Starting phenix.real_space_refine on Wed Mar 4 11:12:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xkv_22226/03_2026/6xkv_22226.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xkv_22226/03_2026/6xkv_22226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xkv_22226/03_2026/6xkv_22226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xkv_22226/03_2026/6xkv_22226.map" model { file = "/net/cci-nas-00/data/ceres_data/6xkv_22226/03_2026/6xkv_22226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xkv_22226/03_2026/6xkv_22226.cif" } resolution = 3.5 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 14 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 31.625 67.838 38.027 0.25105.87 S ATOM 11162 SG CYS E 153 30.491 64.409 37.476 0.25107.21 S ATOM 12381 SG CYS R 133 82.719 27.940 38.570 0.25105.87 S ATOM 12527 SG CYS R 153 83.841 31.371 38.015 0.25107.21 S Residues with excluded nonbonded symmetry interactions: 52 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 40 not shown) Time building chain proxies: 3.14, per 1000 atoms: 0.24 Number of scatterers: 13079 At special positions: 0 Unit cell: (115.6, 96.56, 107.44, 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: 1.16 Conformation dependent library (CDL) restraints added in 587.5 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 135 " pdb="FE2 FES R 501 " - pdb=" ND1 HIS R 156 " pdb="FE1 FES R 501 " - pdb=" SG CYS R 133 " pdb="FE1 FES R 501 " - pdb=" SG CYS R 153 " Number of angles added : 6 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3056 Finding SS restraints... Secondary structure from input PDB file: 61 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: 3.764A pdb=" N GLY C 27 " --> pdb=" O LEU C 23 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE C 33 " --> pdb=" O VAL C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 66 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 90 through 118 removed outlier: 3.757A pdb=" N SER C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 148 removed outlier: 3.860A pdb=" N TRP C 129 " --> pdb=" O ARG C 125 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL C 148 " --> pdb=" O PHE C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 169 removed outlier: 3.623A 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: 3.541A pdb=" N GLY C 167 " --> pdb=" O THR C 163 " (cutoff:3.500A) removed outlier: 4.001A 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: 3.959A 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: 5.577A 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 164 through 168 Processing helix chain 'D' and resid 201 through 218 Processing helix chain 'D' and resid 220 through 250 Processing helix chain 'P' and resid 14 through 19 Processing helix chain 'P' and resid 23 through 33 removed outlier: 3.762A pdb=" N GLY P 27 " --> pdb=" O LEU P 23 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE P 33 " --> pdb=" O VAL P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 66 Processing helix chain 'P' and resid 75 through 86 Processing helix chain 'P' and resid 90 through 118 removed outlier: 3.754A pdb=" N SER P 102 " --> pdb=" O ALA P 98 " (cutoff:3.500A) Processing helix chain 'P' and resid 125 through 148 removed outlier: 3.859A 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: 3.542A 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: 3.669A pdb=" N ILE P 176 " --> pdb=" O ILE P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 187 through 199 Processing helix chain 'P' and resid 200 through 219 removed outlier: 3.957A pdb=" N VAL P 204 " --> pdb=" O LEU P 200 " (cutoff:3.500A) removed outlier: 3.586A 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: 3.847A pdb=" N MET P 343 " --> pdb=" O ALA P 339 " (cutoff:3.500A) Processing helix chain 'P' and resid 347 through 349 No H-bonds generated for 'chain 'P' and resid 347 through 349' Processing helix chain 'P' and resid 356 through 359 Processing helix chain 'P' and resid 360 through 381 Processing helix chain 'P' and resid 388 through 415 removed outlier: 5.576A pdb=" N LEU P 408 " --> pdb=" O PHE P 404 " (cutoff:3.500A) Proline residue: P 409 - end of helix Processing helix chain 'Q' and resid 19 through 33 removed outlier: 3.628A 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: 3.590A pdb=" N ALA Q 49 " --> pdb=" O ARG Q 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 44 through 49' Processing helix chain 'Q' and resid 57 through 67 Processing helix chain 'Q' and resid 127 through 136 Processing helix chain 'Q' and resid 201 through 218 Processing helix chain 'Q' and resid 220 through 250 Processing helix chain 'E' and resid 12 through 37 Proline residue: E 33 - end of helix Processing helix chain 'E' and resid 41 through 46 removed outlier: 3.563A pdb=" N ALA E 46 " --> pdb=" O ALA E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 87 Processing helix chain 'E' and resid 109 through 114 Processing helix chain 'R' and resid 12 through 37 Proline residue: R 33 - end of helix Processing helix chain 'R' and resid 41 through 46 removed outlier: 3.563A pdb=" N ALA R 46 " --> pdb=" O ALA R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 87 Processing helix chain 'R' and resid 109 through 114 Processing 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: 3.606A 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: 4.682A 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: 3.691A pdb=" N TRP E 151 " --> pdb=" O TYR E 160 " (cutoff:3.500A) removed outlier: 3.631A 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: 7.225A pdb=" N GLY R 150 " --> pdb=" O ASP R 143 " (cutoff:3.500A) removed outlier: 3.689A 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) 631 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: 1.95 