Starting phenix.real_space_refine on Wed Mar 4 11:12:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xkt_22224/03_2026/6xkt_22224.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xkt_22224/03_2026/6xkt_22224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xkt_22224/03_2026/6xkt_22224.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xkt_22224/03_2026/6xkt_22224.map" model { file = "/net/cci-nas-00/data/ceres_data/6xkt_22224/03_2026/6xkt_22224.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xkt_22224/03_2026/6xkt_22224.cif" } resolution = 3.75 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= 0.004 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 16 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: "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: 143 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: 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: 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} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11016 SG CYS E 133 30.987 63.086 26.275 0.25105.87 S ATOM 11162 SG CYS E 153 31.786 60.791 23.548 0.25107.21 S ATOM 12381 SG CYS R 133 82.986 37.981 26.362 0.25105.87 S ATOM 12527 SG CYS R 153 82.121 40.213 23.602 0.25107.21 S Residues with excluded nonbonded symmetry interactions: 54 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 42 not shown) Time building chain proxies: 2.76, per 1000 atoms: 0.21 Number of scatterers: 13079 At special positions: 0 Unit cell: (115.6, 102, 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: 1.09 Conformation dependent library (CDL) restraints added in 630.8 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 153 " pdb="FE1 FES R 501 " - pdb=" SG CYS R 133 " 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 51.8% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 33 removed outlier: 3.763A 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: 3.642A 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: 4.863A 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: 3.960A 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: 4.405A 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: 3.848A 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: 4.003A 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: 3.753A 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: 4.002A 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: 3.958A pdb=" N VAL P 204 " --> pdb=" O LEU P 200 " (cutoff:3.500A) removed outlier: 3.586A 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: 4.405A 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: 5.575A 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: 3.672A 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: 3.589A 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 helix chain 'E' and resid 12 through 37 Proline residue: E 33 - end of helix Processing helix chain 'E' and resid 41 through 49 removed outlier: 4.227A pdb=" N ALA E 46 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N MET E 47 " --> pdb=" O ASP E 43 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA E 48 " --> pdb=" O VAL E 44 " (cutoff:3.500A) removed outlier: 4.173A 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 49 removed outlier: 4.225A pdb=" N ALA R 46 " --> pdb=" O ALA R 42 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N MET R 47 " --> pdb=" O ASP R 43 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA R 48 " --> pdb=" O VAL R 44 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER R 49 " --> pdb=" O LYS R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 87 Processing helix chain 'R' and resid 109 through 114 Processing sheet with id=AA1, first strand: chain 'D' and resid 153 through 155 Processing sheet with id=AA2, first strand: chain 'Q' and resid 153 through 155 Processing sheet with id=AA3, first strand: chain 'E' and resid 50 through 52 removed outlier: 3.607A pdb=" N ALA E 181 " --> pdb=" O LYS E 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 64 through 67 Processing sheet with id=AA5, first strand: chain 'E' and resid 141 through 145 removed outlier: 4.683A pdb=" N ASP E 143 " --> pdb=" O GLY E 150 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N GLY E 150 " --> pdb=" O ASP E 143 " (cutoff:3.500A) removed outlier: 3.690A 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=AA6, 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=AA7, first strand: chain 'R' and resid 64 through 67 Processing sheet with id=AA8, first strand: chain 'R' and resid 141 through 145 removed outlier: 4.683A pdb=" N ASP R 143 " --> pdb=" O GLY R 150 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N GLY R 150 " --> pdb=" O ASP R 143 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TRP R 151 " --> pdb=" O TYR R 160 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER R 158 " --> pdb=" O CYS R 153 " (cutoff:3.500A) 629 hydrogen bonds defined for protein. 1812 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: 1.87 Time building geometry restraints manager: 1.48 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: 5787 1.41 - 1.61: 7560 1.61 - 1.80: 109 1.80 - 2.00: 25 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 1.325 0.219 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=" C2D HEC P 501 " pdb=" C3D HEC P 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 - 3.15: 18203 3.15 - 6.31: 270 6.31 - 9.46: 28 9.46 - 12.61: 3 12.61 - 15.76: 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 89.10 -13.44 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 E 501 " pdb="FE2 FES E 501 " pdb=" S2 FES E 501 " ideal model delta sigma weight residual 104.33 90.92 13.41 1.14e+00 7.69e-01 1.38e+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 90.92 13.41 1.14e+00 7.69e-01 1.38e+02 angle pdb=" S1 FES E 501 " pdb="FE1 FES E 501 " pdb=" S2 FES E 501 " ideal model delta sigma weight residual 104.33 90.78 13.55 1.20e+00 6.94e-01 1.27e+02 ... (remaining 18515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 6976 17.90 - 35.79: 536 35.79 - 53.69: 81 53.69 - 71.59: 10 71.59 - 89.48: 22 Dihedral angle restraints: 7625 sinusoidal: 2835 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 -22.24 82.24 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 -22.11 82.11 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 -17.19 77.19 2 1.00e+01 1.00e-02 4.56e+01 ... (remaining 7622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 1925 0.146 - 0.293: 32 0.293 - 0.439: 1 0.439 - 0.585: 10 0.585 - 0.731: 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 1.34e+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 1.32e+01 chirality pdb=" CB THR D 198 " pdb=" CA THR D 198 " pdb=" OG1 THR D 198 " pdb=" CG2 THR D 198 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.53 2.00e-01 2.50e+01 6.92e+00 ... (remaining 1967 not shown) Planarity restraints: 2327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC Q 501 " 0.009 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 4.09e-02 3.76e+01 pdb=" C2C HEC D 501 " 0.109 2.00e-02 2.50e+03 pdb=" C3C HEC D 501 " -0.041 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 " -0.017 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 " -0.002 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 4.26e-02 1.81e+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: 1.73 - 2.37: 46 2.37 - 3.00: 8314 3.00 - 3.63: 18666 3.63 - 4.27: 28692 4.27 - 4.90: 48565 Nonbonded interactions: 104283 Sorted by model distance: nonbonded pdb=" CD2 LEU P 286 " pdb=" CD LYS R 70 " model vdw 1.732 3.860 nonbonded pdb=" CD2 LEU C 286 " pdb=" CD LYS E 70 " model vdw 1.797 3.860 nonbonded pdb=" NH2 ARG P 193 " pdb=" O MET R 38 " model vdw 1.949 3.120 nonbonded pdb=" OD1 ASP Q 75 " pdb=" NZ LYS E 66 " model vdw 1.962 3.120 nonbonded pdb=" O THR R 186 " pdb=" OG1 THR R 187 " model vdw 1.987 3.040 ... (remaining 104278 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: 1.260 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: 0.030 Set scattering table: 0.040 Process input model: 14.100 Find NCS groups from input model: 0.170 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 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= 0.465 Angle : 1.023 23.199 18530 Z= 0.617 Chirality : 0.068 0.731 1970 Planarity : 0.006 0.083 2327 Dihedral : 13.782 89.483 4563 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 25.78 Ramachandran Plot: Outliers : 0.42 % Allowed : 16.47 % Favored : 83.11 % Rotamer: Outliers : 0.08 % Allowed : 2.72 % Favored : 97.20 % 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: -4.20 (0.17), residues: 1658 helix: -1.61 (0.16), residues: 772 sheet: -2.87 (0.52), residues: 64 loop : -4.12 (0.18), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 85 TYR 0.010 0.001 TYR C 297 PHE 0.021 0.001 PHE P 104 TRP 0.012 0.001 TRP P 296 HIS 0.010 0.001 HIS C 111 Details of bonding type rmsd covalent geometry : bond 0.00937 (13509) covalent geometry : angle 0.99033 (18520) SS BOND : bond 0.00126 ( 2) SS BOND : angle 0.54900 ( 4) hydrogen bonds : bond 0.14686 ( 629) hydrogen bonds : angle 6.99060 ( 1812) metal coordination : bond 0.01169 ( 8) metal coordination : angle 14.20470 ( 6) Misc. bond : bond 0.14987 ( 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 446 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 445 time to evaluate : 0.349 Fit side-chains Corrupt residue: chain: C residue: PRO 24 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: P residue: PRO 24 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 132 TYR cc_start: 0.7207 (t80) cc_final: 0.6492 (t80) REVERT: D 155 ASN cc_start: 0.9198 (t0) cc_final: 0.8865 (t0) REVERT: D 160 ILE cc_start: 0.7429 (mt) cc_final: 0.7039 (mt) REVERT: D 208 ASP cc_start: 0.8065 (m-30) cc_final: 0.7448 (m-30) REVERT: P 390 ASP cc_start: 0.7791 (p0) cc_final: 0.7497 (p0) REVERT: Q 132 TYR cc_start: 0.7232 (t80) cc_final: 0.6797 (t80) REVERT: Q 152 TYR cc_start: 0.7987 (m-80) cc_final: 0.7484 (m-10) REVERT: Q 160 ILE cc_start: 0.7502 (mt) cc_final: 0.6960 (mt) REVERT: Q 208 ASP cc_start: 0.7905 (m-30) cc_final: 0.7366 (m-30) REVERT: E 37 GLN cc_start: 0.8286 (pp30) cc_final: 0.7591 (pp30) REVERT: E 102 ASN cc_start: 0.8301 (p0) cc_final: 0.7939 (p0) REVERT: E 114 THR cc_start: 0.7318 (p) cc_final: 0.7059 (p) REVERT: E 134 THR cc_start: 0.4063 (p) cc_final: 0.3535 (t) REVERT: E 136 LEU cc_start: 0.5116 (mt) cc_final: 0.4632 (mt) REVERT: E 165 ARG cc_start: 0.7527 (mtm-85) cc_final: 0.7060 (mtm-85) REVERT: R 19 THR cc_start: 0.6601 (p) cc_final: 0.5895 (p) REVERT: R 136 LEU cc_start: 0.5207 (mt) cc_final: 0.4885 (mt) REVERT: R 140 PRO cc_start: 0.8183 (Cg_exo) cc_final: 0.7909 (Cg_endo) REVERT: R 165 ARG cc_start: 0.8366 (mtm-85) cc_final: 0.7976 (mtm180) outliers start: 1 outliers final: 0 residues processed: 446 average time/residue: 0.1197 time to fit residues: 74.8185 Evaluate side-chains 283 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.0050 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.8980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 HIS ** P 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 217 HIS P 222 ASN P 291 HIS E 17 HIS R 100 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.145493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.112611 restraints weight = 21542.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.115466 restraints weight = 11237.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.117151 restraints weight = 7852.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.117691 restraints weight = 6488.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.118310 restraints weight = 6016.545| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3344 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.328 13529 Z= 0.166 Angle : 0.791 17.796 18530 Z= 0.371 Chirality : 0.047 0.188 1970 Planarity : 0.006 0.080 2327 Dihedral : 8.830 89.943 1858 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.42 % Favored : 87.52 % Rotamer: Outliers : 3.76 % Allowed : 12.49 % Favored : 83.75 % 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: -2.09 (0.19), residues: 1658 helix: 0.33 (0.17), residues: 794 sheet: -1.46 (0.66), residues: 60 loop : -3.35 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 113 TYR 0.012 0.001 TYR R 160 PHE 0.021 0.001 PHE P 104 TRP 0.020 0.001 TRP C 157 HIS 0.003 0.001 HIS P 68 Details of bonding type rmsd covalent geometry : bond 0.00373 (13509) covalent geometry : angle 0.77129 (18520) SS BOND : bond 0.00647 ( 2) SS BOND : angle 2.03404 ( 4) hydrogen bonds : bond 0.05021 ( 629) hydrogen bonds : angle 4.78078 ( 1812) metal coordination : bond 0.01355 ( 8) metal coordination : angle 9.66075 ( 6) Misc. bond : bond 0.18148 ( 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: 47 poor density : 345 time to evaluate : 0.341 Fit side-chains Corrupt residue: chain: C residue: PRO 24 >>> skipping revert: symmetry clash Corrupt residue: chain: P residue: PRO 24 