Starting phenix.real_space_refine on Wed Mar 4 11:11:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xku_22225/03_2026/6xku_22225.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xku_22225/03_2026/6xku_22225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xku_22225/03_2026/6xku_22225.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xku_22225/03_2026/6xku_22225.map" model { file = "/net/cci-nas-00/data/ceres_data/6xku_22225/03_2026/6xku_22225.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xku_22225/03_2026/6xku_22225.cif" } resolution = 4.2 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 10 7.16 5 S 78 5.16 5 C 8578 2.51 5 N 2155 2.21 5 O 2258 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13079 Number of models: 1 Model: "" Number of chains: 12 Chain: "E" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1365 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 170} Chain: "R" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1365 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 170} Chain: "C" Number of atoms: 3244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3244 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 393} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'HIS:plan': 3, 'ASP:plan': 6, 'TYR:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1, 'TRP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 90 Chain: "D" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1801 Classifications: {'peptide': 235} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "P" Number of atoms: 3244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3244 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 393} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'HIS:plan': 3, 'ASP:plan': 6, 'TYR:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1, 'TRP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 90 Chain: "Q" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1794 Classifications: {'peptide': 235} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 15, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 933 SG CYS E 133 30.892 60.280 26.108 0.25105.87 S ATOM 1079 SG CYS E 153 31.686 57.930 23.427 0.25107.21 S ATOM 2298 SG CYS R 133 82.864 27.948 41.694 0.25105.87 S ATOM 2444 SG CYS R 153 83.981 31.374 41.102 0.25107.21 S Residues with excluded nonbonded symmetry interactions: 53 residue: pdb=" N MET E 129 " occ=0.25 ... (6 atoms not shown) pdb=" CE MET E 129 " occ=0.25 residue: pdb=" N GLY E 131 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY E 131 " occ=0.25 residue: pdb=" N VAL E 132 " occ=0.25 ... (5 atoms not shown) pdb=" CG2 VAL E 132 " occ=0.25 residue: pdb=" N CYS E 133 " occ=0.25 ... (4 atoms not shown) pdb=" SG CYS E 133 " occ=0.25 residue: pdb=" N THR E 134 " occ=0.25 ... (5 atoms not shown) pdb=" CG2 THR E 134 " occ=0.25 residue: pdb=" N HIS E 135 " occ=0.25 ... (8 atoms not shown) pdb=" NE2 HIS E 135 " occ=0.25 residue: pdb=" N LEU E 136 " occ=0.25 ... (6 atoms not shown) pdb=" CD2 LEU E 136 " occ=0.25 residue: pdb=" N GLY E 137 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY E 137 " occ=0.25 residue: pdb=" N CYS E 138 " occ=0.25 ... (4 atoms not shown) pdb=" SG CYS E 138 " occ=0.25 residue: pdb=" N VAL E 139 " occ=0.25 ... (5 atoms not shown) pdb=" CG2 VAL E 139 " occ=0.25 residue: pdb=" N PRO E 140 " occ=0.25 ... (5 atoms not shown) pdb=" CD PRO E 140 " occ=0.25 residue: pdb=" N GLY E 142 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY E 142 " occ=0.25 ... (remaining 41 not shown) Time building chain proxies: 3.02, per 1000 atoms: 0.23 Number of scatterers: 13079 At special positions: 0 Unit cell: (114.24, 99.28, 110.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 10 26.01 S 78 16.00 O 2258 8.00 N 2155 7.00 C 8578 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 155 " distance=2.03 Simple disulfide: pdb=" SG CYS R 138 " - pdb=" SG CYS R 155 " distance=2.03 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 581.8 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 501 " pdb="FE2 FES E 501 " - pdb=" ND1 HIS E 135 " pdb="FE2 FES E 501 " - pdb=" ND1 HIS E 156 " pdb="FE1 FES E 501 " - pdb=" SG CYS E 153 " pdb="FE1 FES E 501 " - pdb=" SG CYS E 133 " pdb=" FES R 501 " pdb="FE2 FES R 501 " - pdb=" ND1 HIS R 156 " pdb="FE2 FES R 501 " - pdb=" ND1 HIS R 135 " pdb="FE1 FES R 501 " - pdb=" SG CYS R 133 " pdb="FE1 FES R 501 " - pdb=" SG CYS R 153 " Number of angles added : 6 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3056 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 8 sheets defined 51.6% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'E' and resid 11 through 35 Proline residue: E 33 - end of helix Processing helix chain 'E' and resid 41 through 49 removed outlier: 3.857A pdb=" N ALA E 46 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N MET E 47 " --> pdb=" O ASP E 43 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA E 48 " --> pdb=" O VAL E 44 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 87 Processing helix chain 'E' and resid 109 through 114 Processing helix chain 'R' and resid 12 through 37 Proline residue: R 33 - end of helix Processing helix chain 'R' and resid 41 through 46 removed outlier: 3.562A pdb=" N ALA R 46 " --> pdb=" O ALA R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 87 Processing helix chain 'R' and resid 109 through 114 Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 33 removed outlier: 3.764A pdb=" N GLY C 27 " --> pdb=" O LEU C 23 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE C 33 " --> pdb=" O VAL C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 66 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 90 through 118 removed outlier: 3.757A pdb=" N SER C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 148 removed outlier: 3.860A pdb=" N TRP C 129 " --> pdb=" O ARG C 125 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL C 148 " --> pdb=" O PHE C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 169 removed outlier: 3.624A pdb=" N TRP C 157 " --> pdb=" O GLN C 153 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N PHE C 166 " --> pdb=" O ILE C 162 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY C 167 " --> pdb=" O THR C 163 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 182 removed outlier: 3.668A pdb=" N ILE C 176 " --> pdb=" O ILE C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 199 Processing helix chain 'C' and resid 200 through 219 removed outlier: 3.961A pdb=" N VAL C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE C 216 " --> pdb=" O HIS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 270 Processing helix chain 'C' and resid 276 through 281 Processing helix chain 'C' and resid 298 through 308 removed outlier: 4.406A pdb=" N PHE C 308 " --> pdb=" O ILE C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 321 Processing helix chain 'C' and resid 327 through 346 removed outlier: 3.849A pdb=" N MET C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 356 through 359 Processing helix chain 'C' and resid 360 through 381 Processing helix chain 'C' and resid 388 through 415 removed outlier: 5.576A pdb=" N LEU C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Proline residue: C 409 - end of helix Processing helix chain 'D' and resid 19 through 33 removed outlier: 3.629A pdb=" N LEU D 23 " --> pdb=" O ASP D 19 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU D 32 " --> pdb=" O GLN D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 37 Processing