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.41: 5786 1.41 - 1.61: 7561 1.61 - 1.80: 99 1.80 - 2.00: 35 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 1.19e+02 bond pdb=" C2D HEC C 501 " pdb=" C3D HEC C 501 " ideal model delta sigma weight residual 1.544 1.336 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" CAB HEC C 501 " pdb=" CBB HEC C 501 " ideal model delta sigma weight residual 1.544 1.336 0.208 2.00e-02 2.50e+03 1.08e+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 ... (remaining 13504 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 18183 3.16 - 6.32: 288 6.32 - 9.48: 28 9.48 - 12.63: 4 12.63 - 15.79: 17 Bond angle restraints: 18520 Sorted by residual: angle pdb="FE1 FES R 501 " pdb=" S2 FES R 501 " pdb="FE2 FES R 501 " ideal model delta sigma weight residual 75.66 89.12 -13.46 1.14e+00 7.69e-01 1.39e+02 angle pdb="FE1 FES E 501 " pdb=" S2 FES E 501 " pdb="FE2 FES E 501 " ideal model delta sigma weight residual 75.66 89.10 -13.44 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 90.93 13.40 1.14e+00 7.69e-01 1.38e+02 angle pdb=" S1 FES R 501 " pdb="FE1 FES R 501 " pdb=" S2 FES R 501 " ideal model delta sigma weight residual 104.33 90.79 13.54 1.20e+00 6.94e-01 1.27e+02 ... (remaining 18515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 6978 17.90 - 35.80: 536 35.80 - 53.69: 79 53.69 - 71.59: 10 71.59 - 89.49: 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 -17.15 77.15 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: 1911 0.146 - 0.292: 46 0.292 - 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 1.33e+01 chirality pdb=" CB THR Q 198 " pdb=" CA THR Q 198 " pdb=" OG1 THR Q 198 " pdb=" CG2 THR Q 198 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.53 2.00e-01 2.50e+01 6.91e+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 " -0.110 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 " -0.009 2.00e-02 2.50e+03 4.11e-02 3.79e+01 pdb=" C2C HEC D 501 " 0.109 2.00e-02 2.50e+03 pdb=" C3C HEC D 501 " -0.042 2.00e-02 2.50e+03 pdb=" C4C HEC D 501 " -0.007 2.00e-02 2.50e+03 pdb=" CAC HEC D 501 " -0.007 2.00e-02 2.50e+03 pdb=" CHC HEC D 501 " -0.018 2.00e-02 2.50e+03 pdb=" CHD HEC D 501 " 0.007 2.00e-02 2.50e+03 pdb=" CMC HEC D 501 " -0.031 2.00e-02 2.50e+03 pdb=" NC HEC D 501 " -0.002 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 4.28e-02 1.83e+01 pdb=" C ASN C 222 " 0.074 2.00e-02 2.50e+03 pdb=" O ASN C 222 " -0.028 2.00e-02 2.50e+03 pdb=" N ASN C 223 " -0.025 2.00e-02 2.50e+03 ... (remaining 2324 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 156 2.57 - 3.15: 11758 3.15 - 3.73: 19507 3.73 - 4.32: 27392 4.32 - 4.90: 45655 Nonbonded interactions: 104468 Sorted by model distance: nonbonded pdb=" O THR R 186 " pdb=" OG1 THR R 187 " model vdw 1.987 3.040 nonbonded pdb=" O THR E 186 " pdb=" OG1 THR E 187 " model vdw 1.987 3.040 nonbonded pdb=" OG SER P 120 " pdb=" ND2 ASN P 222 " model vdw 1.988 3.120 nonbonded pdb=" NH2 ARG C 306 " pdb=" O MET C 383 " model vdw 2.006 3.120 nonbonded pdb=" NH2 ARG P 306 " pdb=" O MET P 383 " model vdw 2.007 3.120 ... (remaining 104463 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'P' } ncs_group { reference = (chain 'D' and (resid 5 through 80 or (resid 81 and (name N or name CA or name C \ or name O or name CB )) or resid 82 or (resid 83 and (name N or name CA or name \ C or name O or name CB )) or resid 84 through 501)) selection = chain 'Q' } ncs_group { reference = chain 'E' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.25 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.680 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 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= 0.474 Angle : 1.049 23.239 18530 Z= 0.637 Chirality : 0.070 0.731 1970 Planarity : 0.007 0.082 2327 Dihedral : 13.755 89.490 4563 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 23.04 Ramachandran Plot: Outliers : 0.42 % Allowed : 16.41 % Favored : 83.17 % Rotamer: Outliers : 0.08 % Allowed : 3.04 % Favored : 96.88 % 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: -4.31 (0.17), residues: 1658 helix: -1.65 (0.16), residues: 784 sheet: -3.39 (0.48), residues: 64 loop : -4.22 (0.18), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 75 TYR 0.010 0.001 TYR C 297 PHE 0.021 0.001 PHE P 104 TRP 0.012 0.001 TRP C 296 HIS 0.010 0.001 HIS C 111 Details of bonding type rmsd covalent geometry : bond 0.00945 (13509) covalent geometry : angle 1.01798 (18520) SS BOND : bond 0.00172 ( 2) SS BOND : angle 0.56970 ( 4) hydrogen bonds : bond 0.14451 ( 631) hydrogen bonds : angle 6.99308 ( 1812) metal coordination : bond 0.01145 ( 8) metal coordination : angle 14.22020 ( 6) Misc. bond : bond 0.14979 ( 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 292 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 291 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 231 ARG cc_start: 0.8472 (ptp-170) cc_final: 0.8217 (ptp-170) REVERT: C 351 THR cc_start: 0.8113 (p) cc_final: 0.7535 (p) REVERT: D 14 ILE cc_start: 0.8784 (mp) cc_final: 0.8576 (mt) REVERT: D 165 ASP cc_start: 0.6750 (m-30) cc_final: 0.6382 (m-30) REVERT: D 196 ASP cc_start: 0.8044 (p0) cc_final: 0.7762 (p0) REVERT: P 222 ASN cc_start: 0.7704 (t0) cc_final: 0.7277 (t0) REVERT: P 334 ILE cc_start: 0.8882 (mt) cc_final: 0.8667 (mt) REVERT: Q 14 ILE cc_start: 0.8568 (mp) cc_final: 0.8362 (mt) REVERT: E 13 ASP cc_start: 0.5978 (p0) cc_final: 0.5733 (m-30) REVERT: E 94 ARG cc_start: 0.6015 (ttm-80) cc_final: 0.5513 (mpt180) REVERT: E 118 PHE cc_start: 0.5907 (m-80) cc_final: 0.5506 (m-80) REVERT: E 119 ASP cc_start: 0.5752 (t0) cc_final: 0.4517 (m-30) REVERT: E 165 ARG cc_start: 0.5899 (mtm-85) cc_final: 0.5617 (mtm-85) REVERT: R 139 VAL cc_start: 0.6400 (t) cc_final: 0.5291 (t) REVERT: R 158 SER cc_start: 0.1845 (m) cc_final: 0.1610 (m) REVERT: R 161 ASP cc_start: 0.6263 (p0) cc_final: 0.6008 (p0) outliers start: 1 outliers final: 1 residues processed: 292 average time/residue: 0.1267 time to fit residues: 52.4106 Evaluate side-chains 185 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.0770 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.4980 chunk 149 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 HIS C 153 GLN C 222 ASN D 20 GLN D 159 GLN D 177 HIS P 68 HIS P 153 GLN P 222 ASN E 17 HIS E 100 ASN R 17 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.165932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.133179 restraints weight = 17286.