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7544 (mm-30) REVERT: C 93 MET cc_start: 0.8642 (mmt) cc_final: 0.7849 (mmt) REVERT: D 80 ARG cc_start: 0.8523 (mtp-110) cc_final: 0.8259 (mtm-85) REVERT: D 96 MET cc_start: 0.8415 (mmt) cc_final: 0.8163 (mmt) REVERT: D 99 ASP cc_start: 0.8213 (t0) cc_final: 0.7954 (t70) REVERT: D 158 PHE cc_start: 0.8698 (t80) cc_final: 0.8043 (t80) REVERT: D 160 ILE cc_start: 0.8544 (mt) cc_final: 0.8319 (tp) REVERT: D 204 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.6632 (tm-30) REVERT: D 208 ASP cc_start: 0.8642 (m-30) cc_final: 0.7827 (m-30) REVERT: P 222 ASN cc_start: 0.8897 (t160) cc_final: 0.8466 (t0) REVERT: P 253 LEU cc_start: 0.9236 (mt) cc_final: 0.8996 (mp) REVERT: Q 80 ARG cc_start: 0.8565 (mtp-110) cc_final: 0.8354 (mtm-85) REVERT: Q 96 MET cc_start: 0.8473 (mmt) cc_final: 0.8209 (mmt) REVERT: Q 155 ASN cc_start: 0.9275 (t0) cc_final: 0.9018 (t0) REVERT: Q 158 PHE cc_start: 0.8882 (t80) cc_final: 0.8603 (t80) REVERT: Q 160 ILE cc_start: 0.8726 (mt) cc_final: 0.8427 (mt) REVERT: Q 183 MET cc_start: 0.8818 (ttp) cc_final: 0.8508 (ttp) REVERT: Q 204 GLN cc_start: 0.7470 (mm-40) cc_final: 0.6472 (tm-30) REVERT: Q 208 ASP cc_start: 0.8614 (m-30) cc_final: 0.7942 (m-30) REVERT: E 37 GLN cc_start: 0.8748 (pp30) cc_final: 0.8442 (pp30) REVERT: E 78 ASP cc_start: 0.8644 (t0) cc_final: 0.7915 (m-30) REVERT: E 103 LYS cc_start: 0.7554 (ptpp) cc_final: 0.7087 (ptpt) REVERT: R 37 GLN cc_start: 0.9032 (pp30) cc_final: 0.7955 (pp30) REVERT: R 88 VAL cc_start: 0.6997 (t) cc_final: 0.6714 (p) outliers start: 47 outliers final: 32 residues processed: 366 average time/residue: 0.1118 time to fit residues: 58.8635 Evaluate side-chains 296 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 263 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 272 ASN Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 218 THR Chi-restraints excluded: chain P residue 272 ASN Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain Q residue 94 ASP Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 100 ASN Chi-restraints excluded: chain R residue 187 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 145 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 177 GLN C 217 HIS P 99 ASN P 177 GLN R 36 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.132486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.102275 restraints weight = 22335.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.101441 restraints weight = 14288.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.102613 restraints weight = 11754.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.103100 restraints weight = 8845.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.103197 restraints weight = 8005.515| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.233 13529 Z= 0.168 Angle : 0.758 17.732 18530 Z= 0.349 Chirality : 0.046 0.180 1970 Planarity : 0.006 0.072 2327 Dihedral : 8.435 89.913 1858 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.98 % Favored : 88.90 % Rotamer: Outliers : 5.04 % Allowed : 13.13 % Favored : 81.83 % 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: -1.57 (0.20), residues: 1658 helix: 0.71 (0.17), residues: 838 sheet: -0.33 (0.73), residues: 56 loop : -3.31 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 193 TYR 0.015 0.001 TYR R 160 PHE 0.021 0.001 PHE P 363 TRP 0.028 0.001 TRP E 126 HIS 0.004 0.001 HIS C 111 Details of bonding type rmsd covalent geometry : bond 0.00397 (13509) covalent geometry : angle 0.73699 (18520) SS BOND : bond 0.00379 ( 2) SS BOND : angle 1.31500 ( 4) hydrogen bonds : bond 0.04939 ( 629) hydrogen bonds : angle 4.61056 ( 1812) metal coordination : bond 0.00941 ( 8) metal coordination : angle 9.88132 ( 6) Misc. bond : bond 0.13956 ( 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 342 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 279 time to evaluate : 0.453 Fit side-chains Corrupt residue: chain: C residue: PRO 24 >>> skipping revert: symmetry clash Corrupt residue: chain: P residue: PRO 24 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 LYS cc_start: 0.8646 (mttt) cc_final: 0.7270 (tttm) REVERT: C 177 GLN cc_start: 0.8060 (tt0) cc_final: 0.7846 (mt0) REVERT: C 253 LEU cc_start: 0.9366 (mt) cc_final: 0.9099 (mp) REVERT: D 103 MET cc_start: 0.8954 (mmm) cc_final: 0.8721 (tpt) REVERT: D 158 PHE cc_start: 0.8875 (t80) cc_final: 0.8392 (t80) REVERT: D 183 MET cc_start: 0.8840 (ttp) cc_final: 0.8577 (ttp) REVERT: D 204 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.6630 (tm-30) REVERT: D 208 ASP cc_start: 0.8623 (m-30) cc_final: 0.7894 (m-30) REVERT: D 226 GLN cc_start: 0.7759 (mt0) cc_final: 0.7469 (mp10) REVERT: P 253 LEU cc_start: 0.9353 (mt) cc_final: 0.9061 (mp) REVERT: Q 155 ASN cc_start: 0.9264 (t0) cc_final: 0.8892 (t0) REVERT: Q 158 PHE cc_start: 0.9133 (t80) cc_final: 0.8534 (t80) REVERT: Q 204 GLN cc_start: 0.7705 (mm-40) cc_final: 0.6793 (tm-30) REVERT: Q 208 ASP cc_start: 0.8546 (m-30) cc_final: 0.7902 (m-30) REVERT: Q 226 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7498 (mp10) REVERT: E 37 GLN cc_start: 0.8765 (pp30) cc_final: 0.8116 (pp30) REVERT: E 66 LYS cc_start: 0.8939 (tppt) cc_final: 0.8629 (tppt) REVERT: E 83 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8422 (tp30) REVERT: E 127 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8001 (tp) REVERT: R 37 GLN cc_start: 0.9240 (pp30) cc_final: 0.8428 (pp30) REVERT: R 66 LYS cc_start: 0.9049 (tppt) cc_final: 0.8622 (tppt) REVERT: R 88 VAL cc_start: 0.7297 (t) cc_final: 0.7034 (p) outliers start: 63 outliers final: 48 residues processed: 307 average time/residue: 0.1096 time to fit residues: 49.1127 Evaluate side-chains 308 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 257 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 272 ASN Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 167 CYS Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 169 ILE Chi-restraints excluded: chain P residue 196 SER Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 218 THR Chi-restraints excluded: chain P residue 267 VAL Chi-restraints excluded: chain P residue 272 ASN Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 94 ASP Chi-restraints excluded: chain Q residue 167 CYS Chi-restraints excluded: chain Q residue 226 GLN Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 70 LYS Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain R residue 16 TYR Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 188 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 144 optimal weight: 8.9990 chunk 27 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 217 HIS D 31 ASN R 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.130730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.100392 restraints weight = 22347.