helix chain 'D' and resid 44 through 49 Processing helix chain 'D' and resid 57 through 67 Processing helix chain 'D' and resid 127 through 136 Processing helix chain 'D' and resid 201 through 218 Processing helix chain 'D' and resid 220 through 250 Processing helix chain 'P' and resid 14 through 19 Processing helix chain 'P' and resid 23 through 33 removed outlier: 3.762A pdb=" N GLY P 27 " --> pdb=" O LEU P 23 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE P 33 " --> pdb=" O VAL P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 66 Processing helix chain 'P' and resid 75 through 86 Processing helix chain 'P' and resid 90 through 118 removed outlier: 3.754A pdb=" N SER P 102 " --> pdb=" O ALA P 98 " (cutoff:3.500A) Processing helix chain 'P' and resid 125 through 148 removed outlier: 3.860A pdb=" N TRP P 129 " --> pdb=" O ARG P 125 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL P 148 " --> pdb=" O PHE P 144 " (cutoff:3.500A) Processing helix chain 'P' and resid 153 through 169 removed outlier: 3.623A pdb=" N TRP P 157 " --> pdb=" O GLN P 153 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N PHE P 166 " --> pdb=" O ILE P 162 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY P 167 " --> pdb=" O THR P 163 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE P 169 " --> pdb=" O LEU P 165 " (cutoff:3.500A) Processing helix chain 'P' and resid 172 through 182 removed outlier: 3.668A pdb=" N ILE P 176 " --> pdb=" O ILE P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 187 through 199 Processing helix chain 'P' and resid 200 through 219 removed outlier: 3.957A pdb=" N VAL P 204 " --> pdb=" O LEU P 200 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE P 216 " --> pdb=" O HIS P 212 " (cutoff:3.500A) Processing helix chain 'P' and resid 246 through 270 Processing helix chain 'P' and resid 276 through 281 Processing helix chain 'P' and resid 298 through 308 removed outlier: 4.406A pdb=" N PHE P 308 " --> pdb=" O ILE P 304 " (cutoff:3.500A) Processing helix chain 'P' and resid 316 through 321 Processing helix chain 'P' and resid 327 through 346 removed outlier: 3.848A pdb=" N MET P 343 " --> pdb=" O ALA P 339 " (cutoff:3.500A) Processing helix chain 'P' and resid 347 through 349 No H-bonds generated for 'chain 'P' and resid 347 through 349' Processing helix chain 'P' and resid 356 through 359 Processing helix chain 'P' and resid 360 through 381 Processing helix chain 'P' and resid 388 through 415 removed outlier: 5.576A pdb=" N LEU P 408 " --> pdb=" O PHE P 404 " (cutoff:3.500A) Proline residue: P 409 - end of helix Processing helix chain 'Q' and resid 19 through 33 removed outlier: 3.627A pdb=" N LEU Q 23 " --> pdb=" O ASP Q 19 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU Q 32 " --> pdb=" O GLN Q 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 34 through 37 Processing helix chain 'Q' and resid 44 through 49 removed outlier: 3.567A pdb=" N THR Q 47 " --> pdb=" O PRO Q 44 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU Q 48 " --> pdb=" O ILE Q 45 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA Q 49 " --> pdb=" O ARG Q 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 44 through 49' Processing helix chain 'Q' and resid 57 through 67 Processing helix chain 'Q' and resid 127 through 136 Processing helix chain 'Q' and resid 201 through 218 Processing helix chain 'Q' and resid 220 through 250 Processing sheet with id=AA1, first strand: chain 'E' and resid 50 through 51 removed outlier: 3.606A pdb=" N ALA E 181 " --> pdb=" O LYS E 189 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 64 through 67 Processing sheet with id=AA3, first strand: chain 'E' and resid 141 through 145 removed outlier: 4.682A pdb=" N ASP E 143 " --> pdb=" O GLY E 150 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N GLY E 150 " --> pdb=" O ASP E 143 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TRP E 151 " --> pdb=" O TYR E 160 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER E 158 " --> pdb=" O CYS E 153 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'R' and resid 50 through 52 removed outlier: 3.607A pdb=" N ALA R 181 " --> pdb=" O LYS R 189 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 64 through 67 Processing sheet with id=AA6, first strand: chain 'R' and resid 141 through 145 removed outlier: 4.684A pdb=" N ASP R 143 " --> pdb=" O GLY R 150 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLY R 150 " --> pdb=" O ASP R 143 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TRP R 151 " --> pdb=" O TYR R 160 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER R 158 " --> pdb=" O CYS R 153 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 153 through 155 Processing sheet with id=AA8, first strand: chain 'Q' and resid 153 through 155 626 hydrogen bonds defined for protein. 1806 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.97 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.41: 5785 1.41 - 1.61: 7562 1.61 - 1.80: 103 1.80 - 2.00: 31 2.00 - 2.20: 28 Bond restraints: 13509 Sorted by residual: bond pdb=" CAC HEC C 501 " pdb=" CBC HEC C 501 " ideal model delta sigma weight residual 1.544 1.324 0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" CAC HEC P 501 " pdb=" CBC HEC P 501 " ideal model delta sigma weight residual 1.544 1.324 0.220 2.00e-02 2.50e+03 1.20e+02 bond pdb=" CAB HEC P 501 " pdb=" CBB HEC P 501 " ideal model delta sigma weight residual 1.544 1.336 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C2D HEC C 501 " pdb=" C3D HEC C 501 " ideal model delta sigma weight residual 1.544 1.336 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" CAB HEC C 501 " pdb=" CBB HEC C 501 " ideal model delta sigma weight residual 1.544 1.337 0.207 2.00e-02 2.50e+03 1.08e+02 ... (remaining 13504 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 18209 3.17 - 6.33: 264 6.33 - 9.50: 27 9.50 - 12.67: 4 12.67 - 15.84: 16 Bond angle restraints: 18520 Sorted by residual: angle pdb="FE1 FES R 501 " pdb=" S2 FES R 501 " pdb="FE2 FES R 501 " ideal model delta sigma weight residual 75.66 89.12 -13.46 1.14e+00 7.69e-01 1.39e+02 angle pdb="FE1 FES E 501 " pdb=" S2 FES E 501 " pdb="FE2 FES E 501 " ideal model delta sigma weight residual 75.66 89.08 -13.42 1.14e+00 7.69e-01 1.39e+02 angle pdb=" S1 FES R 501 " pdb="FE2 FES R 501 " pdb=" S2 FES R 501 " ideal model delta sigma weight residual 104.33 90.93 13.40 1.14e+00 7.69e-01 1.38e+02 angle pdb=" S1 FES E 501 " pdb="FE2 FES E 501 " pdb=" S2 FES E 501 " ideal model delta sigma weight residual 104.33 90.94 13.39 1.14e+00 7.69e-01 1.38e+02 angle pdb=" S1 FES R 501 " pdb="FE1 FES R 501 " pdb=" S2 FES R 501 " ideal model delta sigma weight residual 104.33 90.78 13.55 1.20e+00 6.94e-01 1.28e+02 ... (remaining 18515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 6978 17.90 - 35.81: 534 35.81 - 53.71: 82 53.71 - 71.61: 10 71.61 - 89.52: 22 Dihedral angle restraints: 7626 sinusoidal: 2836 harmonic: 4790 Sorted by residual: dihedral pdb=" C2B HEC P 501 " pdb=" C3B HEC P 501 " pdb=" CAB HEC P 501 " pdb=" CBB HEC P 501 " ideal model delta sinusoidal sigma weight residual 60.00 -22.34 82.34 2 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" C2B HEC C 501 " pdb=" C3B HEC C 501 " pdb=" CAB HEC C 501 " pdb=" CBB HEC C 501 " ideal model delta sinusoidal sigma weight residual 60.00 -22.17 82.17 2 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" C2C HEC P 502 " pdb=" C3C HEC P 502 " pdb=" CAC HEC P 502 " pdb=" CBC HEC P 502 " ideal model delta sinusoidal sigma