR C 199 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N ARG C 310 " --> pdb=" O GLN C 196 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU C 198 " --> pdb=" O ARG C 310 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ILE C 312 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE C 200 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N TYR C 314 " --> pdb=" O ILE C 200 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU C 202 " --> pdb=" O TYR C 314 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 228 through 232 removed outlier: 6.602A pdb=" N ARG C 232 " --> pdb=" O LYS C 236 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LYS C 236 " --> pdb=" O ARG C 232 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 219 through 223 removed outlier: 6.898A pdb=" N ILE D 244 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLU D 249 " --> pdb=" O ARG D 253 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ARG D 253 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 228 through 232 removed outlier: 6.763A pdb=" N ARG D 232 " --> pdb=" O LYS D 236 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LYS D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) 628 hydrogen bonds defined for protein. 1836 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: 4.66 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10020 1.03 - 1.23: 42 1.23 - 1.42: 4346 1.42 - 1.62: 5956 1.62 - 1.81: 68 Bond restraints: 20432 Sorted by residual: bond pdb=" C40 1SY C 401 " pdb=" N39 1SY C 401 " ideal model delta sigma weight residual 1.304 1.430 -0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" C40 1SY B 401 " pdb=" N39 1SY B 401 " ideal model delta sigma weight residual 1.304 1.429 -0.125 2.00e-02 2.50e+03 3.93e+01 bond pdb=" C36 1SY C 401 " pdb=" N42 1SY C 401 " ideal model delta sigma weight residual 1.357 1.474 -0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" C36 1SY B 401 " pdb=" N42 1SY B 401 " ideal model delta sigma weight residual 1.357 1.473 -0.116 2.00e-02 2.50e+03 3.39e+01 bond pdb=" C11 Y6H A 401 " pdb=" N12 Y6H A 401 " ideal model delta sigma weight residual 1.374 1.471 -0.097 2.00e-02 2.50e+03 2.37e+01 ... (remaining 20427 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.51: 36809 6.51 - 13.02: 27 13.02 - 19.54: 12 19.54 - 26.05: 2 26.05 - 32.56: 2 Bond angle restraints: 36852 Sorted by residual: angle pdb=" C20 Y6H C 402 " pdb=" C19 Y6H C 402 " pdb=" C22 Y6H C 402 " ideal model delta sigma weight residual 108.62 141.18 -32.56 3.00e+00 1.11e-01 1.18e+02 angle pdb=" C20 Y6H A 401 " pdb=" C19 Y6H A 401 " pdb=" C22 Y6H A 401 " ideal model delta sigma weight residual 108.62 140.61 -31.99 3.00e+00 1.11e-01 1.14e+02 angle pdb=" C18 Y6H C 402 " pdb=" C19 Y6H C 402 " pdb=" C21 Y6H C 402 " ideal model delta sigma weight residual 111.16 137.09 -25.93 3.00e+00 1.11e-01 7.47e+01 angle pdb=" C18 Y6H A 401 " pdb=" C19 Y6H A 401 " pdb=" C21 Y6H A 401 " ideal model delta sigma weight residual 111.16 137.06 -25.90 3.00e+00 1.11e-01 7.45e+01 angle pdb=" O19 1SY C 401 " pdb=" P18 1SY C 401 " pdb=" O44 1SY C 401 " ideal model delta sigma weight residual 123.21 104.84 18.37 3.00e+00 1.11e-01 3.75e+01 ... (remaining 36847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.46: 9110 21.46 - 42.92: 406 42.92 - 64.38: 184 64.38 - 85.83: 8 85.83 - 107.29: 6 Dihedral angle restraints: 9714 sinusoidal: 5450 harmonic: 4264 Sorted by residual: dihedral pdb=" C18 Y6H A 401 " pdb=" C24 Y6H A 401 " pdb=" O23 Y6H A 401 " pdb=" C25 Y6H A 401 " ideal model delta sinusoidal sigma weight residual -58.10 49.19 -107.29 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" C18 Y6H C 402 " pdb=" C24 Y6H C 402 " pdb=" O23 Y6H C 402 " pdb=" C25 Y6H C 402 " ideal model delta sinusoidal sigma weight residual -58.10 48.08 -106.18 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" C27 Y6H C 402 " pdb=" C24 Y6H C 402 " pdb=" C25 Y6H C 402 " pdb=" O23 Y6H C 402 " ideal model delta sinusoidal sigma weight residual -70.26 -171.40 101.14 1 3.00e+01 1.11e-03 