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.099795 restraints weight = 14131.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.100913 restraints weight = 11071.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.101217 restraints weight = 8912.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.101362 restraints weight = 8034.751| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.205 13529 Z= 0.153 Angle : 0.711 21.754 18530 Z= 0.332 Chirality : 0.045 0.178 1970 Planarity : 0.005 0.066 2327 Dihedral : 8.393 88.558 1858 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.43 % Favored : 89.45 % Rotamer: Outliers : 5.12 % Allowed : 15.93 % Favored : 78.94 % 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: -1.19 (0.20), residues: 1658 helix: 0.94 (0.17), residues: 836 sheet: -0.27 (0.76), residues: 56 loop : -2.98 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 86 TYR 0.012 0.001 TYR Q 153 PHE 0.016 0.002 PHE C 216 TRP 0.023 0.001 TRP E 126 HIS 0.004 0.001 HIS P 111 Details of bonding type rmsd covalent geometry : bond 0.00374 (13509) covalent geometry : angle 0.68448 (18520) SS BOND : bond 0.00412 ( 2) SS BOND : angle 1.44539 ( 4) hydrogen bonds : bond 0.04739 ( 629) hydrogen bonds : angle 4.51219 ( 1812) metal coordination : bond 0.01205 ( 8) metal coordination : angle 10.59625 ( 6) Misc. bond : bond 0.10771 ( 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 329 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 265 time to evaluate : 0.416 Fit side-chains Corrupt residue: chain: C residue: PRO 24 >>> skipping Corrupt residue: chain: P residue: PRO 24 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 253 LEU cc_start: 0.9345 (mt) cc_final: 0.9060 (mp) REVERT: D 96 MET cc_start: 0.8951 (mmt) cc_final: 0.8581 (mmm) REVERT: D 103 MET cc_start: 0.9048 (mmm) cc_final: 0.8812 (tpt) REVERT: D 158 PHE cc_start: 0.9033 (t80) cc_final: 0.8537 (t80) REVERT: D 191 GLN cc_start: 0.8395 (mm-40) cc_final: 0.8124 (tp40) REVERT: D 204 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.6553 (tm-30) REVERT: D 205 MET cc_start: 0.7873 (mtp) cc_final: 0.7622 (mtm) REVERT: D 208 ASP cc_start: 0.8650 (m-30) cc_final: 0.7984 (m-30) REVERT: D 226 GLN cc_start: 0.7726 (mt0) cc_final: 0.7468 (mt0) REVERT: Q 96 MET cc_start: 0.8876 (mmt) cc_final: 0.8527 (mmm) REVERT: Q 155 ASN cc_start: 0.9263 (t0) cc_final: 0.8967 (t0) REVERT: Q 204 GLN cc_start: 0.7917 (mm-40) cc_final: 0.6848 (tm-30) REVERT: Q 208 ASP cc_start: 0.8615 (m-30) cc_final: 0.7851 (m-30) REVERT: Q 226 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7435 (mp10) REVERT: E 12 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.5948 (mmt-90) REVERT: E 37 GLN cc_start: 0.8782 (pp30) cc_final: 0.8138 (pp30) REVERT: E 78 ASP cc_start: 0.8358 (t0) cc_final: 0.8088 (m-30) REVERT: R 37 GLN cc_start: 0.9212 (pp30) cc_final: 0.8408 (pp30) REVERT: R 45 LYS cc_start: 0.8967 (mmmm) cc_final: 0.8664 (mtpt) REVERT: R 88 VAL cc_start: 0.7520 (t) cc_final: 0.7209 (p) outliers start: 64 outliers final: 50 residues processed: 301 average time/residue: 0.1038 time to fit residues: 46.8474 Evaluate side-chains 289 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 236 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 272 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 167 CYS Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 169 ILE Chi-restraints excluded: chain P residue 196 SER Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 272 ASN Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain Q residue 94 ASP Chi-restraints excluded: chain Q residue 160 ILE Chi-restraints excluded: chain Q residue 188 VAL Chi-restraints excluded: chain Q residue 226 GLN Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 70 LYS Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 188 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 131 optimal weight: 6.9990 chunk 2 optimal weight: 0.4980 chunk 117 optimal weight: 0.0670 chunk 90 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 148 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 0.0770 chunk 20 optimal weight: 1.9990 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS C 177 GLN C 217 HIS Q 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.131915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.101351 restraints weight = 22355.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.101850 restraints weight = 14407.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.102669 restraints weight = 10800.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.102792 restraints weight = 8587.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.104270 restraints weight = 8244.260| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.5079 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= 0.130 Angle : 0.667 17.787 18530 Z= 0.319 Chirality : 0.044 0.169 1970 Planarity : 0.005 0.061 2327 Dihedral : 8.334 87.944 1858 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.10 % Favored : 88.78 % Rotamer: Outliers : 4.40 % Allowed : 17.77 % Favored : 77.82 % 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: -0.95 (0.21), residues: 1658 helix: 1.10 (0.18), residues: 836 sheet: -0.67 (0.75), residues: 60 loop : -2.77 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 193 TYR 0.013 0.001 TYR Q 153 PHE 0.015 0.001 PHE C 216 TRP 0.021 0.001 TRP E 126 HIS 0.003 0.001 HIS C 111 Details of bonding type rmsd covalent geometry : bond 0.00310 (13509) covalent geometry : angle 0.64576 (18520) SS BOND : bond 0.00465 ( 2) SS BOND : angle 1.36751 ( 4) hydrogen bonds : bond 0.04427 ( 629) hydrogen bonds : angle 4.36229 ( 1812) metal coordination : bond 0.01427 ( 8) metal coordination : angle 9.26543 ( 6) Misc. bond : bond 0.07817 ( 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 324 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 269 time to evaluate : 0.521 Fit side-chains Corrupt residue: chain: C residue: PRO 24 >>> skipping Corrupt residue: chain: P residue: PRO 24 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 222 ASN cc_start: 0.8650 (t0) cc_final: 0.8142 (t0) REVERT: D 96 MET cc_start: 0.8886 (mmt) cc_final: 