weight residual 60.00 -17.13 77.13 2 1.00e+01 1.00e-02 4.56e+01 ... (remaining 7623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 1917 0.146 - 0.292: 40 0.292 - 0.438: 1 0.438 - 0.584: 10 0.584 - 0.729: 2 Chirality restraints: 1970 Sorted by residual: chirality pdb=" CG LEU Q 244 " pdb=" CB LEU Q 244 " pdb=" CD1 LEU Q 244 " pdb=" CD2 LEU Q 244 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" CG LEU D 244 " pdb=" CB LEU D 244 " pdb=" CD1 LEU D 244 " pdb=" CD2 LEU D 244 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" CB THR Q 198 " pdb=" CA THR Q 198 " pdb=" OG1 THR Q 198 " pdb=" CG2 THR Q 198 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.52 2.00e-01 2.50e+01 6.86e+00 ... (remaining 1967 not shown) Planarity restraints: 2327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC Q 501 " 0.010 2.00e-02 2.50e+03 4.12e-02 3.82e+01 pdb=" C2C HEC Q 501 " -0.109 2.00e-02 2.50e+03 pdb=" C3C HEC Q 501 " 0.042 2.00e-02 2.50e+03 pdb=" C4C HEC Q 501 " 0.007 2.00e-02 2.50e+03 pdb=" CAC HEC Q 501 " 0.007 2.00e-02 2.50e+03 pdb=" CHC HEC Q 501 " 0.018 2.00e-02 2.50e+03 pdb=" CHD HEC Q 501 " -0.007 2.00e-02 2.50e+03 pdb=" CMC HEC Q 501 " 0.031 2.00e-02 2.50e+03 pdb=" NC HEC Q 501 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC D 501 " -0.010 2.00e-02 2.50e+03 4.11e-02 3.81e+01 pdb=" C2C HEC D 501 " 0.109 2.00e-02 2.50e+03 pdb=" C3C HEC D 501 " -0.042 2.00e-02 2.50e+03 pdb=" C4C HEC D 501 " -0.007 2.00e-02 2.50e+03 pdb=" CAC HEC D 501 " -0.007 2.00e-02 2.50e+03 pdb=" CHC HEC D 501 " -0.018 2.00e-02 2.50e+03 pdb=" CHD HEC D 501 " 0.007 2.00e-02 2.50e+03 pdb=" CMC HEC D 501 " -0.031 2.00e-02 2.50e+03 pdb=" NC HEC D 501 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 222 " -0.021 2.00e-02 2.50e+03 4.29e-02 1.84e+01 pdb=" C ASN C 222 " 0.074 2.00e-02 2.50e+03 pdb=" O ASN C 222 " -0.028 2.00e-02 2.50e+03 pdb=" N ASN C 223 " -0.025 2.00e-02 2.50e+03 ... (remaining 2324 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 167 2.57 - 3.15: 11801 3.15 - 3.73: 19465 3.73 - 4.32: 27251 4.32 - 4.90: 45455 Nonbonded interactions: 104139 Sorted by model distance: nonbonded pdb=" O THR E 186 " pdb=" OG1 THR E 187 " model vdw 1.987 3.040 nonbonded pdb=" O THR R 186 " pdb=" OG1 THR R 187 " model vdw 1.987 3.040 nonbonded pdb=" OG SER P 120 " pdb=" ND2 ASN P 222 " model vdw 1.988 3.120 nonbonded pdb=" NH2 ARG P 306 " pdb=" O MET P 383 " model vdw 2.007 3.120 nonbonded pdb=" NH2 ARG C 306 " pdb=" O MET C 383 " model vdw 2.007 3.120 ... (remaining 104134 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 'C' selection = chain 'P' } ncs_group { reference = (chain 'D' and (resid 5 through 80 or (resid 81 and (name N or name CA or name C \ or name O or name CB )) or resid 82 or (resid 83 and (name N or name CA or name \ C or name O or name CB )) or resid 84 through 501)) selection = chain 'Q' } ncs_group { reference = chain 'E' selection = chain 'R' } 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=0.25 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.370 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 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 : 0.010 0.220 13529 Z= 0.468 Angle : 1.028 23.204 18530 Z= 0.622 Chirality : 0.069 0.729 1970 Planarity : 0.006 0.082 2327 Dihedral : 13.797 89.516 4564 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 25.23 Ramachandran Plot: Outliers : 0.36 % Allowed : 16.47 % Favored : 83.17 % Rotamer: Outliers : 0.16 % Allowed : 2.80 % Favored : 97.04 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.56 % 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: -4.29 (0.17), residues: 1658 helix: -1.64 (0.16), residues: 782 sheet: -3.48 (0.49), residues: 64 loop : -4.18 (0.18), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 75 TYR 0.010 0.001 TYR C 297 PHE 0.021 0.001 PHE C 104 TRP 0.012 0.001 TRP C 296 HIS 0.010 0.001 HIS P 111 Details of bonding type rmsd covalent geometry : bond 0.00939 (13509) covalent geometry : angle 0.99581 (18520) SS BOND : bond 0.00111 ( 2) SS BOND : angle 0.57340 ( 4) hydrogen bonds : bond 0.14710 ( 626) hydrogen bonds : angle 6.99370 ( 1806) metal coordination : bond 0.01210 ( 8) metal coordination : angle 14.21024 ( 6) Misc. bond : bond 0.14972 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 553 time to evaluate : 0.435 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 102 ASN cc_start: 0.7092 (p0) cc_final: 0.6482 (p0) REVERT: E 167 ARG cc_start: 0.7989 (mtp180) cc_final: 0.7619 (mtp85) REVERT: E 174 ASN cc_start: 0.5896 (p0) cc_final: 0.5205 (p0) REVERT: R 61 THR cc_start: 0.7000 (m) cc_final: 0.6770 (p) REVERT: C 39 LYS cc_start: 0.6276 (mttt) cc_final: 0.5461 (pttt) REVERT: C 70 THR cc_start: 0.8988 (m) cc_final: 0.8394 (p) REVERT: C 94 ARG cc_start: 0.8221 (ttt-90) cc_final: 0.7867 (ttt-90) REVERT: C 110 ILE cc_start: 0.9314 (mt) cc_final: 0.8898 (mm) REVERT: C 139 MET cc_start: 0.8107 (ptm) cc_final: 0.7760 (ptp) REVERT: C 175 SER cc_start: 0.8596 (m) cc_final: 0.8341 (t) REVERT: C 296 TRP cc_start: 0.8221 (p-90) cc_final: 0.7876 (p-90) REVERT: C 299 LEU cc_start: 0.8509 (mt) cc_final: 0.8220 (mt) REVERT: C 302 TYR cc_start: 0.8342 (t80) cc_final: 0.8116 (t80) REVERT: C 374 PHE cc_start: 0.8692 (t80) cc_final: 0.8440 (t80) REVERT: C 408 LEU cc_start: 0.8736 (mt) cc_final: 0.8504 (mm) REVERT: D 210 SER cc_start: 0.9550 (m) cc_final: 0.9223 (t) REVERT: D 254 LYS cc_start: 0.6759 (mttm) cc_final: 0.6196 (tptt) REVERT: P 175 SER cc_start: 0.8368 (m) cc_final: 0.7895 (t) REVERT: Q 32 GLU cc_start: 0.6689 (mt-10) cc_final: 0.5868 (mt-10) REVERT: Q 103 MET cc_start: 0.8767 (tpp) cc_final: 0.8535 (mmm) REVERT: Q 134 TYR cc_start: 0.7640 (t80) cc_final: 0.7149 (t80) REVERT: Q 155 ASN cc_start: 0.5971 (t0) cc_final: 0.5424 (t0) REVERT: Q 188 VAL cc_start: 0.7600 (t) cc_final: 0.6999 (m) REVERT: Q 229 LEU cc_start: 0.8754 (tp) cc_final: 0.8534 (tt) outliers start: 2 outliers final: 1 residues processed: 555 average time/residue: 0.1225 time to fit residues: 96.3124 Evaluate side-chains 269 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 268 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.0970 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 100 ASN C 72 HIS C 192 ASN C 217 HIS C 222 ASN ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 222 ASN P 282 GLN Q 177 HIS ** Q 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 204 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.114463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.093289 restraints weight = 38229.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.095380 restraints weight = 21113.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.096661 restraints weight = 14502.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.097397 restraints weight = 11585.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.097693 restraints weight = 10187.647| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3315 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.285 13529 Z= 0.164 Angle : 0.777 12.788 18530 Z= 0.373 Chirality : 0.047 0.184 1970 Planarity : 0.007 0.082 2327 Dihedral : 8.867 89.419 1858 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.64 % Favored : 88.30 % Rotamer: Outliers : 0.32 % Allowed : 5.20 % Favored : 94.