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.131951 restraints weight = 19071.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.132447 restraints weight = 16258.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.132957 restraints weight = 12686.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.133031 restraints weight = 11567.375| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3461 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.263 13529 Z= 0.157 Angle : 0.738 10.969 18530 Z= 0.356 Chirality : 0.046 0.192 1970 Planarity : 0.006 0.077 2327 Dihedral : 8.635 87.793 1861 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.16 % Favored : 88.66 % Rotamer: Outliers : 2.24 % Allowed : 10.49 % Favored : 87.27 % 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: -2.27 (0.19), residues: 1658 helix: 0.23 (0.17), residues: 814 sheet: -2.03 (0.60), residues: 64 loop : -3.55 (0.18), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 167 TYR 0.024 0.001 TYR C 199 PHE 0.022 0.001 PHE P 113 TRP 0.017 0.001 TRP P 157 HIS 0.003 0.001 HIS P 217 Details of bonding type rmsd covalent geometry : bond 0.00354 (13509) covalent geometry : angle 0.72559 (18520) SS BOND : bond 0.00052 ( 2) SS BOND : angle 0.44035 ( 4) hydrogen bonds : bond 0.05057 ( 631) hydrogen bonds : angle 4.74793 ( 1812) metal coordination : bond 0.01255 ( 8) metal coordination : angle 7.55693 ( 6) Misc. bond : bond 0.14697 ( 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 246 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 218 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 252 ASP cc_start: 0.7470 (m-30) cc_final: 0.7270 (m-30) REVERT: D 14 ILE cc_start: 0.8811 (mp) cc_final: 0.8609 (mt) REVERT: D 218 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7981 (tp30) REVERT: P 349 LEU cc_start: 0.8571 (mt) cc_final: 0.8305 (mp) REVERT: Q 79 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7283 (mm-30) REVERT: Q 87 MET cc_start: 0.8853 (mtt) cc_final: 0.8280 (mtt) REVERT: Q 218 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7959 (tp30) REVERT: E 94 ARG cc_start: 0.6230 (ttm-80) cc_final: 0.5801 (mpt180) REVERT: E 119 ASP cc_start: 0.6043 (t0) cc_final: 0.4649 (m-30) REVERT: R 53 ASP cc_start: 0.5505 (t70) cc_final: 0.5086 (m-30) outliers start: 28 outliers final: 15 residues processed: 235 average time/residue: 0.1146 time to fit residues: 38.8581 Evaluate side-chains 195 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 179 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 145 optimal weight: 10.0000 chunk 70 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 144 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 0.0970 chunk 36 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 153 optimal weight: 4.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 HIS C 99 ASN D 20 GLN P 99 ASN R 36 ASN R 100 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.153453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.119105 restraints weight = 17501.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.118222 restraints weight = 19821.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.119683 restraints weight = 16587.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.119376 restraints weight = 13598.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.119649 restraints weight = 12206.975| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3255 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.198 13529 Z= 0.145 Angle : 0.684 13.257 18530 Z= 0.327 Chirality : 0.045 0.184 1970 Planarity : 0.005 0.064 2327 Dihedral : 8.366 85.469 1858 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.16 % Favored : 88.72 % Rotamer: Outliers : 2.96 % Allowed : 13.13 % Favored : 83.91 % 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: -1.40 (0.20), residues: 1658 helix: 0.89 (0.18), residues: 818 sheet: -1.37 (0.65), residues: 68 loop : -3.10 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 77 TYR 0.016 0.001 TYR D 153 PHE 0.024 0.001 PHE C 104 TRP 0.013 0.001 TRP C 157 HIS 0.005 0.001 HIS P 212 Details of bonding type rmsd covalent geometry : bond 0.00334 (13509) covalent geometry : angle 0.67570 (18520) SS BOND : bond 0.00213 ( 2) SS BOND : angle 0.40922 ( 4) hydrogen bonds : bond 0.04848 ( 631) hydrogen bonds : angle 4.55344 ( 1812) metal coordination : bond 0.00993 ( 8) metal coordination : angle 6.06847 ( 6) Misc. bond : bond 0.11727 ( 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 240 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 252 ASP cc_start: 0.7647 (m-30) cc_final: 0.7356 (m-30) REVERT: D 50 ASP cc_start: 0.8088 (m-30) cc_final: 0.7518 (m-30) REVERT: D 159 GLN cc_start: 0.8415 (mm-40) cc_final: 0.8185 (mm110) REVERT: D 160 ILE cc_start: 0.8953 (mm) cc_final: 0.8715 (mm) REVERT: D 183 MET cc_start: 0.8638 (ttp) cc_final: 0.8322 (ttm) REVERT: Q 50 ASP cc_start: 0.8027 (m-30) cc_final: 0.7607 (m-30) REVERT: Q 78 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7409 (mt-10) REVERT: Q 79 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7383 (mm-30) REVERT: Q 87 MET cc_start: 0.8979 (mtt) cc_final: 0.8526 (mtt) REVERT: Q 227 MET cc_start: 0.8181 (ttp) cc_final: 