1.27e+01 ... (remaining 9711 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1381 0.046 - 0.092: 144 0.092 - 0.138: 53 0.138 - 0.184: 0 0.184 - 0.230: 4 Chirality restraints: 1582 Sorted by residual: chirality pdb=" C2' 1SY C 401 " pdb=" C1' 1SY C 401 " pdb=" C3' 1SY C 401 " pdb=" O2' 1SY C 401 " both_signs ideal model delta sigma weight residual False -2.74 -2.51 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" C2' 1SY B 401 " pdb=" C1' 1SY B 401 " pdb=" C3' 1SY B 401 " pdb=" O2' 1SY B 401 " both_signs ideal model delta sigma weight residual False -2.74 -2.52 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C22 1SY C 401 " pdb=" C21 1SY C 401 " pdb=" C24 1SY C 401 " pdb=" O23 1SY C 401 " both_signs ideal model delta sigma weight residual False -2.70 -2.48 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1579 not shown) Planarity restraints: 2972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 225 " 0.023 5.00e-02 4.00e+02 3.54e-02 2.01e+00 pdb=" N PRO B 226 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 226 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 226 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 225 " 0.023 5.00e-02 4.00e+02 3.54e-02 2.01e+00 pdb=" N PRO D 226 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO D 226 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 226 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 91 " 0.016 5.00e-02 4.00e+02 2.40e-02 9.25e-01 pdb=" N PRO A 92 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 92 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 92 " 0.014 5.00e-02 4.00e+02 ... (remaining 2969 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 810 2.18 - 2.78: 40438 2.78 - 3.39: 57382 3.39 - 3.99: 74673 3.99 - 4.60: 118185 Nonbonded interactions: 291488 Sorted by model distance: nonbonded pdb=" OD1 ASN B 211 " pdb=" HG SER B 213 " model vdw 1.572 2.450 nonbonded pdb=" OD1 ASN D 211 " pdb=" HG SER D 213 " model vdw 1.573 2.450 nonbonded pdb=" O PHE C 269 " pdb=" HG SER C 272 " model vdw 1.672 2.450 nonbonded pdb=" O PHE A 269 " pdb=" HG SER A 272 " model vdw 1.672 2.450 nonbonded pdb=" OE1 GLU A 316 " pdb=" H GLU A 316 " model vdw 1.685 2.450 ... (remaining 291483 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 4 through 335) selection = (chain 'B' and resid 4 through 335) selection = (chain 'C' and resid 4 through 335) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.130 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 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 0.126 10372 Z= 0.306 Angle : 0.966 32.561 14104 Z= 0.369 Chirality : 0.035 0.230 1582 Planarity : 0.003 0.035 1780 Dihedral : 13.245 107.292 3974 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.31 % Allowed : 6.55 % Favored : 92.13 % 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: 1.64 (0.24), residues: 1240 helix: 2.21 (0.19), residues: 724 sheet: -1.09 (0.44), residues: 112 loop : -0.30 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 45 TYR 0.007 0.001 TYR C 261 PHE 0.008 0.001 PHE C 279 TRP 0.009 0.001 TRP A 161 HIS 0.002 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00621 / 0.31 (10372) covalent geometry : angle 0.96591 / 0.37 (14104) hydrogen bonds : bond 0.15291 / 10.40 ( 628) hydrogen bonds : angle 6.69792 / 4.98 ( 1836) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Evaluate side-chains 247 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 233 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.7667 (ttt-90) cc_final: 0.7390 (ttt180) REVERT: A 107 TYR cc_start: 0.6085 (OUTLIER) cc_final: 0.4884 (m-80) REVERT: A 180 ARG cc_start: 0.6236 (mtm110) cc_final: 0.5760 (ptp-110) REVERT: A 184 GLN cc_start: 0.6609 (OUTLIER) cc_final: 0.6133 (mp10) REVERT: A 218 ASN cc_start: 0.7126 (m-40) cc_final: 0.6864 (m-40) REVERT: B 78 ARG cc_start: 0.7990 (mtp85) cc_final: 0.7744 (mtp180) REVERT: B 260 GLU cc_start: 0.8101 (pt0) cc_final: 0.7873 (pt0) REVERT: C 86 ARG cc_start: 0.7568 (ttt-90) cc_final: 0.7276 (ttt180) REVERT: C 107 TYR cc_start: 