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.34 (0.19), residues: 1658 helix: 0.05 (0.17), residues: 804 sheet: -1.92 (0.66), residues: 52 loop : -3.38 (0.19), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 165 TYR 0.021 0.002 TYR P 199 PHE 0.021 0.001 PHE P 401 TRP 0.021 0.001 TRP E 126 HIS 0.005 0.001 HIS P 217 Details of bonding type rmsd covalent geometry : bond 0.00372 (13509) covalent geometry : angle 0.76379 (18520) SS BOND : bond 0.00156 ( 2) SS BOND : angle 0.56519 ( 4) hydrogen bonds : bond 0.05031 ( 626) hydrogen bonds : angle 4.91508 ( 1806) metal coordination : bond 0.01068 ( 8) metal coordination : angle 7.91579 ( 6) Misc. bond : bond 0.15476 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 388 time to evaluate : 0.474 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 70 LYS cc_start: 0.8185 (pttp) cc_final: 0.7907 (pttp) REVERT: R 35 ILE cc_start: 0.9306 (mm) cc_final: 0.9044 (mm) REVERT: R 50 ILE cc_start: 0.7217 (tp) cc_final: 0.6918 (tp) REVERT: R 127 LEU cc_start: 0.7734 (mp) cc_final: 0.7485 (mp) REVERT: R 130 LEU cc_start: 0.9098 (mt) cc_final: 0.8243 (mt) REVERT: C 39 LYS cc_start: 0.7759 (mttt) cc_final: 0.5786 (tttm) REVERT: C 93 MET cc_start: 0.9379 (mmm) cc_final: 0.8740 (mmm) REVERT: C 110 ILE cc_start: 0.9567 (mt) cc_final: 0.9209 (tt) REVERT: C 175 SER cc_start: 0.9052 (m) cc_final: 0.8655 (t) REVERT: C 296 TRP cc_start: 0.8590 (p-90) cc_final: 0.7978 (p-90) REVERT: C 306 ARG cc_start: 0.8668 (ttp80) cc_final: 0.8188 (ttt-90) REVERT: C 350 ASP cc_start: 0.7472 (t70) cc_final: 0.7024 (t0) REVERT: D 180 TRP cc_start: 0.7513 (m100) cc_final: 0.6719 (m100) REVERT: D 195 GLU cc_start: 0.7673 (mp0) cc_final: 0.7467 (mp0) REVERT: P 120 SER cc_start: 0.8839 (m) cc_final: 0.8602 (m) REVERT: P 121 TYR cc_start: 0.7546 (p90) cc_final: 0.6534 (p90) REVERT: P 287 SER cc_start: 0.8378 (m) cc_final: 0.7972 (p) REVERT: P 305 LEU cc_start: 0.8870 (mt) cc_final: 0.8667 (mt) REVERT: P 343 MET cc_start: 0.8248 (mtp) cc_final: 0.8029 (ttm) REVERT: P 374 PHE cc_start: 0.9055 (t80) cc_final: 0.8750 (t80) REVERT: P 378 THR cc_start: 0.9510 (m) cc_final: 0.9291 (p) REVERT: P 390 ASP cc_start: 0.8327 (p0) cc_final: 0.8084 (p0) REVERT: Q 28 GLN cc_start: 0.8174 (tp-100) cc_final: 0.7779 (tp-100) REVERT: Q 43 VAL cc_start: 0.9219 (t) cc_final: 0.8874 (p) REVERT: Q 96 MET cc_start: 0.8504 (mmp) cc_final: 0.7859 (mmm) REVERT: Q 204 GLN cc_start: 0.8923 (tp-100) cc_final: 0.8337 (tp-100) REVERT: Q 214 MET cc_start: 0.8447 (tpp) cc_final: 0.7898 (tpt) outliers start: 4 outliers final: 2 residues processed: 390 average time/residue: 0.1047 time to fit residues: 60.2026 Evaluate side-chains 243 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 241 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 145 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 35 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 36 optimal weight: 0.0770 chunk 73 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 153 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 36 ASN R 62 GLN C 68 HIS C 217 HIS ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 GLN ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 72 HIS P 282 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.101813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.082292 restraints weight = 40683.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.084436 restraints weight = 21703.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.085804 restraints weight = 14444.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.086366 restraints weight = 11215.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.086947 restraints weight = 9910.777| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.364 13529 Z= 0.148 Angle : 0.742 14.450 18530 Z= 0.347 Chirality : 0.045 0.173 1970 Planarity : 0.006 0.058 2327 Dihedral : 8.632 89.368 1858 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.70 % Favored : 88.24 % Rotamer: Outliers : 0.24 % Allowed : 2.80 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.65 (0.20), residues: 1658 helix: 0.56 (0.18), residues: 818 sheet: -0.79 (0.69), residues: 58 loop : -3.09 (0.20), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 12 TYR 0.037 0.001 TYR C 109 PHE 0.026 0.001 PHE C 330 TRP 0.024 0.001 TRP E 151 HIS 0.005 0.001 HIS C 291 Details of bonding type rmsd covalent geometry : bond 0.00334 (13509) covalent geometry : angle 0.72607 (18520) SS BOND : bond 0.00137 ( 2) SS BOND : angle 0.45670 ( 4) hydrogen bonds : bond 0.04611 ( 626) hydrogen bonds : angle 4.74897 ( 1806) metal coordination : bond 0.01187 ( 8) metal coordination : angle 8.66506 ( 6) Misc. bond : bond 0.18705 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 355 time to evaluate : 0.447 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: E 93 LEU cc_start: 0.6548 (mm) cc_final: 0.6346 (mm) REVERT: E 130 LEU cc_start: 0.8859 (tp) cc_final: 0.8325 (tp) REVERT: E 145 SER cc_start: 0.8617 (m) cc_final: 0.8307 (m) REVERT: R 66 LYS cc_start: 0.9182 (tmtt) cc_final: 0.8970 (tmtt) REVERT: R 160 TYR cc_start: 0.7819 (m-80) cc_final: 0.7552 (m-80) REVERT: C 39 LYS cc_start: 0.7836 (mttt) cc_final: 0.5722 (tttm) REVERT: C 93 MET cc_start: 0.9445 (mmm) cc_final: 0.8832 (mmm) REVERT: C 94 ARG cc_start: 0.8618 (ttt-90) cc_final: 0.8269 (ttt-90) REVERT: C 110 ILE cc_start: 0.9503 (mt) cc_final: 0.9266 (tt) REVERT: C 175 SER cc_start: 0.8671 (m) cc_final: 0.8365 (t) REVERT: C 193 ARG cc_start: 0.7930 (mtt90) cc_final: 0.7680 (mtt-85) REVERT: C 296 TRP cc_start: 0.8815 (p-90) cc_final: 0.8178 (p-90) REVERT: C 372 LEU cc_start: 0.9237 (tp) cc_final: 0.8845 (tt) REVERT: D 22 GLN cc_start: 0.8411 (tp-100) cc_final: 0.8118 (tp-100) REVERT: D 27 PHE cc_start: 0.8874 (t80) cc_final: 0.8548 (t80) REVERT: D 31 ASN cc_start: 0.9193 (p0) cc_final: 0.8798 (p0) REVERT: D 180 TRP cc_start: 0.7647 (m100) cc_final: 0.6826 (m100) REVERT: P 120 SER cc_start: 0.8929 (m) cc_final: 0.8448 (p) REVERT: P 121 TYR cc_start: 0.7812 (p90) cc_final: 0.7090 (p90) REVERT: P 165 LEU cc_start: 0.9359 (mp) cc_final: 0.8983 (mp) REVERT: P 374 PHE cc_start: 0.9115 (t80) cc_final: 0.8836 (t80) REVERT: P 378 THR cc_start: 0.9484 (m) cc_final: 0.9176 (p) REVERT: Q 28 GLN cc_start: 0.8316 (tp-100) cc_final: 0.7042 (tp-100) REVERT: Q 32 GLU cc_start: 0.7868 (mt-10) cc_final: 0.6865 (mt-10) REVERT: Q 96 MET cc_start: 0.8561 (mmp) cc_final: 0.8176 (mmm) REVERT: Q 155 ASN cc_start: 0.6572 (t0) cc_final: 0.6115 (t0) REVERT: Q 204 GLN cc_start: 0.8979 (tp-100) cc_final: 0.8505 (tp-100) outliers start: 3 outliers final: 2 residues processed: 356 average time/residue: 0.0977 time to fit residues: 51.9363 Evaluate side-chains 243 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 241 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 144 optimal weight: 6.9990 chunk 27 optimal weight: 0.5980 chunk 23 optimal weight: 0.1980 chunk 124 optimal weight: 10.0000 chunk 42 optimal weight: 0.0050 chunk 92 optimal weight: 0.0570 chunk 77 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.3512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 36 ASN ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 62 GLN C 99 ASN C 217 HIS D 20 GLN D 159 GLN ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.101859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.082185 restraints weight = 40008.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.084472 restraints weight = 20877.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.085988 restraints weight = 13609.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.086626 restraints weight = 10362.