0.8558 (mmm) REVERT: D 101 SER cc_start: 0.9159 (OUTLIER) cc_final: 0.8657 (p) REVERT: D 103 MET cc_start: 0.8914 (mmm) cc_final: 0.8705 (tpt) REVERT: D 158 PHE cc_start: 0.9049 (t80) cc_final: 0.8542 (t80) REVERT: D 191 GLN cc_start: 0.8342 (mm-40) cc_final: 0.8083 (tp40) REVERT: D 204 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.6688 (tm-30) REVERT: D 208 ASP cc_start: 0.8617 (m-30) cc_final: 0.7936 (m-30) REVERT: D 226 GLN cc_start: 0.7733 (mt0) cc_final: 0.7313 (mp10) REVERT: D 248 ARG cc_start: 0.7581 (ttp-170) cc_final: 0.7205 (ttp-170) REVERT: P 104 PHE cc_start: 0.8890 (t80) cc_final: 0.8654 (t80) REVERT: P 372 LEU cc_start: 0.8795 (tp) cc_final: 0.8563 (tt) REVERT: P 398 THR cc_start: 0.9146 (t) cc_final: 0.8942 (t) REVERT: Q 31 ASN cc_start: 0.8475 (t0) cc_final: 0.8117 (t0) REVERT: Q 96 MET cc_start: 0.8891 (mmt) cc_final: 0.8553 (mmm) REVERT: Q 155 ASN cc_start: 0.9124 (t0) cc_final: 0.8813 (t0) REVERT: Q 204 GLN cc_start: 0.7912 (mm-40) cc_final: 0.6948 (tm-30) REVERT: Q 208 ASP cc_start: 0.8605 (m-30) cc_final: 0.7921 (m-30) REVERT: Q 226 GLN cc_start: 0.7911 (mt0) cc_final: 0.7519 (mp10) REVERT: E 12 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.5950 (mmt-90) REVERT: E 66 LYS cc_start: 0.8475 (tppt) cc_final: 0.8137 (mmtm) REVERT: R 37 GLN cc_start: 0.9166 (pp30) cc_final: 0.8344 (pp30) REVERT: R 45 LYS cc_start: 0.8919 (mmmm) cc_final: 0.8581 (mtpt) REVERT: R 88 VAL cc_start: 0.7623 (t) cc_final: 0.7313 (p) outliers start: 55 outliers final: 39 residues processed: 303 average time/residue: 0.1028 time to fit residues: 46.3817 Evaluate side-chains 290 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 248 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 217 HIS Chi-restraints excluded: chain C residue 272 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 94 ASP Chi-restraints excluded: chain Q residue 160 ILE Chi-restraints excluded: chain Q residue 188 VAL Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 70 LYS Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 188 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 77 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 138 optimal weight: 9.9990 chunk 39 optimal weight: 0.5980 chunk 157 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.127236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.096420 restraints weight = 22078.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.096990 restraints weight = 14455.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.097759 restraints weight = 11074.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.097847 restraints weight = 9144.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.099248 restraints weight = 8644.494| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.5350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.217 13529 Z= 0.178 Angle : 0.739 19.325 18530 Z= 0.342 Chirality : 0.045 0.178 1970 Planarity : 0.005 0.058 2327 Dihedral : 8.421 89.452 1858 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.31 % Favored : 89.57 % Rotamer: Outliers : 5.28 % Allowed : 18.33 % Favored : 76.38 % 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: -0.90 (0.21), residues: 1658 helix: 1.12 (0.18), residues: 832 sheet: -1.04 (0.63), residues: 76 loop : -2.69 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 193 TYR 0.012 0.001 TYR Q 153 PHE 0.021 0.001 PHE C 216 TRP 0.024 0.001 TRP E 126 HIS 0.015 0.002 HIS C 217 Details of bonding type rmsd covalent geometry : bond 0.00441 (13509) covalent geometry : angle 0.71451 (18520) SS BOND : bond 0.00389 ( 2) SS BOND : angle 1.47162 ( 4) hydrogen bonds : bond 0.04868 ( 629) hydrogen bonds : angle 4.48923 ( 1812) metal coordination : bond 0.01132 ( 8) metal coordination : angle 10.42884 ( 6) Misc. bond : bond 0.11493 ( 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 333 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 265 time to evaluate : 0.464 Fit side-chains Corrupt residue: chain: C residue: PRO 24 >>> skipping Corrupt residue: chain: P residue: PRO 24 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 MET cc_start: 0.9470 (mmm) cc_final: 0.9258 (mmm) REVERT: D 96 MET cc_start: 0.8964 (mmt) cc_final: 0.8634 (mmm) REVERT: D 103 MET cc_start: 0.9157 (mmm) cc_final: 0.8804 (tpt) REVERT: D 191 GLN cc_start: 0.8389 (mm-40) cc_final: 0.8073 (tp40) REVERT: D 204 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.6824 (tm-30) REVERT: D 208 ASP cc_start: 0.8598 (m-30) cc_final: 0.7929 (m-30) REVERT: D 226 GLN cc_start: 0.7520 (mt0) cc_final: 0.7094 (mp10) REVERT: P 40 ASN cc_start: 0.8172 (t0) cc_final: 0.7580 (t0) REVERT: Q 96 MET cc_start: 0.8937 (mmt) cc_final: 0.8578 (mmm) REVERT: Q 155 ASN cc_start: 0.9206 (t0) cc_final: 0.8847 (t0) REVERT: Q 204 GLN cc_start: 0.7962 (mm-40) cc_final: 0.6925 (tm-30) REVERT: Q 208 ASP cc_start: 0.8636 (m-30) cc_final: 0.7919 (m-30) REVERT: Q 226 GLN cc_start: 0.7918 (mt0) cc_final: 0.7459 (mp10) REVERT: Q 241 MET cc_start: 0.8109 (tmm) cc_final: 0.7830 (tmm) REVERT: E 12 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.5987 (mmm-85) REVERT: E 37 GLN cc_start: 0.8864 (pp30) cc_final: 0.8621 (pp30) REVERT: E 66 LYS cc_start: 0.8573 (tppt) cc_final: 0.8290 (mmtm) REVERT: R 37 GLN cc_start: 0.9254 (pp30) cc_final: 0.8403 (pp30) REVERT: R 45 LYS cc_start: 0.8960 (mmmm) cc_final: 0.8646 (mtpt) REVERT: R 88 VAL cc_start: 0.7794 (t) cc_final: 0.7350 (p) REVERT: R 93 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7202 (mp) outliers start: 68 outliers final: 56 residues processed: 305 average time/residue: 0.1028 time to fit residues: 46.9666 Evaluate side-chains 313 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 254 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 PRO Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 272 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain P residue 24 PRO Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 169 ILE Chi-restraints excluded: chain P residue 196 SER Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 229 VAL Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 94 ASP Chi-restraints excluded: chain Q residue 188 VAL Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 70 LYS Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain R residue 16 TYR Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 110 ASP Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 187 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 161 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 0.0470 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 217 HIS ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.129217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.098472 restraints weight = 22200.