0.6390 (OUTLIER) cc_final: 0.5246 (m-80) REVERT: C 184 GLN cc_start: 0.6514 (OUTLIER) cc_final: 0.6188 (mp10) REVERT: C 216 ASP cc_start: 0.6409 (t0) cc_final: 0.6163 (t0) REVERT: C 217 PRO cc_start: 0.7748 (Cg_exo) cc_final: 0.7498 (Cg_endo) REVERT: C 223 ASP cc_start: 0.6617 (t70) cc_final: 0.6381 (t70) REVERT: C 286 GLU cc_start: 0.7512 (tt0) cc_final: 0.7183 (tp30) REVERT: D 78 ARG cc_start: 0.7952 (mtp85) cc_final: 0.7736 (mtp180) REVERT: D 307 ASN cc_start: 0.6428 (m-40) cc_final: 0.5802 (m-40) outliers start: 14 outliers final: 4 residues processed: 242 average time/residue: 1.5624 time to fit residues: 399.3303 Evaluate side-chains 180 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 172 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain C residue 107 TYR Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 184 GLN Chi-restraints excluded: chain D residue 323 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 65 optimal weight: 0.0570 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 308 ASN B 128 GLN B 273 GLN B 276 GLN C 176 GLN C 196 GLN C 308 ASN D 273 GLN D 276 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.145240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.124170 restraints weight = 33775.707| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.46 r_work: 0.3265 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10372 Z= 0.147 Angle : 0.555 5.977 14104 Z= 0.277 Chirality : 0.036 0.141 1582 Planarity : 0.005 0.049 1780 Dihedral : 6.763 54.888 1636 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.90 % Allowed : 11.52 % Favored : 85.58 % 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: 2.04 (0.24), residues: 1240 helix: 2.57 (0.18), residues: 728 sheet: -0.99 (0.43), residues: 120 loop : -0.20 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 281 TYR 0.013 0.001 TYR C 106 PHE 0.012 0.002 PHE C 279 TRP 0.011 0.002 TRP A 161 HIS 0.002 0.001 HIS A 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (10372) covalent geometry : angle 0.55494 / 0.28 (14104) hydrogen bonds : bond 0.04477 / 3.04 ( 628) hydrogen bonds : angle 5.01941 / 3.71 ( 1836) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Evaluate side-chains 221 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.7827 (ttt-90) cc_final: 0.7511 (ttt180) REVERT: A 107 TYR cc_start: 0.6307 (OUTLIER) cc_final: 0.5101 (m-80) REVERT: A 216 ASP cc_start: 0.6642 (t0) cc_final: 0.6398 (t0) REVERT: B 12 CYS cc_start: 0.7692 (m) cc_final: 0.7479 (m) REVERT: B 71 ARG cc_start: 0.7659 (mtt180) cc_final: 0.7456 (mtt180) REVERT: B 315 GLN cc_start: 0.7768 (tt0) cc_final: 0.7111 (mm110) REVERT: B 328 GLU cc_start: 0.6850 (mm-30) cc_final: 0.6424 (mm-30) REVERT: C 68 GLU cc_start: 0.7764 (tp30) cc_final: 0.7518 (tp30) REVERT: C 107 TYR cc_start: 0.6451 (OUTLIER) cc_final: 0.5320 (m-80) REVERT: C 216 ASP cc_start: 0.6631 (t0) cc_final: 0.6339 (t0) REVERT: C 217 PRO cc_start: 0.7649 (Cg_exo) cc_final: 0.7390 (Cg_endo) REVERT: C 218 ASN cc_start: 0.7134 (m-40) cc_final: 0.6658 (m-40) REVERT: C 223 ASP cc_start: 0.6948 (t70) cc_final: 0.6714 (t70) REVERT: C 286 GLU cc_start: 0.7597 (tt0) cc_final: 0.7341 (tp30) REVERT: D 12 CYS cc_start: 0.7842 (m) cc_final: 0.7598 (m) outliers start: 31 outliers final: 17 residues processed: 205 average time/residue: 1.3986 time to fit residues: 304.7597 Evaluate side-chains 189 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 308 ASN Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 107 TYR Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 296 GLU Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 323 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 49 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN A 308 ASN C 131 ASN C 196 GLN D 128 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.141236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.119800 restraints weight = 34380.044| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.47 r_work: 0.3223 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10372 