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.087200 restraints weight = 9058.155| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.167 13529 Z= 0.131 Angle : 0.698 10.415 18530 Z= 0.335 Chirality : 0.044 0.178 1970 Planarity : 0.005 0.058 2327 Dihedral : 8.561 88.702 1858 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.31 % Favored : 89.63 % Rotamer: Outliers : 0.24 % Allowed : 2.48 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.28 (0.21), residues: 1658 helix: 0.73 (0.18), residues: 823 sheet: -0.60 (0.72), residues: 52 loop : -2.75 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 77 TYR 0.030 0.001 TYR P 199 PHE 0.020 0.001 PHE C 330 TRP 0.016 0.001 TRP E 151 HIS 0.004 0.001 HIS C 291 Details of bonding type rmsd covalent geometry : bond 0.00296 (13509) covalent geometry : angle 0.68186 (18520) SS BOND : bond 0.00054 ( 2) SS BOND : angle 0.30453 ( 4) hydrogen bonds : bond 0.04342 ( 626) hydrogen bonds : angle 4.57704 ( 1806) metal coordination : bond 0.00626 ( 8) metal coordination : angle 8.44901 ( 6) Misc. bond : bond 0.10616 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 359 time to evaluate : 0.554 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: symmetry clash REVERT: E 145 SER cc_start: 0.8579 (m) cc_final: 0.8171 (t) REVERT: R 50 ILE cc_start: 0.7682 (tp) cc_final: 0.7477 (tp) REVERT: R 66 LYS cc_start: 0.9160 (tmtt) cc_final: 0.8894 (tmtt) REVERT: R 160 TYR cc_start: 0.7995 (m-80) cc_final: 0.7693 (m-80) REVERT: C 39 LYS cc_start: 0.7755 (mttt) cc_final: 0.6057 (pttp) REVERT: C 84 MET cc_start: 0.9219 (mmm) cc_final: 0.8503 (mmm) REVERT: C 93 MET cc_start: 0.9451 (mmm) cc_final: 0.8756 (mmm) REVERT: C 94 ARG cc_start: 0.8631 (ttt-90) cc_final: 0.7687 (ttt180) REVERT: C 110 ILE cc_start: 0.9498 (mt) cc_final: 0.9245 (tt) REVERT: C 133 MET cc_start: 0.8606 (mmp) cc_final: 0.8287 (mmm) REVERT: C 175 SER cc_start: 0.8661 (m) cc_final: 0.8384 (t) REVERT: C 196 SER cc_start: 0.9640 (t) cc_final: 0.9302 (m) REVERT: C 199 TYR cc_start: 0.9238 (t80) cc_final: 0.8617 (t80) REVERT: C 296 TRP cc_start: 0.8738 (p-90) cc_final: 0.8193 (p-90) REVERT: D 22 GLN cc_start: 0.8464 (tp-100) cc_final: 0.8090 (tp-100) REVERT: D 31 ASN cc_start: 0.9199 (p0) cc_final: 0.8852 (p0) REVERT: D 48 LEU cc_start: 0.9242 (mt) cc_final: 0.8822 (mp) REVERT: D 87 MET cc_start: 0.8215 (mtm) cc_final: 0.7935 (mtm) REVERT: D 232 MET cc_start: 0.7942 (tmm) cc_final: 0.7720 (tmm) REVERT: P 121 TYR cc_start: 0.7909 (p90) cc_final: 0.7151 (p90) REVERT: P 165 LEU cc_start: 0.9210 (mp) cc_final: 0.8980 (mp) REVERT: P 260 LEU cc_start: 0.9756 (mp) cc_final: 0.9492 (mm) REVERT: P 270 MET cc_start: 0.8067 (mpp) cc_final: 0.7786 (mpp) REVERT: P 278 ASP cc_start: 0.8561 (m-30) cc_final: 0.8277 (m-30) REVERT: P 287 SER cc_start: 0.8724 (m) cc_final: 0.8337 (p) REVERT: P 295 GLU cc_start: 0.8732 (tp30) cc_final: 0.8473 (tp30) REVERT: P 343 MET cc_start: 0.8581 (ttm) cc_final: 0.8272 (mmm) REVERT: P 350 ASP cc_start: 0.7961 (m-30) cc_final: 0.6896 (m-30) REVERT: P 374 PHE cc_start: 0.9088 (t80) cc_final: 0.8886 (t80) REVERT: P 378 THR cc_start: 0.9452 (m) cc_final: 0.9155 (p) REVERT: Q 28 GLN cc_start: 0.8420 (tp-100) cc_final: 0.7846 (tp-100) REVERT: Q 41 LYS cc_start: 0.8018 (pttp) cc_final: 0.7771 (pttp) REVERT: Q 96 MET cc_start: 0.8331 (mmp) cc_final: 0.7967 (mmm) REVERT: Q 155 ASN cc_start: 0.6697 (t0) cc_final: 0.6155 (t0) REVERT: Q 204 GLN cc_start: 0.8957 (tp-100) cc_final: 0.8430 (tp-100) outliers start: 3 outliers final: 2 residues processed: 360 average time/residue: 0.1065 time to fit residues: 57.6513 Evaluate side-chains 250 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 248 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 131 optimal weight: 0.9980 chunk 2 optimal weight: 0.4980 chunk 117 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 43 optimal weight: 0.2980 chunk 20 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 36 ASN ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 217 HIS P 68 HIS P 99 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.100063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.080382 restraints weight = 40362.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.082596 restraints weight = 21197.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.084047 restraints weight = 13840.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.084619 restraints weight = 10595.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.085227 restraints weight = 9291.030| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.5568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.168 13529 Z= 0.136 Angle : 0.712 11.790 18530 Z= 0.337 Chirality : 0.045 0.182 1970 Planarity : 0.005 0.058 2327 Dihedral : 8.417 89.025 1858 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.55 % Favored : 89.32 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.01 (0.21), residues: 1658 helix: 0.91 (0.18), residues: 824 sheet: -0.28 (0.70), residues: 58 loop : -2.59 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 68 TYR 0.016 0.001 TYR D 134 PHE 0.011 0.001 PHE Q 158 TRP 0.015 0.001 TRP E 151 HIS 0.005 0.001 HIS P 68 Details of bonding type rmsd covalent geometry : bond 0.00326 (13509) covalent geometry : angle 0.69325 (18520) SS BOND : bond 0.00101 ( 2) SS BOND : angle 0.28120 ( 4) hydrogen bonds : bond 0.04242 ( 626) hydrogen bonds : angle 4.49167 ( 1806) metal coordination : bond 0.00854 ( 8) metal coordination : angle 9.10912 ( 6) Misc. bond : bond 0.10262 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 0.502 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: E 145 SER cc_start: 0.8619 (m) cc_final: 0.8282 (t) REVERT: E 166 ILE cc_start: 0.7326 (tp) cc_final: 0.7050 (tp) REVERT: R 35 ILE cc_start: 0.9466 (mm) cc_final: 0.8969 (tp) REVERT: R 66 LYS cc_start: 0.9159 (tmtt) cc_final: 0.8887 (tmtt) REVERT: R 70 LYS cc_start: 0.9135 (mptt) cc_final: 0.8928 (mppt) REVERT: R 81 ASP cc_start: 0.7829 (t0) cc_final: 0.7506 (t0) REVERT: R 129 MET cc_start: 0.8712 (ttm) cc_final: 0.8245 (ttt) REVERT: R 160 TYR cc_start: 0.8133 (m-80) cc_final: 0.7778 (m-80) REVERT: R 175 LEU cc_start: 0.9434 (mt) cc_final: 0.9229 (mt) REVERT: C 39 LYS cc_start: 0.7832 (mttt) cc_final: 0.5927 (tttm) REVERT: C 93 MET cc_start: 0.9375 (mmm) cc_final: 0.8388 (mmm) REVERT: C 175 SER cc_start: 0.8707 (m) cc_final: 0.8417 (t) REVERT: C 222 ASN cc_start: 0.8452 (t0) cc_final: 0.8205 (t0) REVERT: C 223 ASN cc_start: 0.8386 (t0) cc_final: 0.8186 (t0) REVERT: C 296 TRP cc_start: 0.8840 (p-90) cc_final: 0.8276 (p-90) REVERT: C 365 MET cc_start: 0.8760 (ppp) cc_final: 0.8303 (ppp) REVERT: D 22 GLN cc_start: 0.8543 (tp-100) cc_final: 0.8103 (tp-100) REVERT: D 27 PHE cc_start: 0.8732 (t80) cc_final: 0.8398 (t80) REVERT: D 31 ASN cc_start: 0.9151 (p0) cc_final: 0.8906 (p0) REVERT: D 87 MET cc_start: 0.8353 (mtm) cc_final: 0.8130 (mtm) REVERT: D 214 MET cc_start: 0.9070 (tpp) cc_final: 0.8520 (tpt) REVERT: D 232 MET cc_start: 0.8148 (tmm) cc_final: 0.7893 (tmm) REVERT: D 241 MET cc_start: 0.9289 (ttm) cc_final: 0.9059 (ttm) REVERT: P 58 GLN cc_start: 0.8891 (mm-40) cc_final: 0.8605 (tp-100) REVERT: P 120 SER cc_start: 0.9031 (m) cc_final: 0.8439 (p) REVERT: P 165 LEU cc_start: 0.9212 (mp) cc_final: 0.8974 (mp) REVERT: P 187 ASP cc_start: 0.9031 (t0) cc_final: 0.8444 (m-30) REVERT: P 278 ASP cc_start: 0.8587 (m-30) cc_final: 0.8385 (m-30) REVERT: P 378 THR cc_start: 0.9431 (m) cc_final: 0.9199 (p) REVERT: Q 28 GLN cc_start: 0.8461 (tp-100) cc_final: 0.7832 (tp40) REVERT: Q 96 MET cc_start: 0.8363 (mmp) cc_final: 0.8029 (mmm) REVERT: Q 155 ASN cc_start: 0.6700 (t0) cc_final: 0.6175 (t0) REVERT: Q 204 GLN cc_start: 0.8985 (tp-100) cc_final: 0.8514 (tp-100) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.1036 time to fit residues: 53.6435 Evaluate side-chains 241 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 77 optimal weight: 0.3980 chunk 124 optimal weight: 6.9990 chunk 2 optimal weight: 0.0070 chunk 138 optimal weight: 0.0000 chunk 39 optimal weight: 1.9990 chunk 157 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 107 optimal weight: 0.5980 chunk 93 optimal weight: 7.9990 chunk 119 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 overall best weight: 0.