0.7980 (tmm) REVERT: E 94 ARG cc_start: 0.6417 (ttm-80) cc_final: 0.5837 (mpt180) REVERT: E 113 ARG cc_start: 0.5700 (tpt170) cc_final: 0.5291 (tmt-80) REVERT: R 36 ASN cc_start: 0.8627 (t0) cc_final: 0.7925 (t0) REVERT: R 113 ARG cc_start: 0.6498 (tpt90) cc_final: 0.6243 (tpt170) outliers start: 37 outliers final: 22 residues processed: 231 average time/residue: 0.1134 time to fit residues: 37.7790 Evaluate side-chains 196 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 167 CYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 334 ILE Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 84 GLU Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain R residue 128 VAL 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: 1.9990 chunk 23 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 221 ASN R 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.149847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.113954 restraints weight = 17655.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.113833 restraints weight = 20021.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.114681 restraints weight = 15774.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.114801 restraints weight = 12423.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.114929 restraints weight = 11215.936| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.183 13529 Z= 0.159 Angle : 0.683 11.459 18530 Z= 0.328 Chirality : 0.045 0.188 1970 Planarity : 0.005 0.060 2327 Dihedral : 8.313 88.860 1858 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.16 % Favored : 88.72 % Rotamer: Outliers : 3.28 % Allowed : 14.81 % Favored : 81.91 % 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: -1.08 (0.21), residues: 1658 helix: 1.15 (0.18), residues: 812 sheet: -1.22 (0.65), residues: 68 loop : -2.90 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 193 TYR 0.017 0.001 TYR D 153 PHE 0.017 0.002 PHE P 113 TRP 0.011 0.001 TRP R 67 HIS 0.005 0.001 HIS P 212 Details of bonding type rmsd covalent geometry : bond 0.00381 (13509) covalent geometry : angle 0.67275 (18520) SS BOND : bond 0.00231 ( 2) SS BOND : angle 0.48522 ( 4) hydrogen bonds : bond 0.04936 ( 631) hydrogen bonds : angle 4.48057 ( 1812) metal coordination : bond 0.00915 ( 8) metal coordination : angle 6.44730 ( 6) Misc. bond : bond 0.10948 ( 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 247 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 206 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: C 93 MET cc_start: 0.8420 (mmp) cc_final: 0.8194 (mmt) REVERT: C 193 ARG cc_start: 0.8370 (mtt90) cc_final: 0.8038 (mtt90) REVERT: C 252 ASP cc_start: 0.7813 (m-30) cc_final: 0.7444 (m-30) REVERT: D 50 ASP cc_start: 0.8240 (m-30) cc_final: 0.7816 (m-30) REVERT: D 159 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8254 (mm110) REVERT: D 165 ASP cc_start: 0.7155 (m-30) cc_final: 0.6925 (m-30) REVERT: D 248 ARG cc_start: 0.8469 (ttm170) cc_final: 0.7139 (ttt180) REVERT: P 193 ARG cc_start: 0.8414 (mtt90) cc_final: 0.8070 (mtt90) REVERT: Q 50 ASP cc_start: 0.8138 (m-30) cc_final: 0.7757 (m-30) REVERT: Q 78 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7370 (mt-10) REVERT: Q 79 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7441 (mm-30) REVERT: Q 87 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8576 (mtt) REVERT: Q 208 ASP cc_start: 0.8040 (m-30) cc_final: 0.7779 (m-30) REVERT: Q 218 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8092 (tp30) REVERT: Q 227 MET cc_start: 0.8326 (ttp) cc_final: 0.8051 (tmm) REVERT: Q 248 ARG cc_start: 0.8439 (ttm170) cc_final: 0.7182 (ttt180) REVERT: E 94 ARG cc_start: 0.6549 (ttm-80) cc_final: 0.6293 (mpt180) REVERT: E 113 ARG cc_start: 0.5803 (tpt170) cc_final: 0.5380 (tmt-80) REVERT: R 38 MET cc_start: 0.8562 (mtm) cc_final: 0.8305 (mtp) outliers start: 41 outliers final: 25 residues processed: 234 average time/residue: 0.1222 time to fit residues: 40.4017 Evaluate side-chains 216 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 167 CYS Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain P residue 165 LEU Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain P residue 334 ILE Chi-restraints excluded: chain P residue 351 THR Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 87 MET Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 167 CYS Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain R residue 43 ASP Chi-restraints excluded: chain R residue 128 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 131 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 148 optimal weight: 0.1980 chunk 35 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 16 optimal weight: 0.0060 chunk 43 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 ASN C 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.151139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.115102 restraints weight = 17711.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.116561 restraints weight = 18033.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.116999 restraints weight = 14121.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.116913 restraints weight = 12061.