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.099256 restraints weight = 14361.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.100076 restraints weight = 11478.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.100690 restraints weight = 8175.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.100790 restraints weight = 7398.524| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.5569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.149 13529 Z= 0.141 Angle : 0.696 18.413 18530 Z= 0.328 Chirality : 0.044 0.167 1970 Planarity : 0.005 0.055 2327 Dihedral : 8.370 89.815 1858 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.04 % Favored : 88.84 % Rotamer: Outliers : 4.80 % Allowed : 19.38 % Favored : 75.82 % 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: -0.72 (0.21), residues: 1658 helix: 1.23 (0.18), residues: 836 sheet: -1.19 (0.60), residues: 76 loop : -2.54 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 193 TYR 0.012 0.001 TYR D 153 PHE 0.017 0.001 PHE P 104 TRP 0.024 0.001 TRP E 126 HIS 0.005 0.001 HIS C 217 Details of bonding type rmsd covalent geometry : bond 0.00344 (13509) covalent geometry : angle 0.67206 (18520) SS BOND : bond 0.00368 ( 2) SS BOND : angle 1.23465 ( 4) hydrogen bonds : bond 0.04494 ( 629) hydrogen bonds : angle 4.35836 ( 1812) metal coordination : bond 0.00920 ( 8) metal coordination : angle 10.13897 ( 6) Misc. bond : bond 0.08048 ( 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 332 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 271 time to evaluate : 0.384 Fit side-chains Corrupt residue: chain: C residue: PRO 24 >>> skipping Corrupt residue: chain: P residue: PRO 24 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 MET cc_start: 0.9429 (mmm) cc_final: 0.9199 (mmm) REVERT: C 398 THR cc_start: 0.9191 (t) cc_final: 0.8963 (t) REVERT: D 96 MET cc_start: 0.8931 (mmt) cc_final: 0.8603 (mmm) REVERT: D 99 ASP cc_start: 0.8297 (t70) cc_final: 0.8077 (t0) REVERT: D 103 MET cc_start: 0.9142 (mmm) cc_final: 0.8557 (tpt) REVERT: D 191 GLN cc_start: 0.8270 (mm-40) cc_final: 0.7954 (tp40) REVERT: D 204 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.6809 (tm-30) REVERT: D 208 ASP cc_start: 0.8597 (m-30) cc_final: 0.7940 (m-30) REVERT: D 226 GLN cc_start: 0.7483 (mt0) cc_final: 0.7038 (mp10) REVERT: P 40 ASN cc_start: 0.8162 (t0) cc_final: 0.7587 (t0) REVERT: P 104 PHE cc_start: 0.8970 (t80) cc_final: 0.8501 (t80) REVERT: P 337 PHE cc_start: 0.7637 (m-10) cc_final: 0.7413 (m-10) REVERT: P 372 LEU cc_start: 0.8743 (tp) cc_final: 0.8499 (tt) REVERT: Q 96 MET cc_start: 0.8945 (mmt) cc_final: 0.8612 (mmm) REVERT: Q 155 ASN cc_start: 0.9110 (t0) cc_final: 0.8737 (t0) REVERT: Q 204 GLN cc_start: 0.7894 (mm-40) cc_final: 0.6800 (tm-30) REVERT: Q 208 ASP cc_start: 0.8642 (m-30) cc_final: 0.7866 (m-30) REVERT: Q 226 GLN cc_start: 0.7964 (mt0) cc_final: 0.7659 (mp10) REVERT: E 12 ARG cc_start: 0.7158 (OUTLIER) cc_final: 0.5851 (mmt-90) REVERT: E 45 LYS cc_start: 0.8819 (mmmm) cc_final: 0.8502 (ttpt) REVERT: E 66 LYS cc_start: 0.8540 (tppt) cc_final: 0.8227 (mmtm) REVERT: R 37 GLN cc_start: 0.9177 (pp30) cc_final: 0.8334 (pp30) REVERT: R 45 LYS cc_start: 0.8946 (mmmm) cc_final: 0.8644 (mtpt) REVERT: R 66 LYS cc_start: 0.8564 (tppt) cc_final: 0.8259 (mmtm) REVERT: R 88 VAL cc_start: 0.7832 (t) cc_final: 0.7525 (p) outliers start: 61 outliers final: 47 residues processed: 309 average time/residue: 0.0967 time to fit residues: 45.3322 Evaluate side-chains 300 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 251 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 272 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain P residue 24 PRO Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 169 ILE Chi-restraints excluded: chain P residue 196 SER Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 229 VAL Chi-restraints excluded: chain P residue 272 ASN Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 94 ASP Chi-restraints excluded: chain Q residue 188 VAL Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain R residue 16 TYR Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 187 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 62 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 ASN ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 72 HIS ** R 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.124946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.094719 restraints weight = 22360.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.095695 restraints weight = 15282.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.096420 restraints weight = 10836.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.096689 restraints weight = 8840.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.096841 restraints weight = 8789.182| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.5801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.262 13529 Z= 0.205 Angle : 0.768 20.823 18530 Z= 0.356 Chirality : 0.046 0.182 1970 Planarity : 0.005 0.055 2327 Dihedral : 8.540 88.576 1858 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.04 % Favored : 88.84 % Rotamer: Outliers : 4.88 % Allowed : 20.02 % Favored : 75.10 % 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: -0.83 (0.21), residues: 1658 helix: 1.12 (0.17), residues: 836 sheet: -1.23 (0.59), residues: 76 loop : -2.56 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 193 TYR 0.011 0.001 TYR C 199 PHE 0.019 0.002 PHE P 104 TRP 0.024 0.001 TRP E 126 HIS 0.005 0.001 HIS C 212 Details of bonding type rmsd covalent geometry : bond 0.00509 (13509) covalent geometry : angle 0.74048 (18520) SS BOND : bond 0.00452 ( 2) SS BOND : angle 1.51320 ( 4) hydrogen bonds : bond 0.05083 ( 629) hydrogen bonds : angle 4.58118 ( 1812) metal coordination : bond 0.01154 ( 8) metal coordination : angle 11.33097 ( 6) Misc. bond : bond 0.13074 ( 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 320 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 257 time to evaluate : 0.410 Fit side-chains Corrupt residue: chain: C residue: PRO 24 >>> skipping Corrupt residue: chain: P residue: PRO 24 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 96 MET cc_start: 0.8964 (mmt) cc_final: 0.8677 (mmm) REVERT: D 99 