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 217 HIS D 159 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.101582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.082132 restraints weight = 39841.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.084234 restraints weight = 21592.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.085649 restraints weight = 14573.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.086207 restraints weight = 11294.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.086676 restraints weight = 9923.134| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.5886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 13529 Z= 0.127 Angle : 0.687 11.703 18530 Z= 0.328 Chirality : 0.044 0.163 1970 Planarity : 0.005 0.057 2327 Dihedral : 8.247 82.951 1858 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.83 % Favored : 90.05 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.21), residues: 1658 helix: 1.04 (0.18), residues: 817 sheet: 0.13 (0.74), residues: 53 loop : -2.48 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 68 TYR 0.031 0.001 TYR C 199 PHE 0.011 0.001 PHE Q 158 TRP 0.017 0.001 TRP E 151 HIS 0.005 0.001 HIS C 291 Details of bonding type rmsd covalent geometry : bond 0.00299 (13509) covalent geometry : angle 0.66495 (18520) SS BOND : bond 0.00031 ( 2) SS BOND : angle 0.09628 ( 4) hydrogen bonds : bond 0.04107 ( 626) hydrogen bonds : angle 4.33411 ( 1806) metal coordination : bond 0.00586 ( 8) metal coordination : angle 9.59491 ( 6) Misc. bond : bond 0.08021 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 0.483 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: 0.7921 (tpt) cc_final: 0.7386 (tpp) REVERT: E 145 SER cc_start: 0.8735 (m) cc_final: 0.8464 (t) REVERT: R 35 ILE cc_start: 0.9459 (mm) cc_final: 0.8967 (tp) REVERT: R 66 LYS cc_start: 0.9136 (tmtt) cc_final: 0.8919 (tmtt) REVERT: R 90 LEU cc_start: 0.8415 (mp) cc_final: 0.8146 (tt) REVERT: R 160 TYR cc_start: 0.8255 (m-80) cc_final: 0.7884 (m-80) REVERT: C 84 MET cc_start: 0.9326 (mmm) cc_final: 0.9009 (mmm) REVERT: C 93 MET cc_start: 0.9339 (mmm) cc_final: 0.8415 (mmm) REVERT: C 175 SER cc_start: 0.8773 (m) cc_final: 0.8452 (t) REVERT: C 199 TYR cc_start: 0.9200 (t80) cc_final: 0.8580 (t80) REVERT: C 222 ASN cc_start: 0.8475 (t0) cc_final: 0.8217 (t0) REVERT: C 223 ASN cc_start: 0.8294 (t0) cc_final: 0.8087 (t0) REVERT: C 296 TRP cc_start: 0.8630 (p-90) cc_final: 0.8141 (p-90) REVERT: C 365 MET cc_start: 0.8852 (ppp) cc_final: 0.8315 (ppp) REVERT: D 22 GLN cc_start: 0.8515 (tp-100) cc_final: 0.8151 (tp-100) REVERT: D 232 MET cc_start: 0.8212 (tmm) cc_final: 0.7984 (tmm) REVERT: P 58 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8396 (mm-40) REVERT: P 118 TYR cc_start: 0.8608 (m-80) cc_final: 0.8219 (m-10) REVERT: P 165 LEU cc_start: 0.9135 (mp) cc_final: 0.8852 (mp) REVERT: P 187 ASP cc_start: 0.9023 (t0) cc_final: 0.8344 (m-30) REVERT: P 188 ASN cc_start: 0.9030 (p0) cc_final: 0.8420 (p0) REVERT: P 305 LEU cc_start: 0.8918 (mt) cc_final: 0.8674 (mt) REVERT: P 378 THR cc_start: 0.9439 (m) cc_final: 0.9212 (p) REVERT: Q 28 GLN cc_start: 0.8469 (tp-100) cc_final: 0.7832 (tp-100) REVERT: Q 155 ASN cc_start: 0.6786 (t0) cc_final: 0.6250 (t0) REVERT: Q 204 GLN cc_start: 0.9079 (tp-100) cc_final: 0.8463 (tp-100) REVERT: Q 235 LEU cc_start: 0.9392 (mp) cc_final: 0.9169 (mm) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.0988 time to fit residues: 50.7192 Evaluate side-chains 243 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 161 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 147 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 36 ASN ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 HIS D 246 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.099109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.079875 restraints weight = 40484.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.081969 restraints weight = 22397.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.083308 restraints weight = 15081.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.083936 restraints weight = 11704.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.084369 restraints weight = 10238.126| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.6172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.145 13529 Z= 0.151 Angle : 0.724 12.121 18530 Z= 0.343 Chirality : 0.046 0.210 1970 Planarity : 0.005 0.057 2327 Dihedral : 8.192 84.399 1858 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.43 % Favored : 89.45 % Rotamer: Outliers : 0.08 % Allowed : 0.96 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.21), residues: 1658 helix: 1.09 (0.18), residues: 820 sheet: 0.37 (0.75), residues: 53 loop : -2.35 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 68 TYR 0.044 0.002 TYR P 199 PHE 0.025 0.001 PHE P 104 TRP 0.023 0.001 TRP E 151 HIS 0.005 0.001 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00375 (13509) covalent geometry : angle 0.70152 (18520) SS BOND : bond 0.00101 ( 2) SS BOND : angle 0.16604 ( 4) hydrogen bonds : bond 0.04263 ( 626) hydrogen bonds : angle 4.37765 ( 1806) metal coordination : bond 0.00763 ( 8) metal coordination : angle 10.06987 ( 6) Misc. bond : bond 0.08068 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 330 time to evaluate : 0.487 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 145 SER cc_start: 0.8792 (m) cc_final: 0.8524 (t) REVERT: E 182 PHE cc_start: 0.6663 (m-10) cc_final: 0.6225 (m-80) REVERT: R 35 ILE cc_start: 0.9480 (mm) cc_final: 0.9040 (tp) REVERT: R 130 LEU cc_start: 0.9336 (mt) cc_final: 0.8962 (mt) REVERT: C 39 LYS cc_start: 0.7777 (mttt) cc_final: 0.5954 (tttm) REVERT: C 93 MET cc_start: 0.9253 (mmm) cc_final: 0.8305 (mmm) REVERT: C 133 MET cc_start: 0.8453 (mmp) cc_final: 0.8247 (mmm) REVERT: C 136 TYR cc_start: 0.8803 (t80) cc_final: 0.8594 (t80) REVERT: C 175 SER cc_start: 0.8817 (m) cc_final: 0.8496 (t) REVERT: C 222 ASN cc_start: 0.8312 (t0) cc_final: 0.8092 (t0) REVERT: C 223 ASN cc_start: 0.8349 (t0) cc_final: 0.8129 (t0) REVERT: C 296 TRP cc_start: 0.8789 (p-90) cc_final: 0.8367 (p-90) REVERT: C 365 MET cc_start: 0.8875 (ppp) cc_final: 0.8275 (ppp) REVERT: D 27 PHE cc_start: 0.8845 (t80) cc_final: 0.8446 (t80) REVERT: D 31 ASN cc_start: 0.9173 (p0) cc_final: 0.8739 (p0) REVERT: D 87 MET cc_start: 0.8238 (mtm) cc_final: 0.7836 (mtm) REVERT: D 180 TRP cc_start: 0.8111 (m100) cc_final: 0.7239 (m100) REVERT: P 58 GLN cc_start: 0.9158 (mm-40) cc_final: 0.8586 (mm-40) REVERT: P 118 TYR cc_start: 0.8664 (m-80) cc_final: 0.8155 (m-10) REVERT: P 187 ASP cc_start: 0.9017 (t0) cc_final: 0.8449 (m-30) REVERT: P 188 ASN cc_start: 0.9143 (p0) cc_final: 0.8689 (p0) REVERT: P 260 LEU cc_start: 0.9782 (mp) cc_final: 0.9511 (mm) REVERT: P 305 LEU cc_start: 0.8928 (mt) cc_final: 0.8356 (mt) REVERT: P 378 THR cc_start: 0.9427 (m) cc_final: 0.9182 (p) REVERT: Q 28 GLN cc_start: 0.8415 (tp-100) cc_final: 0.7760 (tp-100) REVERT: Q 40 MET cc_start: 0.7636 (mmp) cc_final: 0.7143 (mmp) REVERT: Q 41 LYS cc_start: 0.8408 (pttp) cc_final: 0.7933 (pttm) REVERT: Q 155 ASN cc_start: 0.6882 (t0) cc_final: 0.6406 (t0) REVERT: Q 204 GLN cc_start: 0.8977 (tp-100) cc_final: 0.8151 (tp-100) outliers start: 1 outliers final: 0 residues processed: 331 average time/residue: 0.1017 time to fit residues: 51.0445 Evaluate side-chains 240 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 62 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 36 ASN ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 HIS C 222 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 ASN P 291 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.095216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.075659 restraints weight = 40490.