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.117044 restraints weight = 9713.156| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 13529 Z= 0.125 Angle : 0.644 10.257 18530 Z= 0.311 Chirality : 0.043 0.176 1970 Planarity : 0.005 0.058 2327 Dihedral : 8.178 88.966 1858 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.98 % Favored : 88.90 % Rotamer: Outliers : 2.56 % Allowed : 16.57 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.21), residues: 1658 helix: 1.39 (0.18), residues: 814 sheet: -1.09 (0.65), residues: 68 loop : -2.65 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 193 TYR 0.015 0.001 TYR D 153 PHE 0.017 0.001 PHE P 216 TRP 0.010 0.001 TRP C 400 HIS 0.004 0.001 HIS P 212 Details of bonding type rmsd covalent geometry : bond 0.00286 (13509) covalent geometry : angle 0.63515 (18520) SS BOND : bond 0.00150 ( 2) SS BOND : angle 0.31210 ( 4) hydrogen bonds : bond 0.04471 ( 631) hydrogen bonds : angle 4.33074 ( 1812) metal coordination : bond 0.00606 ( 8) metal coordination : angle 5.85056 ( 6) Misc. bond : bond 0.09722 ( 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 232 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: C 193 ARG cc_start: 0.8217 (mtt90) cc_final: 0.7981 (mtt90) REVERT: C 252 ASP cc_start: 0.7917 (m-30) cc_final: 0.7536 (m-30) REVERT: D 50 ASP cc_start: 0.8118 (m-30) cc_final: 0.7643 (m-30) REVERT: D 183 MET cc_start: 0.8362 (ttp) cc_final: 0.8085 (ttm) REVERT: D 248 ARG cc_start: 0.8489 (ttm170) cc_final: 0.7200 (ttt180) REVERT: P 193 ARG cc_start: 0.8240 (mtt90) cc_final: 0.7967 (mtt90) REVERT: P 231 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7959 (mtt-85) REVERT: Q 78 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7453 (mt-10) REVERT: Q 79 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7415 (mm-30) REVERT: Q 87 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8508 (mtt) REVERT: Q 183 MET cc_start: 0.8488 (ttp) cc_final: 0.7964 (ttm) REVERT: Q 208 ASP cc_start: 0.8036 (m-30) cc_final: 0.7789 (m-30) REVERT: Q 227 MET cc_start: 0.8232 (ttp) cc_final: 0.8015 (tmm) REVERT: Q 248 ARG cc_start: 0.8420 (ttm170) cc_final: 0.7175 (ttt180) REVERT: E 68 ARG cc_start: 0.7422 (ttt180) cc_final: 0.7176 (ttt180) REVERT: E 94 ARG cc_start: 0.6647 (ttm-80) cc_final: 0.6325 (mpt180) REVERT: E 113 ARG cc_start: 0.5831 (tpt170) cc_final: 0.5522 (tmt-80) REVERT: E 173 ARG cc_start: 0.7615 (mpp80) cc_final: 0.7259 (mtm180) REVERT: R 36 ASN cc_start: 0.8802 (t0) cc_final: 0.8076 (t0) REVERT: R 38 MET cc_start: 0.8542 (mtm) cc_final: 0.8302 (mtp) REVERT: R 148 PHE cc_start: 0.6946 (m-80) cc_final: 0.6741 (m-80) outliers start: 32 outliers final: 20 residues processed: 223 average time/residue: 0.1167 time to fit residues: 37.2268 Evaluate side-chains 205 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 167 CYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain P residue 231 ARG Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 84 GLU Chi-restraints excluded: chain Q residue 87 MET Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain R residue 43 ASP Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 158 SER 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: 0.9990 chunk 2 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 28 optimal weight: 0.0170 chunk 107 optimal weight: 3.9990 chunk 93 optimal weight: 0.3980 chunk 119 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 72 HIS P 222 ASN E 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.149645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.113722 restraints weight = 17636.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.115236 restraints weight = 18404.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.115486 restraints weight = 14117.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.115359 restraints weight = 12196.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.115482 restraints weight = 9872.363| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.158 13529 Z= 0.137 Angle : 0.660 14.421 18530 Z= 0.315 Chirality : 0.043 0.183 1970 Planarity : 0.005 0.059 2327 Dihedral : 8.152 88.194 1858 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.55 % Favored : 89.32 % Rotamer: Outliers : 2.48 % Allowed : 18.09 % Favored : 79.42 % 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: -0.61 (0.21), residues: 1658 helix: 1.45 (0.18), residues: 814 sheet: -0.14 (0.76), residues: 50 loop : -2.59 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 193 TYR 0.015 0.001 TYR D 153 PHE 0.018 0.001 PHE P 216 TRP 0.009 0.001 TRP P 400 HIS 0.005 0.001 HIS P 212 Details of bonding type rmsd covalent geometry : bond 0.00328 (13509) covalent geometry : angle 0.65110 (18520) SS BOND : bond 0.00206 ( 2) SS BOND : angle 0.49758 ( 4) hydrogen bonds : bond 0.04589 ( 631) hydrogen bonds : angle 4.31476 ( 1812) metal coordination : bond 0.00766 ( 8) metal coordination : angle 5.89986 ( 6) Misc. bond : bond 0.09304 ( 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 218 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: C 193 ARG cc_start: 0.8233 (mtt90) cc_final: 0.7991 (mtt90) REVERT: C 252 ASP cc_start: 0.8035 (m-30) cc_final: 0.7660 (m-30) REVERT: D 50 ASP cc_start: 0.8188 (m-30) cc_final: 0.7726 (m-30) REVERT: D 55 GLN cc_start: 0.8409 (mp10) cc_final: 0.8186 (mp10) REVERT: D 79 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: D 183 MET cc_start: 0.8540 (ttp) cc_final: 0.7958 (ttm) REVERT: D 248 ARG cc_start: 0.8506 (ttm170) cc_final: 0.7244 (ttt180) REVERT: P 193 ARG cc_start: 0.8264 (mtt90) cc_final: 0.7976 (mtt90) REVERT: P 231 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7968 (mtt-85) REVERT: Q 78 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7432 (mt-10) REVERT: Q 87 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8335 (mtt) REVERT: Q 183 MET cc_start: 0.8596 (ttp) cc_final: 0.8122 (ttm) REVERT: Q 208 ASP cc_start: 0.8097 (m-30) cc_final: 0.7821 (m-30) REVERT: Q 227 MET cc_start: 0.8274 (ttp) cc_final: 0.8016 (tmm) REVERT: Q 248 ARG cc_start: 0.8391 (ttm170) cc_final: 0.7797 (ttt180) REVERT: E 94 ARG cc_start: 0.6654 (ttm-80) cc_final: 0.5946 (mpt180) REVERT: E 173 ARG cc_start: 0.7545 (mpp80) cc_final: 0.7142 (mtm180) REVERT: R 36 ASN cc_start: 0.8857 (t0) cc_final: 0.8122 (t0) REVERT: R 38 MET cc_start: 0.8605 (mtm) cc_final: 0.8355 (mtp) outliers start: 31 outliers final: 22 residues processed: 211 average time/residue: 0.1207 time to fit residues: 36.8440 Evaluate side-chains 205 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 167 CYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain P residue 231 ARG Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 84 GLU Chi-restraints excluded: chain Q residue 87 MET Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 167 CYS Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain R residue 43 ASP Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 158 SER 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: 0.9980 chunk 165 optimal weight: 7.9990 chunk 117 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 57 optimal weight: 5.9990 chunk 147 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.149179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.112953 restraints weight = 17774.