Z= 0.166 Angle : 0.553 4.112 14104 Z= 0.279 Chirality : 0.036 0.133 1582 Planarity : 0.005 0.043 1780 Dihedral : 6.178 55.642 1630 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.28 % Allowed : 13.39 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.24), residues: 1240 helix: 2.38 (0.19), residues: 728 sheet: -0.74 (0.39), residues: 160 loop : 0.13 (0.36), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 281 TYR 0.012 0.002 TYR C 106 PHE 0.013 0.002 PHE A 279 TRP 0.013 0.002 TRP B 161 HIS 0.006 0.001 HIS D 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (10372) covalent geometry : angle 0.55297 / 0.28 (14104) hydrogen bonds : bond 0.04474 / 3.04 ( 628) hydrogen bonds : angle 4.85254 / 3.59 ( 1836) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Evaluate side-chains 203 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.7827 (ttt-90) cc_final: 0.7506 (ttt180) REVERT: A 218 ASN cc_start: 0.7417 (m-40) cc_final: 0.7081 (m-40) REVERT: A 220 ARG cc_start: 0.7004 (OUTLIER) cc_final: 0.6680 (mtt-85) REVERT: A 290 LEU cc_start: 0.8518 (tp) cc_final: 0.8316 (tp) REVERT: C 218 ASN cc_start: 0.7241 (m-40) cc_final: 0.6905 (m-40) REVERT: D 137 LYS cc_start: 0.7426 (mmtm) cc_final: 0.7212 (mmtm) REVERT: D 248 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6640 (mp) outliers start: 35 outliers final: 19 residues processed: 189 average time/residue: 1.5627 time to fit residues: 312.2205 Evaluate side-chains 178 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 308 ASN Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 107 TYR Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 184 GLN Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 323 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN C 307 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.140536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.119074 restraints weight = 34562.426| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.47 r_work: 0.3113 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10372 Z= 0.167 Angle : 0.553 4.603 14104 Z= 0.279 Chirality : 0.036 0.136 1582 Planarity : 0.006 0.056 1780 Dihedral : 6.163 56.869 1630 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.28 % Allowed : 14.14 % Favored : 82.58 % 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: 1.94 (0.24), residues: 1240 helix: 2.36 (0.18), residues: 728 sheet: -0.78 (0.39), residues: 160 loop : 0.09 (0.36), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 83 TYR 0.011 0.001 TYR C 106 PHE 0.012 0.002 PHE C 279 TRP 0.012 0.002 TRP B 161 HIS 0.005 0.001 HIS C 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (10372) covalent geometry : angle 0.55291 / 0.28 (14104) hydrogen bonds : bond 0.04238 / 2.89 ( 628) hydrogen bonds : angle 4.76886 / 3.52 ( 1836) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.6401 (tt0) REVERT: A 218 ASN cc_start: 0.7387 (m-40) cc_final: 0.6921 (m-40) REVERT: A 290 LEU cc_start: 0.8512 (tp) cc_final: 0.8297 (tp) REVERT: C 19 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7593 (mm-40) REVERT: C 38 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6459 (tt0) REVERT: C 218 ASN cc_start: 0.7332 (m-40) cc_final: 0.6820 (m-40) REVERT: C 223 ASP cc_start: 0.6764 (t70) cc_final: 0.6431 (t70) REVERT: D 59 LEU cc_start: 0.8225 (tm) cc_final: 0.7834 (tp) REVERT: D 137 LYS cc_start: 0.7467 (mmtm) cc_final: 0.7228 (mmtm) REVERT: D 248 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6613 (mp) outliers start: 35 outliers final: 19 residues processed: 182 average time/residue: 1.6089 time to fit residues: 309.3365 Evaluate side-chains 177 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 308 ASN Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 107 TYR Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 184 GLN Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 307 ASN Chi-restraints excluded: chain D residue 323 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 50 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 13 optimal