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.077667 restraints weight = 21907.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.078702 restraints weight = 14620.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.079744 restraints weight = 11685.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.080181 restraints weight = 9837.764| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.6503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.182 13529 Z= 0.182 Angle : 0.778 14.742 18530 Z= 0.368 Chirality : 0.046 0.192 1970 Planarity : 0.005 0.057 2327 Dihedral : 8.249 86.965 1858 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.98 % Favored : 88.90 % Rotamer: Outliers : 0.08 % Allowed : 1.76 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.21), residues: 1658 helix: 1.09 (0.18), residues: 819 sheet: 0.32 (0.74), residues: 53 loop : -2.46 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 76 TYR 0.021 0.002 TYR P 199 PHE 0.026 0.002 PHE P 105 TRP 0.030 0.001 TRP E 151 HIS 0.018 0.002 HIS P 291 Details of bonding type rmsd covalent geometry : bond 0.00464 (13509) covalent geometry : angle 0.76023 (18520) SS BOND : bond 0.00141 ( 2) SS BOND : angle 0.13389 ( 4) hydrogen bonds : bond 0.04503 ( 626) hydrogen bonds : angle 4.45393 ( 1806) metal coordination : bond 0.00903 ( 8) metal coordination : angle 9.25627 ( 6) Misc. bond : bond 0.08247 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 312 time to evaluate : 0.548 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: E 47 MET cc_start: 0.8045 (tpt) cc_final: 0.7636 (tmm) REVERT: E 182 PHE cc_start: 0.6699 (m-10) cc_final: 0.6295 (m-80) REVERT: R 35 ILE cc_start: 0.9538 (mm) cc_final: 0.9120 (tp) REVERT: R 70 LYS cc_start: 0.9321 (mptt) cc_final: 0.9101 (mmmt) REVERT: R 129 MET cc_start: 0.9060 (ttm) cc_final: 0.8773 (ttt) REVERT: C 39 LYS cc_start: 0.7929 (mttt) cc_final: 0.6018 (tttm) REVERT: C 46 ILE cc_start: 0.8772 (pt) cc_final: 0.8363 (tp) REVERT: C 84 MET cc_start: 0.9183 (mmm) cc_final: 0.8977 (mmm) REVERT: C 93 MET cc_start: 0.9443 (mmm) cc_final: 0.8815 (mmm) REVERT: C 175 SER cc_start: 0.8832 (m) cc_final: 0.8562 (t) REVERT: C 199 TYR cc_start: 0.9223 (t80) cc_final: 0.9018 (t80) REVERT: C 222 ASN cc_start: 0.8559 (t160) cc_final: 0.8253 (t0) REVERT: C 223 ASN cc_start: 0.8570 (t0) cc_final: 0.8319 (t0) REVERT: C 365 MET cc_start: 0.8802 (ppp) cc_final: 0.8292 (ppp) REVERT: D 27 PHE cc_start: 0.8990 (t80) cc_final: 0.8589 (t80) REVERT: D 31 ASN cc_start: 0.9233 (p0) cc_final: 0.8745 (p0) REVERT: D 141 ASN cc_start: 0.7402 (OUTLIER) cc_final: 0.6846 (t0) REVERT: D 180 TRP cc_start: 0.8197 (m100) cc_final: 0.7313 (m100) REVERT: D 214 MET cc_start: 0.8740 (tpp) cc_final: 0.8427 (tpt) REVERT: D 232 MET cc_start: 0.8294 (tmm) cc_final: 0.8035 (tmm) REVERT: P 58 GLN cc_start: 0.9173 (mm-40) cc_final: 0.8775 (tp-100) REVERT: P 118 TYR cc_start: 0.8688 (m-80) cc_final: 0.8225 (m-10) REVERT: P 187 ASP cc_start: 0.9147 (t0) cc_final: 0.8549 (m-30) REVERT: P 188 ASN cc_start: 0.9142 (p0) cc_final: 0.8769 (p0) REVERT: P 260 LEU cc_start: 0.9765 (mp) cc_final: 0.9496 (mm) REVERT: P 305 LEU cc_start: 0.9163 (mt) cc_final: 0.8704 (mt) REVERT: P 378 THR cc_start: 0.9489 (m) cc_final: 0.9237 (p) REVERT: Q 28 GLN cc_start: 0.8481 (tp-100) cc_final: 0.7809 (tp-100) REVERT: Q 40 MET cc_start: 0.7851 (mmp) cc_final: 0.7519 (mmp) REVERT: Q 155 ASN cc_start: 0.7151 (t0) cc_final: 0.6772 (t0) REVERT: Q 204 GLN cc_start: 0.9039 (tp-100) cc_final: 0.8188 (tp-100) REVERT: Q 241 MET cc_start: 0.8558 (ttp) cc_final: 0.8012 (tmm) REVERT: Q 245 THR cc_start: 0.9052 (p) cc_final: 0.8718 (p) outliers start: 1 outliers final: 0 residues processed: 313 average time/residue: 0.1016 time to fit residues: 48.3479 Evaluate side-chains 236 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 72 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 153 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 162 optimal weight: 0.4980 chunk 157 optimal weight: 7.9990 chunk 14 optimal weight: 0.0010 chunk 97 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 142 optimal weight: 8.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 36 ASN ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 HIS D 246 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.097337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.077944 restraints weight = 40279.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.080009 restraints weight = 21807.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.081307 restraints weight = 14530.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.082224 restraints weight = 11276.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.082523 restraints weight = 9560.620| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.6704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 13529 Z= 0.138 Angle : 0.733 11.974 18530 Z= 0.353 Chirality : 0.046 0.184 1970 Planarity : 0.005 0.055 2327 Dihedral : 8.202 89.280 1858 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.25 % Favored : 89.63 % Rotamer: Outliers : 0.16 % Allowed : 0.96 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.21), residues: 1658 helix: 1.11 (0.18), residues: 818 sheet: 0.36 (0.75), residues: 53 loop : -2.41 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 224 TYR 0.030 0.001 TYR P 199 PHE 0.021 0.001 PHE P 367 TRP 0.034 0.001 TRP E 151 HIS 0.006 0.001 HIS P 276 Details of bonding type rmsd covalent geometry : bond 0.00328 (13509) covalent geometry : angle 0.71448 (18520) SS BOND : bond 0.00062 ( 2) SS BOND : angle 0.16621 ( 4) hydrogen bonds : bond 0.04281 ( 626) hydrogen bonds : angle 4.38684 ( 1806) metal coordination : bond 0.00455 ( 8) metal coordination : angle 9.25431 ( 6) Misc. bond : bond 0.07346 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 321 time to evaluate : 0.494 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: symmetry clash REVERT: E 128 VAL cc_start: 0.8908 (p) cc_final: 0.8624 (m) REVERT: E 129 MET cc_start: 0.7875 (ptt) cc_final: 0.7409 (ptp) REVERT: E 145 SER cc_start: 0.8870 (m) cc_final: 0.8606 (t) REVERT: E 182 PHE cc_start: 0.6566 (m-10) cc_final: 0.6206 (m-80) REVERT: R 35 ILE cc_start: 0.9553 (mm) cc_final: 0.9128 (tp) REVERT: R 66 LYS cc_start: 0.9364 (tptp) cc_final: 0.9121 (tptp) REVERT: R 70 LYS cc_start: 0.9300 (mptt) cc_final: 0.9056 (mmmt) REVERT: R 129 MET cc_start: 0.8925 (ttm) cc_final: 0.8639 (ttt) REVERT: C 39 LYS cc_start: 0.7819 (mttt) cc_final: 0.5982 (tttm) REVERT: C 93 MET cc_start: 0.9436 (mmm) cc_final: 0.8768 (mmm) REVERT: C 175 SER cc_start: 0.8842 (m) cc_final: 0.8571 (t) REVERT: C 199 TYR cc_start: 0.8338 (t80) cc_final: 0.8122 (t80) REVERT: C 365 MET cc_start: 0.8870 (ppp) cc_final: 0.8319 (ppp) REVERT: D 31 ASN cc_start: 0.9174 (p0) cc_final: 0.8839 (p0) REVERT: D 87 MET