ASP cc_start: 0.8325 (t70) cc_final: 0.8108 (t0) REVERT: D 103 MET cc_start: 0.9276 (mmm) cc_final: 0.8656 (tpt) REVERT: D 204 GLN cc_start: 0.7910 (mm-40) cc_final: 0.6596 (tm-30) REVERT: D 208 ASP cc_start: 0.8576 (m-30) cc_final: 0.7881 (m-30) REVERT: D 226 GLN cc_start: 0.7516 (mt0) cc_final: 0.7095 (mt0) REVERT: P 104 PHE cc_start: 0.8881 (t80) cc_final: 0.8666 (t80) REVERT: P 383 MET cc_start: 0.8380 (mmm) cc_final: 0.8033 (mmm) REVERT: Q 96 MET cc_start: 0.8984 (mmt) cc_final: 0.8698 (mmm) REVERT: Q 99 ASP cc_start: 0.8063 (t0) cc_final: 0.7463 (m-30) REVERT: Q 155 ASN cc_start: 0.9186 (t0) cc_final: 0.8827 (t0) REVERT: Q 204 GLN cc_start: 0.7759 (mm-40) cc_final: 0.7023 (tm-30) REVERT: Q 226 GLN cc_start: 0.7943 (mt0) cc_final: 0.7625 (mp10) REVERT: E 12 ARG cc_start: 0.7068 (OUTLIER) cc_final: 0.5854 (mmt-90) REVERT: E 66 LYS cc_start: 0.8355 (tppt) cc_final: 0.8127 (mmtm) REVERT: R 37 GLN cc_start: 0.9239 (pp30) cc_final: 0.8401 (pp30) REVERT: R 45 LYS cc_start: 0.8948 (mmmm) cc_final: 0.8608 (mtpt) REVERT: R 66 LYS cc_start: 0.8692 (tppt) cc_final: 0.8368 (mmtm) REVERT: R 93 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.7069 (mp) outliers start: 63 outliers final: 54 residues processed: 296 average time/residue: 0.0987 time to fit residues: 44.3955 Evaluate side-chains 300 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 244 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 PRO Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 272 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain P residue 24 PRO Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 169 ILE Chi-restraints excluded: chain P residue 177 GLN Chi-restraints excluded: chain P residue 196 SER Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 267 VAL Chi-restraints excluded: chain P residue 272 ASN Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 94 ASP Chi-restraints excluded: chain Q residue 188 VAL Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain R residue 16 TYR Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 188 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 72 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 162 optimal weight: 8.9990 chunk 157 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 chunk 142 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 159 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.127041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.098021 restraints weight = 22477.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.096969 restraints weight = 16014.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.097893 restraints weight = 12849.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.098335 restraints weight = 10173.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.098485 restraints weight = 8974.004| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.5933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.225 13529 Z= 0.152 Angle : 0.732 18.955 18530 Z= 0.338 Chirality : 0.044 0.168 1970 Planarity : 0.005 0.053 2327 Dihedral : 8.456 89.888 1858 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.10 % Favored : 88.78 % Rotamer: Outliers : 3.76 % Allowed : 20.66 % Favored : 75.58 % 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: -0.72 (0.21), residues: 1658 helix: 1.15 (0.18), residues: 836 sheet: -1.34 (0.58), residues: 76 loop : -2.41 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 193 TYR 0.012 0.001 TYR D 153 PHE 0.017 0.001 PHE P 104 TRP 0.024 0.001 TRP E 126 HIS 0.005 0.001 HIS P 111 Details of bonding type rmsd covalent geometry : bond 0.00372 (13509) covalent geometry : angle 0.70141 (18520) SS BOND : bond 0.00212 ( 2) SS BOND : angle 1.18612 ( 4) hydrogen bonds : bond 0.04705 ( 629) hydrogen bonds : angle 4.43810 ( 1812) metal coordination : bond 0.01160 ( 8) metal coordination : angle 11.68053 ( 6) Misc. bond : bond 0.10700 ( 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 307 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 259 time to evaluate : 0.409 Fit side-chains Corrupt residue: chain: C residue: PRO 24 >>> skipping Corrupt residue: chain: P residue: PRO 24 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 407 ILE cc_start: 0.9191 (mm) cc_final: 0.8954 (mp) REVERT: D 96 MET cc_start: 0.8995 (mmt) cc_final: 0.8699 (mmm) REVERT: D 99 ASP cc_start: 0.8386 (t70) cc_final: 0.8139 (t0) REVERT: D 103 MET cc_start: 0.9225 (mmm) cc_final: 0.8600 (tpt) REVERT: D 204 GLN cc_start: 0.7926 (mm-40) cc_final: 0.6747 (tm-30) REVERT: D 208 ASP cc_start: 0.8592 (m-30) cc_final: 0.7906 (m-30) REVERT: D 226 GLN cc_start: 0.7501 (mt0) cc_final: 0.7056 (mp10) REVERT: P 104 PHE cc_start: 0.8964 (OUTLIER) cc_final: 0.8568 (t80) REVERT: P 372 LEU cc_start: 0.8775 (tp) cc_final: 0.8535 (tt) REVERT: P 383 MET cc_start: 0.8437 (mmm) cc_final: 0.8136 (mmm) REVERT: Q 96 MET cc_start: 0.8937 (mmt) cc_final: 0.8624 (mmm) REVERT: Q 99 ASP cc_start: 0.8070 (t0) cc_final: 0.7430 (m-30) REVERT: Q 155 ASN cc_start: 0.9119 (t0) cc_final: 0.8746 (t0) REVERT: Q 182 ARG cc_start: 0.7668 (ttm-80) cc_final: 0.7211 (ttm-80) REVERT: Q 204 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7155 (tm-30) REVERT: Q 226 GLN cc_start: 0.7932 (mt0) cc_final: 0.7591 (mp10) REVERT: E 12 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.5658 (mmt-90) REVERT: E 66 LYS cc_start: 0.8316 (tppt) cc_final: 0.8102 (mmtm) REVERT: R 37 GLN cc_start: 0.9169 (pp30) cc_final: 0.8317 (pp30) REVERT: R 45 LYS cc_start: 0.8929 (mmmm) cc_final: 0.8548 (mtpt) REVERT: R 47 MET cc_start: 0.8466 (mmt) cc_final: 0.8205 (mmm) REVERT: R 66 LYS cc_start: 0.8651 (tppt) cc_final: 0.8344 (mmtm) outliers start: 48 outliers final: 41 residues processed: 290 average time/residue: 0.0988 time to fit residues: 43.1700 Evaluate side-chains 293 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 250 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 272 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain P residue 24 PRO Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 104 PHE Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 169 ILE Chi-restraints excluded: chain P residue 196 SER Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 272 ASN Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain Q residue 188 VAL Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain R residue 16 TYR Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 188 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 112 optimal weight: 0.0170 chunk 117 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 135 optimal weight: 0.9990 chunk 146 optimal weight: 0.0270 chunk 149 optimal weight: 0.9990 chunk 31 optimal weight: 0.0020 overall best weight: 0.