weight: 0.2980 chunk 66 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN A 308 ASN B 276 GLN B 307 ASN C 307 ASN D 276 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.140099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.118723 restraints weight = 34475.973| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.46 r_work: 0.3180 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10372 Z= 0.176 Angle : 0.561 4.622 14104 Z= 0.283 Chirality : 0.036 0.133 1582 Planarity : 0.006 0.050 1780 Dihedral : 6.196 57.808 1630 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.37 % Allowed : 14.51 % Favored : 82.12 % 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: 1.85 (0.24), residues: 1240 helix: 2.24 (0.18), residues: 732 sheet: -0.81 (0.38), residues: 160 loop : 0.13 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 281 TYR 0.010 0.002 TYR C 106 PHE 0.012 0.002 PHE C 279 TRP 0.012 0.002 TRP D 161 HIS 0.003 0.001 HIS B 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (10372) covalent geometry : angle 0.56106 / 0.28 (14104) hydrogen bonds : bond 0.04314 / 2.94 ( 628) hydrogen bonds : angle 4.76817 / 3.52 ( 1836) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Evaluate side-chains 189 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 153 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: A 38 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6477 (tt0) REVERT: A 218 ASN cc_start: 0.7433 (m-40) cc_final: 0.7062 (m-40) REVERT: A 220 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.6781 (mtt-85) REVERT: A 290 LEU cc_start: 0.8553 (tp) cc_final: 0.8347 (tp) REVERT: C 19 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7629 (mm-40) REVERT: C 38 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6478 (tt0) REVERT: C 218 ASN cc_start: 0.7391 (m-40) cc_final: 0.6962 (m-40) REVERT: D 248 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6676 (mp) outliers start: 36 outliers final: 21 residues processed: 173 average time/residue: 1.5407 time to fit residues: 281.6637 Evaluate side-chains 175 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 308 ASN Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 107 TYR Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 184 GLN Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 296 GLU Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 307 ASN Chi-restraints excluded: chain D residue 323 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 75 optimal weight: 0.3980 chunk 102 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 276 GLN ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.140739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.119440 restraints weight = 34543.177| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.46 r_work: 0.3203 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10372 Z= 0.142 Angle : 0.528 4.510 14104 Z= 0.267 Chirality : 0.035 0.135 1582 Planarity : 0.005 0.055 1780 Dihedral : 5.993 58.863 1630 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.18 % Allowed : 14.70 % Favored : 82.12 % 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: 1.92 (0.24), residues: 1240 helix: 2.42 (0.18), residues: 728 sheet: -1.17 (0.37), residues: 180 loop : 0.21 (0.38), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 281 TYR 0.010 0.001 TYR C 106 PHE 0.010 0.002 PHE C 279 TRP 0.011 0.002 TRP D 161 HIS 0.002 0.001 HIS D 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (10372) covalent geometry : angle 0.52773 / 0.27 (14104) hydrogen bonds : bond 0.04046 / 2.76 ( 628) hydrogen bonds : angle 4.64979 / 3.43 ( 1836) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7571 (mm-40) REVERT: A 38 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.6405 (tt0) REVERT: A 86 ARG cc_start: 0.7956 (ttt-90) cc_final: 0.7627 (ttt180) REVERT: A 218 ASN cc_start: 0.7433 (m-40) cc_final: 0.7077 (m-40) REVERT: A 220 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.6643 (mtt-85) REVERT: C 19 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7610 (mm-40) REVERT: C 38 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6371 (tt0) REVERT: C 223 ASP cc_start: 0.6772 (t70) cc_final: 0.6432 (t70) REVERT: D 59 LEU cc_start: 0.8244 (tm) cc_final: 0.7846 (tp) REVERT: D 248 LEU cc_start: 0.6981 (OUTLIER) cc_final: 0.6704 (mp) outliers start: 34 outliers final: 20 residues processed: 181 average time/residue: 1.4952 time to fit residues: 286.6714 Evaluate side-chains 182 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 308 ASN Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 107 TYR Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 184 GLN Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 296 GLU Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 323 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN C 307 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.139899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.118609 restraints weight = 34686.880| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.46 r_work: 0.3194 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10372 Z= 0.169 Angle : 0.556 4.813 14104 Z= 0.282 Chirality : 0.036 0.161 1582 Planarity : 0.006 0.058 1780 Dihedral : 6.167 59.414 1630 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.18 % Allowed : 15.54 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.81 (0.24), residues: 1240 helix: 2.30 (0.18), residues: 732 sheet: -1.15 (0.37), residues: 180 loop : 0.18 (0.38), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 281 TYR 0.012 0.002 TYR A 199 PHE 0.011 0.002 PHE C 279 TRP 0.012 0.002 TRP B 161 HIS 0.003 0.001 HIS D 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (10372) covalent geometry : angle 0.55647 / 0.28 (14104) hydrogen bonds : bond 0.04227 / 2.88 ( 628) hydrogen bonds : angle 4.72147 / 3.48 ( 1836) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7571 (mm-40) REVERT: A 38 GLU cc_start: 0.6760 (OUTLIER) cc_final: 0.6372 (tt0) REVERT: A 218 ASN cc_start: 0.7493 (m-40) cc_final: 0.7135 (m-40) REVERT: A 220 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6662 (mtt-85) REVERT: A 223 ASP cc_start: 0.6710 (t70) cc_final: 0.6324 (t70) REVERT: C 19 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7603 (mm-40) REVERT: C 38 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6478 (tt0) REVERT: D 248 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6850 (mp) REVERT: D 307 ASN cc_start: 0.7019 (p0) cc_final: 0.6796 (p0) outliers start: 34 outliers final: 22 residues processed: 174 average time/residue: 1.5387 time to fit residues: 283.9857 Evaluate side-chains 175 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 308 ASN Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 107 TYR Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 184 GLN Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 296 GLU Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 323 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 94 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 96 optimal weight: 0.1980 chunk 71 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 307 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.141023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.119755 restraints weight = 34600.588| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.46 r_work: 0.3195 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10372 Z= 0.127 Angle : 0.518 5.011 14104 Z= 0.263 Chirality : 0.035 0.144 1582 Planarity : 0.006 0.066 1780 Dihedral : 5.874 59.681 1630 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.90 % Allowed : 16.01 % Favored : 81.09 % 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: 2.02 (0.25), residues: 1240 helix: 2.40 (0.18), residues: 740 sheet: -1.14 (0.36), residues: 180 loop : 0.45 (0.39), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 331 TYR 0.010 0.001 TYR C 106 PHE 0.010 0.001 PHE B 279 TRP 0.011 0.002 TRP B 161 HIS 0.002 0.001 HIS C 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (10372) covalent geometry : angle 0.51791 / 0.26 (14104) hydrogen