cc_start: 0.8360 (mtp) cc_final: 0.7946 (mtm) REVERT: D 180 TRP cc_start: 0.8070 (m100) cc_final: 0.7404 (m100) REVERT: D 210 SER cc_start: 0.9689 (t) cc_final: 0.9437 (p) REVERT: D 214 MET cc_start: 0.8947 (tpp) cc_final: 0.8545 (tpt) REVERT: P 58 GLN cc_start: 0.9092 (mm-40) cc_final: 0.8695 (tp-100) REVERT: P 118 TYR cc_start: 0.8644 (m-80) cc_final: 0.8095 (m-10) REVERT: P 129 TRP cc_start: 0.8864 (t-100) cc_final: 0.8597 (t-100) REVERT: P 187 ASP cc_start: 0.9029 (t0) cc_final: 0.8407 (m-30) REVERT: P 188 ASN cc_start: 0.9161 (p0) cc_final: 0.8743 (p0) REVERT: P 349 LEU cc_start: 0.8942 (mp) cc_final: 0.8598 (tt) REVERT: P 378 THR cc_start: 0.9438 (m) cc_final: 0.9131 (p) REVERT: Q 28 GLN cc_start: 0.8494 (tp-100) cc_final: 0.7804 (tp-100) REVERT: Q 40 MET cc_start: 0.7458 (mmp) cc_final: 0.7250 (mmp) REVERT: Q 87 MET cc_start: 0.6818 (ttm) cc_final: 0.6580 (ttm) REVERT: Q 132 TYR cc_start: 0.8615 (t80) cc_final: 0.8380 (t80) REVERT: Q 134 TYR cc_start: 0.9355 (t80) cc_final: 0.9057 (t80) REVERT: Q 155 ASN cc_start: 0.7153 (t0) cc_final: 0.6609 (t0) REVERT: Q 204 GLN cc_start: 0.9064 (tp-100) cc_final: 0.8184 (tp-100) outliers start: 2 outliers final: 1 residues processed: 322 average time/residue: 0.0995 time to fit residues: 49.1840 Evaluate side-chains 237 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 236 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 112 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 92 optimal weight: 0.0040 chunk 20 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 chunk 135 optimal weight: 0.0010 chunk 146 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 overall best weight: 0.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 36 ASN ** E 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.098546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.079130 restraints weight = 40837.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.081255 restraints weight = 22127.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.082511 restraints weight = 14660.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.083476 restraints weight = 11413.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.084064 restraints weight = 9660.996| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.6921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.158 13529 Z= 0.132 Angle : 0.724 10.457 18530 Z= 0.346 Chirality : 0.045 0.209 1970 Planarity : 0.006 0.072 2327 Dihedral : 8.088 83.894 1858 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.59 % Favored : 90.29 % Rotamer: Outliers : 0.08 % Allowed : 0.48 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.21), residues: 1658 helix: 1.21 (0.18), residues: 812 sheet: 0.41 (0.79), residues: 48 loop : -2.34 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 224 TYR 0.025 0.001 TYR C 136 PHE 0.024 0.001 PHE P 367 TRP 0.015 0.001 TRP C 379 HIS 0.006 0.001 HIS C 217 Details of bonding type rmsd covalent geometry : bond 0.00307 (13509) covalent geometry : angle 0.70521 (18520) SS BOND : bond 0.00077 ( 2) SS BOND : angle 0.10626 ( 4) hydrogen bonds : bond 0.04148 ( 626) hydrogen bonds : angle 4.32617 ( 1806) metal coordination : bond 0.00414 ( 8) metal coordination : angle 9.03222 ( 6) Misc. bond : bond 0.08122 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 333 time to evaluate : 0.503 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: E 58 GLU cc_start: 0.8207 (tt0) cc_final: 0.7991 (pt0) REVERT: E 70 LYS cc_start: 0.8054 (ptpp) cc_final: 0.7848 (ptpp) REVERT: E 145 SER cc_start: 0.8827 (m) cc_final: 0.8594 (t) REVERT: E 182 PHE cc_start: 0.6391 (m-10) cc_final: 0.5867 (m-80) REVERT: R 35 ILE cc_start: 0.9522 (mm) cc_final: 0.9132 (tp) REVERT: R 66 LYS cc_start: 0.9375 (tptp) cc_final: 0.9090 (tptp) REVERT: R 70 LYS cc_start: 0.9285 (mptt) cc_final: 0.9041 (mmmt) REVERT: R 129 MET cc_start: 0.8923 (ttm) cc_final: 0.8623 (ttt) REVERT: C 46 ILE cc_start: 0.8431 (pt) cc_final: 0.8108 (tp) REVERT: C 93 MET cc_start: 0.9364 (mmm) cc_final: 0.8595 (mmm) REVERT: C 175 SER cc_start: 0.8837 (m) cc_final: 0.8573 (t) REVERT: C 365 MET cc_start: 0.8931 (ppp) cc_final: 0.8343 (ppp) REVERT: D 28 GLN cc_start: 0.8801 (tm-30) cc_final: 0.8207 (tm-30) REVERT: D 87 MET cc_start: 0.8454 (mtp) cc_final: 0.7984 (ptp) REVERT: D 134 TYR cc_start: 0.8984 (t80) cc_final: 0.8659 (t80) REVERT: D 180 TRP cc_start: 0.8098 (m100) cc_final: 0.7615 (m100) REVERT: D 229 LEU cc_start: 0.9039 (mm) cc_final: 0.7907 (mm) REVERT: P 58 GLN cc_start: 0.9084 (mm-40) cc_final: 0.8722 (tp-100) REVERT: P 154 MET cc_start: 0.6943 (tmm) cc_final: 0.6492 (tmm) REVERT: P 165 LEU cc_start: 0.9049 (mp) cc_final: 0.8825 (mp) REVERT: P 187 ASP cc_start: 0.8978 (t0) cc_final: 0.8360 (m-30) REVERT: P 188 ASN cc_start: 0.9121 (p0) cc_final: 0.8683 (p0) REVERT: P 295 GLU cc_start: 0.8861 (tp30) cc_final: 0.8568 (tp30) REVERT: P 378 THR cc_start: 0.9404 (m) cc_final: 0.9113 (p) REVERT: Q 28 GLN cc_start: 0.8503 (tp-100) cc_final: 0.7800 (tp-100) REVERT: Q 68 LEU cc_start: 0.8837 (mt) cc_final: 0.8577 (mt) REVERT: Q 87 MET cc_start: 0.6999 (ttm) cc_final: 0.6781 (ttm) REVERT: Q 155 ASN cc_start: 0.7235 (t0) cc_final: 0.6592 (t0) REVERT: Q 204 GLN cc_start: 0.9049 (tp-100) cc_final: 0.8335 (tp-100) REVERT: Q 241 MET cc_start: 0.8696 (ttp) cc_final: 0.8438 (tmm) REVERT: Q 245 THR cc_start: 0.9066 (p) cc_final: 0.8807 (p) outliers start: 1 outliers final: 0 residues processed: 333 average time/residue: 0.0984 time to fit residues: 50.4171 Evaluate side-chains 239 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 135 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 146 optimal weight: 20.0000 chunk 78 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 107 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 36 ASN E 62 GLN ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 HIS C 276 HIS D 28 GLN D 246 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.096739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.077421 restraints weight = 40523.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.079358 restraints weight = 22041.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.080681 restraints weight = 14765.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.081606 restraints weight = 11490.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.081869 restraints weight = 9702.767| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.7050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.132 13529 Z= 0.148 Angle : 0.753 10.718 18530 Z= 0.358 Chirality : 0.046 0.217 1970 Planarity : 0.006 0.078 2327 Dihedral : 8.118 83.923 1858 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.62 % Favored : 89.26 % Rotamer: Outliers : 0.08 % Allowed : 0.96 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.21), residues: 1658 helix: 1.20 (0.18), residues: 810 sheet: 0.22 (0.77), residues: 48 loop : -2.37 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 224 TYR 0.017 0.001 TYR P 69 PHE 0.040 0.001 PHE P 104 TRP 0.016 0.001 TRP P 400 HIS 0.006 0.001 HIS C 217 Details of bonding type rmsd covalent geometry : bond 0.00370 (13509) covalent geometry : angle 0.73896 (18520) SS BOND : bond 0.00101 ( 2) SS BOND : angle 0.10547 ( 4) hydrogen bonds : bond 0.04314 ( 626) hydrogen bonds : angle 4.38824 ( 1806) metal coordination : bond 0.00531 ( 8) metal coordination : angle 8.22976 ( 6) Misc. bond : bond 0.07654 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2320.87 seconds wall clock time: 40 minutes 45.10 seconds (2445.10 seconds total)