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.113182 restraints weight = 19325.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.113527 restraints weight = 15450.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.113717 restraints weight = 14025.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.114034 restraints weight = 11422.867| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.153 13529 Z= 0.144 Angle : 0.665 14.922 18530 Z= 0.320 Chirality : 0.043 0.180 1970 Planarity : 0.005 0.064 2327 Dihedral : 8.123 84.019 1858 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.80 % Favored : 89.08 % Rotamer: Outliers : 2.56 % Allowed : 18.09 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.21), residues: 1658 helix: 1.39 (0.18), residues: 818 sheet: -0.60 (0.65), residues: 70 loop : -2.56 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 12 TYR 0.015 0.001 TYR D 153 PHE 0.022 0.001 PHE P 104 TRP 0.009 0.001 TRP P 400 HIS 0.005 0.001 HIS C 212 Details of bonding type rmsd covalent geometry : bond 0.00349 (13509) covalent geometry : angle 0.65660 (18520) SS BOND : bond 0.00293 ( 2) SS BOND : angle 0.64730 ( 4) hydrogen bonds : bond 0.04705 ( 631) hydrogen bonds : angle 4.36523 ( 1812) metal coordination : bond 0.00789 ( 8) metal coordination : angle 5.86755 ( 6) Misc. bond : bond 0.08966 ( 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 215 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 0.549 Fit side-chains revert: symmetry clash REVERT: C 193 ARG cc_start: 0.8247 (mtt90) cc_final: 0.8026 (mtt90) REVERT: C 252 ASP cc_start: 0.8067 (m-30) cc_final: 0.7684 (m-30) REVERT: D 50 ASP cc_start: 0.8149 (m-30) cc_final: 0.7724 (m-30) REVERT: D 55 GLN cc_start: 0.8396 (mp10) cc_final: 0.8195 (mp10) REVERT: D 79 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7478 (mp0) REVERT: D 183 MET cc_start: 0.8543 (ttp) cc_final: 0.8145 (ttm) REVERT: D 248 ARG cc_start: 0.8446 (ttm170) cc_final: 0.7553 (ttt180) REVERT: P 193 ARG cc_start: 0.8321 (mtt90) cc_final: 0.8052 (mtt90) REVERT: P 231 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7893 (mtt-85) REVERT: Q 79 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7445 (mm-30) REVERT: Q 87 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8344 (mtt) REVERT: Q 183 MET cc_start: 0.8608 (ttp) cc_final: 0.8149 (ttm) REVERT: Q 208 ASP cc_start: 0.8091 (m-30) cc_final: 0.7832 (m-30) REVERT: Q 227 MET cc_start: 0.8305 (ttp) cc_final: 0.7960 (tmm) REVERT: Q 247 LYS cc_start: 0.8700 (tttp) cc_final: 0.8409 (tttm) REVERT: E 47 MET cc_start: 0.2969 (tmm) cc_final: 0.2756 (tmm) REVERT: E 152 PHE cc_start: 0.7199 (t80) cc_final: 0.6509 (t80) REVERT: E 173 ARG cc_start: 0.7500 (mpp80) cc_final: 0.7163 (mtm180) REVERT: R 36 ASN cc_start: 0.8842 (t0) cc_final: 0.8069 (t0) REVERT: R 38 MET cc_start: 0.8587 (mtm) cc_final: 0.8342 (mtp) outliers start: 32 outliers final: 23 residues processed: 207 average time/residue: 0.1243 time to fit residues: 36.8121 Evaluate side-chains 201 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 167 CYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain P residue 231 ARG Chi-restraints excluded: chain P residue 334 ILE Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 84 GLU Chi-restraints excluded: chain Q residue 87 MET Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 167 CYS Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain R residue 43 ASP Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 158 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 62 optimal weight: 0.6980 chunk 68 optimal weight: 0.0980 chunk 30 optimal weight: 4.9990 chunk 162 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 143 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.147711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.111160 restraints weight = 17656.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.111673 restraints weight = 19965.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.111930 restraints weight = 15290.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.112096 restraints weight = 14525.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.112611 restraints weight = 11534.788| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.160 13529 Z= 0.140 Angle : 0.658 14.036 18530 Z= 0.318 Chirality : 0.043 0.182 1970 Planarity : 0.005 0.058 2327 Dihedral : 8.040 82.355 1858 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.43 % Favored : 89.45 % Rotamer: Outliers : 2.32 % Allowed : 19.14 % Favored : 78.54 % 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: -0.53 (0.21), residues: 1658 helix: 1.47 (0.18), residues: 818 sheet: -0.41 (0.65), residues: 70 loop : -2.54 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 76 TYR 0.015 0.001 TYR D 153 PHE 0.020 0.001 PHE P 104 TRP 0.010 0.001 TRP R 67 HIS 0.005 0.001 HIS P 212 Details of bonding type rmsd covalent geometry : bond 0.00339 (13509) covalent geometry : angle 0.64989 (18520) SS BOND : bond 0.00280 ( 2) SS