bonds : bond 0.03896 / 2.66 ( 628) hydrogen bonds : angle 4.56933 / 3.37 ( 1836) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Evaluate side-chains 188 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7551 (mm-40) REVERT: A 38 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6342 (tt0) REVERT: A 86 ARG cc_start: 0.7953 (ttt-90) cc_final: 0.7609 (ttt180) REVERT: A 218 ASN cc_start: 0.7444 (m-40) cc_final: 0.7079 (m-40) REVERT: A 220 ARG cc_start: 0.6971 (OUTLIER) cc_final: 0.6753 (mtt-85) REVERT: A 223 ASP cc_start: 0.6697 (t70) cc_final: 0.6307 (t70) REVERT: B 139 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7671 (mp) REVERT: C 19 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7548 (mm-40) REVERT: C 38 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.6427 (tt0) REVERT: C 86 ARG cc_start: 0.7944 (ttt-90) cc_final: 0.7597 (ttt180) REVERT: C 223 ASP cc_start: 0.6701 (t70) cc_final: 0.6332 (t70) REVERT: D 248 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6867 (mp) outliers start: 31 outliers final: 17 residues processed: 176 average time/residue: 1.4788 time to fit residues: 275.9548 Evaluate side-chains 178 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 308 ASN Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 107 TYR Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 184 GLN Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 296 GLU Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 323 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 46 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 307 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.138589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.117214 restraints weight = 34756.585| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.46 r_work: 0.3160 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 10372 Z= 0.249 Angle : 0.641 6.278 14104 Z= 0.323 Chirality : 0.039 0.139 1582 Planarity : 0.007 0.065 1780 Dihedral : 6.835 59.975 1630 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.56 % Allowed : 15.54 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.24), residues: 1240 helix: 2.00 (0.18), residues: 732 sheet: -1.13 (0.37), residues: 180 loop : 0.08 (0.38), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 331 TYR 0.013 0.002 TYR C 106 PHE 0.014 0.002 PHE C 279 TRP 0.014 0.003 TRP B 161 HIS 0.004 0.001 HIS D 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.25 (10372) covalent geometry : angle 0.64131 / 0.32 (14104) hydrogen bonds : bond 0.04688 / 3.18 ( 628) hydrogen bonds : angle 4.89202 / 3.62 ( 1836) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: A 19 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7604 (mm-40) REVERT: A 38 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6410 (tt0) REVERT: A 86 ARG cc_start: 0.7980 (ttt-90) cc_final: 0.7659 (ttt180) REVERT: A 218 ASN cc_start: 0.7565 (m-40) cc_final: 0.7202 (m-40) REVERT: A 220 ARG cc_start: 0.7008 (OUTLIER) cc_final: 0.6750 (mtt-85) REVERT: A 223 ASP cc_start: 0.6709 (t70) cc_final: 0.6336 (t70) REVERT: B 139 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7654 (mp) REVERT: C 19 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7637 (mm-40) REVERT: C 38 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6475 (tt0) REVERT: C 86 ARG cc_start: 0.7973 (ttt-90) cc_final: 0.7658 (ttt180) REVERT: C 334 ARG cc_start: 0.6167 (OUTLIER) cc_final: 0.5589 (mtt90) REVERT: D 139 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7632 (mp) REVERT: D 248 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6900 (mp) outliers start: 38 outliers final: 23 residues processed: 173 average time/residue: 1.4589 time to fit residues: 267.8596 Evaluate side-chains 173 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 308 ASN Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 107 TYR Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 184 GLN Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 296 GLU Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 