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.130250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.100379 restraints weight = 22325.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.101013 restraints weight = 14435.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.101651 restraints weight = 11968.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.102384 restraints weight = 8763.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.102373 restraints weight = 7815.966| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.6085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.182 13529 Z= 0.129 Angle : 0.705 17.646 18530 Z= 0.328 Chirality : 0.043 0.167 1970 Planarity : 0.005 0.054 2327 Dihedral : 8.297 87.620 1858 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.68 % Favored : 89.20 % Rotamer: Outliers : 2.64 % Allowed : 22.18 % Favored : 75.18 % 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: -0.55 (0.21), residues: 1658 helix: 1.28 (0.18), residues: 836 sheet: -1.35 (0.60), residues: 76 loop : -2.30 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 193 TYR 0.013 0.001 TYR D 153 PHE 0.015 0.001 PHE P 104 TRP 0.027 0.001 TRP E 126 HIS 0.004 0.001 HIS P 111 Details of bonding type rmsd covalent geometry : bond 0.00308 (13509) covalent geometry : angle 0.67622 (18520) SS BOND : bond 0.00198 ( 2) SS BOND : angle 0.87680 ( 4) hydrogen bonds : bond 0.04316 ( 629) hydrogen bonds : angle 4.27492 ( 1812) metal coordination : bond 0.00943 ( 8) metal coordination : angle 11.16288 ( 6) Misc. bond : bond 0.07733 ( 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 314 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 280 time to evaluate : 0.467 Fit side-chains Corrupt residue: chain: C residue: PRO 24 >>> skipping Corrupt residue: chain: P residue: PRO 24 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 MET cc_start: 0.9271 (mmm) cc_final: 0.8878 (mmm) REVERT: C 383 MET cc_start: 0.8473 (mmm) cc_final: 0.8174 (mmm) REVERT: D 96 MET cc_start: 0.8944 (mmt) cc_final: 0.8675 (mmm) REVERT: D 99 ASP cc_start: 0.8412 (t70) cc_final: 0.8166 (t0) REVERT: D 103 MET cc_start: 0.9189 (mmm) cc_final: 0.8562 (tpt) REVERT: D 204 GLN cc_start: 0.7907 (mm-40) cc_final: 0.6690 (tm-30) REVERT: D 208 ASP cc_start: 0.8580 (m-30) cc_final: 0.7944 (m-30) REVERT: D 226 GLN cc_start: 0.7539 (mt0) cc_final: 0.7123 (mp10) REVERT: P 104 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.8547 (t80) REVERT: P 372 LEU cc_start: 0.8776 (tp) cc_final: 0.8525 (tt) REVERT: Q 96 MET cc_start: 0.8935 (mmt) cc_final: 0.8612 (mmm) REVERT: Q 155 ASN cc_start: 0.9089 (t0) cc_final: 0.8678 (t0) REVERT: Q 182 ARG cc_start: 0.7617 (ttm-80) cc_final: 0.7276 (ttm-80) REVERT: Q 204 GLN cc_start: 0.7899 (mm-40) cc_final: 0.6774 (tm-30) REVERT: Q 208 ASP cc_start: 0.8602 (m-30) cc_final: 0.8069 (m-30) REVERT: Q 226 GLN cc_start: 0.7940 (mt0) cc_final: 0.7616 (mp10) REVERT: E 12 ARG cc_start: 0.6914 (OUTLIER) cc_final: 0.5708 (mmt-90) REVERT: E 37 GLN cc_start: 0.8864 (pp30) cc_final: 0.7810 (pp30) REVERT: E 39 ASN cc_start: 0.8597 (m-40) cc_final: 0.8180 (m-40) REVERT: E 66 LYS cc_start: 0.8257 (tppt) cc_final: 0.8009 (mmtm) REVERT: E 89 PRO cc_start: 0.7892 (Cg_endo) cc_final: 0.7498 (Cg_exo) REVERT: R 37 GLN cc_start: 0.9115 (pp30) cc_final: 0.8266 (pp30) REVERT: R 45 LYS cc_start: 0.8806 (mmmm) cc_final: 0.8486 (mtpt) REVERT: R 47 MET cc_start: 0.8354 (mmt) cc_final: 0.8106 (mmm) REVERT: R 59 VAL cc_start: 0.5642 (m) cc_final: 0.5029 (m) REVERT: R 66 LYS cc_start: 0.8514 (tppt) cc_final: 0.8212 (mmtm) REVERT: R 189 LYS cc_start: 0.8584 (tttt) cc_final: 0.8313 (tttm) outliers start: 34 outliers final: 28 residues processed: 295 average time/residue: 0.0995 time to fit residues: 43.5304 Evaluate side-chains 300 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 270 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 272 ASN Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain P residue 24 PRO Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 104 PHE Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 196 SER Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 272 ASN Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain R residue 16 TYR Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 187 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 135 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 146 optimal weight: 0.0010 chunk 78 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 68 optimal weight: 0.3980 chunk 110 optimal weight: 0.2980 chunk 108 optimal weight: 0.5980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.130397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.100530 restraints weight = 22186.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.101206 restraints weight = 14476.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.101873 restraints weight = 12094.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.102688 restraints weight = 8665.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.102713 restraints weight = 7566.444| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.6195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.182 13529 Z= 0.135 Angle : 0.734 18.274 18530 Z= 0.341 Chirality : 0.044 0.164 1970 Planarity : 0.005 0.052 2327 Dihedral : 8.316 89.522 1858 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.25 % Favored : 89.63 % Rotamer: Outliers : 3.12 % Allowed : 22.66 % Favored : 74.22 % 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: -0.54 (0.21), residues: 1658 helix: 1.22 (0.18), residues: 846 sheet: -1.50 (0.60), residues: 76 loop : -2.24 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 193 TYR 0.020 0.001 TYR C 399 PHE 0.022 0.001 PHE R 73 TRP 0.030 0.001 TRP E 126 HIS 0.004 0.001 HIS Q 38 Details of bonding type rmsd covalent geometry : bond 0.00328 (13509) covalent geometry : angle 0.70554 (18520) SS BOND : bond 0.00196 ( 2) SS BOND : angle 0.85260 ( 4) hydrogen bonds : bond 0.04406 ( 629) hydrogen bonds : angle 4.26104 ( 1812) metal coordination : bond 0.00907 ( 8) metal coordination : angle 11.20802 ( 6) Misc. bond : bond 0.07619 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2084.24 seconds wall clock time: 36 minutes 34.13 seconds (2194.13 seconds total)