BOND : angle 0.46136 ( 4) hydrogen bonds : bond 0.04617 ( 631) hydrogen bonds : angle 4.34668 ( 1812) metal coordination : bond 0.00638 ( 8) metal coordination : angle 5.92097 ( 6) Misc. bond : bond 0.09025 ( 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 208 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: C 93 MET cc_start: 0.8346 (mmp) cc_final: 0.8081 (mmt) REVERT: C 193 ARG cc_start: 0.8216 (mtt90) cc_final: 0.8015 (mtt90) REVERT: C 252 ASP cc_start: 0.7991 (m-30) cc_final: 0.7603 (m-30) REVERT: D 50 ASP cc_start: 0.8150 (m-30) cc_final: 0.7714 (m-30) REVERT: D 55 GLN cc_start: 0.8368 (mp10) cc_final: 0.8134 (mp10) REVERT: D 87 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8657 (mmm) REVERT: D 140 GLU cc_start: 0.7959 (mp0) cc_final: 0.7640 (mp0) REVERT: D 183 MET cc_start: 0.8591 (ttp) cc_final: 0.8216 (ttm) REVERT: D 248 ARG cc_start: 0.8410 (ttm170) cc_final: 0.7605 (ttt180) REVERT: Q 87 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8326 (mtt) REVERT: Q 140 GLU cc_start: 0.7926 (mp0) cc_final: 0.7708 (mp0) REVERT: Q 183 MET cc_start: 0.8598 (ttp) cc_final: 0.8123 (ttm) REVERT: Q 208 ASP cc_start: 0.8047 (m-30) cc_final: 0.7796 (m-30) REVERT: Q 227 MET cc_start: 0.8300 (ttp) cc_final: 0.7984 (tmm) REVERT: E 47 MET cc_start: 0.3485 (tmm) cc_final: 0.3220 (tmm) REVERT: E 94 ARG cc_start: 0.6500 (ttt180) cc_final: 0.6251 (ttt180) REVERT: E 173 ARG cc_start: 0.7452 (mpp80) cc_final: 0.7118 (mtm180) REVERT: R 36 ASN cc_start: 0.8866 (t0) cc_final: 0.8108 (t0) REVERT: R 43 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.8254 (t70) outliers start: 29 outliers final: 20 residues processed: 202 average time/residue: 0.1293 time to fit residues: 37.3398 Evaluate side-chains 196 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain P residue 231 ARG Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 84 GLU Chi-restraints excluded: chain Q residue 87 MET Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 167 CYS Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain R residue 43 ASP Chi-restraints excluded: chain R residue 128 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 72 optimal weight: 0.0010 chunk 119 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 1 optimal weight: 0.0470 chunk 162 optimal weight: 8.9990 chunk 157 optimal weight: 7.9990 chunk 14 optimal weight: 0.0470 chunk 97 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 112 optimal weight: 0.0670 chunk 142 optimal weight: 5.9990 overall best weight: 0.1520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.152213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.117001 restraints weight = 17764.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.116889 restraints weight = 21461.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.118233 restraints weight = 16483.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.118097 restraints weight = 13511.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.118170 restraints weight = 12746.637| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.122 13529 Z= 0.117 Angle : 0.630 14.868 18530 Z= 0.304 Chirality : 0.042 0.166 1970 Planarity : 0.005 0.057 2327 Dihedral : 7.860 78.628 1858 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.07 % Favored : 89.81 % Rotamer: Outliers : 1.92 % Allowed : 19.38 % Favored : 78.70 % 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: -0.18 (0.21), residues: 1658 helix: 1.83 (0.18), residues: 802 sheet: 0.68 (0.76), residues: 52 loop : -2.39 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 193 TYR 0.014 0.001 TYR D 153 PHE 0.019 0.001 PHE E 152 TRP 0.014 0.001 TRP P 296 HIS 0.003 0.001 HIS P 212 Details of bonding type rmsd covalent geometry : bond 0.00263 (13509) covalent geometry : angle 0.62641 (18520) SS BOND : bond 0.00112 ( 2) SS BOND : angle 0.45303 ( 4) hydrogen bonds : bond 0.04037 ( 631) hydrogen bonds : angle 4.17256 ( 1812) metal coordination : bond 0.00616 ( 8) metal coordination : angle 3.98375 ( 6) Misc. bond : bond 0.07750 ( 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 226 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 0.496 Fit side-chains REVERT: C 93 MET cc_start: 0.8223 (mmp) cc_final: 0.7976 (mmt) REVERT: C 180 LEU cc_start: 0.9364 (tp) cc_final: 0.9041 (mt) REVERT: C 252 ASP cc_start: 0.7834 (m-30) cc_final: 0.7438 (m-30) REVERT: D 50 ASP cc_start: 0.8056 (m-30) cc_final: 0.7601 (m-30) REVERT: D 78 GLU cc_start: 0.7431 (tm-30) cc_final: 0.7176 (mp0) REVERT: D 87 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8575 (mmm) REVERT: D 140 GLU cc_start: 0.7947 (mp0) cc_final: 0.7644 (mp0) REVERT: D 159 GLN cc_start: 0.8496 (mm110) cc_final: 0.8237 (mm-40) REVERT: D 183 MET cc_start: 0.8334 (ttp) cc_final: 0.7986 (ttm) REVERT: D 227 MET cc_start: 0.8117 (ttp) cc_final: 0.7811 (tmm) REVERT: D 232 MET cc_start: 0.8068 (mmp) cc_final: 0.7808 (mmm) REVERT: D 248 ARG cc_start: 0.8340 (ttm170) cc_final: 0.7576 (ttt180) REVERT: P 231 ARG cc_start: 0.8455 (ptp-170) cc_final: 0.7907 (mtt-85) REVERT: Q 78 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7501 (mt-10) REVERT: Q 87 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8323 (mtt) REVERT: Q 140 GLU cc_start: 0.8023 (mp0) cc_final: 0.7779 (mp0) REVERT: Q 183 MET cc_start: 0.8444 (ttp) cc_final: 0.8054 (ttm) REVERT: Q 208 ASP cc_start: 0.8090 (m-30) cc_final: 0.7828 (m-30) REVERT: Q 227 MET cc_start: 0.8168 (ttp) cc_final: 0.7842 (tmm) REVERT: E 70 LYS cc_start: 0.8337 (mtmt) cc_final: 0.8133 (mttp) REVERT: E 94 ARG cc_start: 0.6400 (ttt180) cc_final: 0.5580 (ttm170) REVERT: E 173 ARG cc_start: 0.7404 (mpp80) cc_final: 0.7134 (mtm180) REVERT: R 36 ASN cc_start: 0.8839 (t0) cc_final: 0.8136 (t0) REVERT: R 43 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.8163 (t70) outliers start: 24 outliers final: 15 residues processed: 217 average time/residue: 0.1219 time to fit residues: 38.1355 Evaluate side-chains 199 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 87 MET Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain R residue 43 ASP Chi-restraints excluded: chain R residue 128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 112 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 107 optimal weight: 0.1980 chunk 92 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 135 optimal weight: 0.9980 chunk 146 optimal weight: 0.6980 chunk 149 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 36 ASN E 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.147567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.111858 restraints weight = 17832.