323 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN B 276 GLN ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 307 ASN D 276 GLN ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.140206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.118903 restraints weight = 34611.805| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.46 r_work: 0.3181 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10372 Z= 0.151 Angle : 0.550 5.087 14104 Z= 0.281 Chirality : 0.035 0.145 1582 Planarity : 0.006 0.068 1780 Dihedral : 6.187 59.937 1630 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.00 % Allowed : 16.48 % Favored : 80.52 % 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: 1.69 (0.25), residues: 1240 helix: 2.20 (0.19), residues: 732 sheet: -1.17 (0.37), residues: 180 loop : 0.12 (0.38), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 331 TYR 0.011 0.001 TYR C 106 PHE 0.010 0.002 PHE C 279 TRP 0.012 0.002 TRP B 161 HIS 0.003 0.001 HIS D 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (10372) covalent geometry : angle 0.55031 / 0.28 (14104) hydrogen bonds : bond 0.04162 / 2.83 ( 628) hydrogen bonds : angle 4.70702 / 3.48 ( 1836) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7535 (mm-40) REVERT: A 38 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6370 (tt0) REVERT: A 86 ARG cc_start: 0.7974 (ttt-90) cc_final: 0.7645 (ttt180) REVERT: A 218 ASN cc_start: 0.7468 (m-40) cc_final: 0.7126 (m-40) REVERT: A 220 ARG cc_start: 0.7008 (OUTLIER) cc_final: 0.6774 (mtt-85) REVERT: A 223 ASP cc_start: 0.6676 (t70) cc_final: 0.6265 (t70) REVERT: B 59 LEU cc_start: 0.8276 (tm) cc_final: 0.7870 (tp) REVERT: B 139 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7639 (mp) REVERT: C 19 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7553 (mm-40) REVERT: C 38 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.6480 (tt0) REVERT: C 86 ARG cc_start: 0.7963 (ttt-90) cc_final: 0.7637 (ttt180) REVERT: C 223 ASP cc_start: 0.6674 (t70) cc_final: 0.6334 (t70) REVERT: D 59 LEU cc_start: 0.8270 (tm) cc_final: 0.7848 (tp) REVERT: D 139 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7604 (mp) REVERT: D 248 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6918 (mp) outliers start: 32 outliers final: 19 residues processed: 168 average time/residue: 1.3951 time to fit residues: 249.6277 Evaluate side-chains 170 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 308 ASN Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 107 TYR Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 184 GLN Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 296 GLU Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 323 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 88 optimal weight: 2.9990 chunk 94 optimal weight: 0.0050 chunk 45 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN C 307 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.141317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.120049 restraints weight = 34493.775| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.46 r_work: 0.3134 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 10372 Z= 0.112 Angle : 0.513 5.385 14104 Z= 0.264 Chirality : 0.035 0.174 1582 Planarity : 0.005 0.068 1780 Dihedral : 5.770 58.178 1630 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.43 % Allowed : 16.95 % Favored : 80.62 % 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: 1.99 (0.25), residues: 1240 helix: 2.36 (0.18), residues: 744 sheet: -1.16 (0.36), residues: 180 loop : 0.46 (0.40), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 331 TYR 0.010 0.001 TYR C 106 PHE 0.010 0.001 PHE B 279 TRP 0.010 0.002 TRP D 161 HIS 0.003 0.001 HIS A 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (10372) covalent geometry : angle 0.51346 / 0.26 (14104) hydrogen bonds : bond 0.03814 / 2.59 ( 628) hydrogen bonds : angle 4.52659 / 3.33 ( 1836) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7323.24 seconds wall clock time: 124 minutes 28.20 seconds (7468.20 seconds total)