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.111245 restraints weight = 25437.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.112784 restraints weight = 17470.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.112633 restraints weight = 13333.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.112806 restraints weight = 13308.229| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.5115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.133 13529 Z= 0.143 Angle : 0.665 13.043 18530 Z= 0.318 Chirality : 0.043 0.180 1970 Planarity : 0.005 0.056 2327 Dihedral : 7.918 81.056 1858 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.55 % Favored : 89.32 % Rotamer: Outliers : 1.60 % Allowed : 19.70 % Favored : 78.70 % 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: -0.17 (0.21), residues: 1658 helix: 1.87 (0.18), residues: 796 sheet: -0.42 (0.60), residues: 82 loop : -2.37 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 193 TYR 0.015 0.001 TYR D 153 PHE 0.028 0.001 PHE E 152 TRP 0.015 0.001 TRP P 179 HIS 0.005 0.001 HIS P 212 Details of bonding type rmsd covalent geometry : bond 0.00352 (13509) covalent geometry : angle 0.65944 (18520) SS BOND : bond 0.00237 ( 2) SS BOND : angle 0.41790 ( 4) hydrogen bonds : bond 0.04513 ( 631) hydrogen bonds : angle 4.25657 ( 1812) metal coordination : bond 0.00558 ( 8) metal coordination : angle 4.90982 ( 6) Misc. bond : bond 0.07396 ( 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 202 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 0.536 Fit side-chains REVERT: C 252 ASP cc_start: 0.7836 (m-30) cc_final: 0.7426 (m-30) REVERT: C 351 THR cc_start: 0.8601 (p) cc_final: 0.8321 (t) REVERT: D 50 ASP cc_start: 0.8158 (m-30) cc_final: 0.7723 (m-30) REVERT: D 78 GLU cc_start: 0.7460 (tm-30) cc_final: 0.7193 (mp0) REVERT: D 87 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8656 (mmm) REVERT: D 140 GLU cc_start: 0.7918 (mp0) cc_final: 0.7624 (mp0) REVERT: D 159 GLN cc_start: 0.8516 (mm110) cc_final: 0.8227 (mm-40) REVERT: D 248 ARG cc_start: 0.8359 (ttm170) cc_final: 0.7611 (ttt180) REVERT: P 166 PHE cc_start: 0.8874 (m-80) cc_final: 0.8600 (m-80) REVERT: P 187 ASP cc_start: 0.8107 (t0) cc_final: 0.7820 (t0) REVERT: Q 87 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8340 (mtt) REVERT: Q 140 GLU cc_start: 0.7992 (mp0) cc_final: 0.7770 (mp0) REVERT: Q 208 ASP cc_start: 0.8053 (m-30) cc_final: 0.7801 (m-30) REVERT: Q 227 MET cc_start: 0.8313 (ttp) cc_final: 0.7971 (tmm) REVERT: E 94 ARG cc_start: 0.6444 (ttt180) cc_final: 0.5853 (ttt180) REVERT: E 173 ARG cc_start: 0.7481 (mpp80) cc_final: 0.7263 (mtm180) REVERT: R 36 ASN cc_start: 0.8870 (t0) cc_final: 0.8120 (t0) outliers start: 20 outliers final: 15 residues processed: 197 average time/residue: 0.1220 time to fit residues: 34.5070 Evaluate side-chains 187 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain P residue 351 THR Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 87 MET Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain R residue 128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 135 optimal weight: 0.2980 chunk 113 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 68 optimal weight: 0.0170 chunk 110 optimal weight: 0.0870 chunk 108 optimal weight: 0.9980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 36 ASN E 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.147718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.111688 restraints weight = 17731.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.111189 restraints weight = 19994.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.111877 restraints weight = 17269.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.111962 restraints weight = 15186.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.112303 restraints weight = 12484.141| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.5120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.156 13529 Z= 0.186 Angle : 0.889 59.200 18530 Z= 0.486 Chirality : 0.043 0.389 1970 Planarity : 0.005 0.056 2327 Dihedral : 7.916 80.904 1858 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.62 % Favored : 89.20 % Rotamer: Outliers : 1.68 % Allowed : 19.70 % Favored : 78.62 % 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: -0.20 (0.21), residues: 1658 helix: 1.79 (0.18), residues: 804 sheet: -0.42 (0.60), residues: 82 loop : -2.37 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 68 TYR 0.014 0.001 TYR D 153 PHE 0.021 0.001 PHE E 152 TRP 0.013 0.001 TRP P 179 HIS 0.004 0.001 HIS P 212 Details of bonding type rmsd covalent geometry : bond 0.00399 (13509) covalent geometry : angle 0.88500 (18520) SS BOND : bond 0.00233 ( 2) SS BOND : angle 0.42396 ( 4) hydrogen bonds : bond 0.04495 ( 631) hydrogen bonds : angle 4.25862 ( 1812) metal coordination : bond 0.00540 ( 8) metal coordination : angle 4.90743 ( 6) Misc. bond : bond 0.08171 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2019.09 seconds wall clock time: 35 minutes 37.30 seconds (2137.30 seconds total)