Starting phenix.real_space_refine on Wed Mar 4 11:11:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xi0_22189/03_2026/6xi0_22189.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xi0_22189/03_2026/6xi0_22189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xi0_22189/03_2026/6xi0_22189.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xi0_22189/03_2026/6xi0_22189.map" model { file = "/net/cci-nas-00/data/ceres_data/6xi0_22189/03_2026/6xi0_22189.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xi0_22189/03_2026/6xi0_22189.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 10 7.16 5 S 78 5.16 5 C 8578 2.51 5 N 2155 2.21 5 O 2258 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13079 Number of models: 1 Model: "" Number of chains: 12 Chain: "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: "C" Number of atoms: 3244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3244 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 393} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'HIS:plan': 3, 'ASP:plan': 6, 'TYR:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1, 'TRP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 90 Chain: "D" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1801 Classifications: {'peptide': 235} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "P" Number of atoms: 3244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3244 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 393} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 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: "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: "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: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} 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 933 SG CYS E 133 30.849 65.240 37.564 0.25105.87 S ATOM 1079 SG CYS E 153 29.828 61.763 37.104 0.25107.21 S ATOM 12381 SG CYS R 133 83.431 27.174 37.574 0.25105.87 S ATOM 12527 SG CYS R 153 84.451 30.652 37.124 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: 2.70, per 1000 atoms: 0.21 Number of scatterers: 13079 At special positions: 0 Unit cell: (115.6, 93.84, 106.08, 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: 1.12 Conformation dependent library (CDL) restraints added in 542.9 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 133 " pdb="FE1 FES E 501 " - pdb=" SG CYS E 153 " pdb=" FES R 501 " pdb="FE2 FES R 501 " - pdb=" ND1 HIS R 156 " pdb="FE2 FES R 501 " - pdb=" ND1 HIS R 135 " pdb="FE1 FES R 501 " - pdb=" SG CYS R 133 " pdb="FE1 FES R 501 " - pdb=" SG CYS R 153 " Number of angles added : 6 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3056 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 8 sheets defined 51.5% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'E' and resid 11 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 '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: 3.756A 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: 4.002A pdb=" N ILE C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 182 removed outlier: 3.668A pdb=" N ILE C 176 " --> pdb=" O ILE C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 199 Processing helix chain 'C' and resid 200 through 219 removed outlier: 3.960A pdb=" N VAL C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE C 216 " --> pdb=" O HIS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 270 Processing helix chain 'C' and resid 276 through 281 Processing helix chain 'C' and resid 298 through 308 removed outlier: 4.405A pdb=" N PHE C 308 " --> pdb=" O ILE C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 321 Processing helix chain 'C' and resid 327 through 346 removed outlier: 3.848A pdb=" N MET C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 356 through 359 Processing helix chain 'C' and resid 360 through 381 Processing helix chain 'C' and resid 388 through 415 removed outlier: 5.576A pdb=" N LEU C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Proline residue: C 409 - end of helix Processing helix chain 'D' and resid 19 through 33 removed outlier: 3.629A pdb=" N LEU D 23 " --> pdb=" O ASP D 19 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU D 32 " --> pdb=" O GLN D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 37 Processing helix chain 'D' and resid 44 through 49 Processing helix chain 'D' and resid 57 through 67 Processing helix chain 'D' and resid 127 through 136 Processing helix chain 'D' and resid 201 through 218 Processing helix chain 'D' and resid 220 through 250 Processing helix chain 'P' and resid 14 through 19 Processing helix chain 'P' and resid 23 through 33 removed outlier: 3.763A pdb=" N GLY P 27 " --> pdb=" O LEU P 23 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE P 33 " --> pdb=" O VAL P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 66 Processing helix chain 'P' and resid 75 through 86 Processing helix chain 'P' and resid 90 through 118 removed outlier: 3.754A pdb=" N SER P 102 " --> pdb=" O ALA P 98 " (cutoff:3.500A) Processing helix chain 'P' and resid 125 through 148 removed outlier: 3.860A pdb=" N TRP P 129 " --> pdb=" O ARG P 125 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL P 148 " --> pdb=" O PHE P 144 " (cutoff:3.500A) Processing helix chain 'P' and resid 153 through 169 removed outlier: 3.623A pdb=" N TRP P 157 " --> pdb=" O GLN P 153 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N PHE P 166 " --> pdb=" O ILE P 162 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY P 167 " --> pdb=" O THR P 163 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE P 169 " --> pdb=" O LEU P 165 " (cutoff:3.500A) Processing helix chain 'P' and resid 172 through 182 removed outlier: 3.668A pdb=" N ILE P 176 " --> pdb=" O ILE P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 187 through 199 Processing helix chain 'P' and resid 200 through 219 removed outlier: 3.957A pdb=" N VAL P 204 " --> pdb=" O LEU P 200 " (cutoff:3.500A) removed outlier: 3.586A 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: 5.575A pdb=" N LEU P 408 " --> pdb=" O PHE P 404 " (cutoff:3.500A) Proline residue: P 409 - end of helix Processing helix chain 'Q' and resid 19 through 33 removed outlier: 3.628A 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 '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 'E' and resid 50 through 52 removed outlier: 3.607A pdb=" N ALA E 181 " --> pdb=" O LYS E 189 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 64 through 67 Processing sheet with id=AA3, first strand: chain 'E' and resid 141 through 145 removed outlier: 4.683A pdb=" N ASP E 143 " --> pdb=" O GLY E 150 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLY E 150 " --> pdb=" O ASP E 143 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TRP E 151 " --> pdb=" O TYR E 160 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER E 158 " --> pdb=" O CYS E 153 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 153 through 155 Processing sheet with id=AA5, first strand: chain 'Q' and resid 153 through 155 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: 3.631A pdb=" N SER R 158 " --> pdb=" O CYS R 153 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1815 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: 2.14 Time building geometry restraints manager: 1.35 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: 103 1.80 - 2.00: 31 2.00 - 2.20: 28 Bond restraints: 13509 Sorted by residual: bond pdb=" CAC HEC C 501 " pdb=" CBC HEC C 501 " ideal model delta sigma weight residual 1.544 1.324 0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" CAC HEC P 501 " pdb=" CBC HEC P 501 " ideal model delta sigma weight residual 1.544 1.325 0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" CAB HEC P 501 " pdb=" CBB HEC P 501 " ideal model delta sigma weight residual 1.544 1.336 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C2D HEC C 501 " pdb=" C3D HEC C 501 " ideal model delta sigma weight residual 1.544 1.336 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C2D HEC P 501 " pdb=" C3D HEC P 501 " ideal model delta sigma weight residual 1.544 1.337 0.207 2.00e-02 2.50e+03 1.08e+02 ... (remaining 13504 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 18189 3.16 - 6.32: 279 6.32 - 9.49: 31 9.49 - 12.65: 5 12.65 - 15.81: 16 Bond angle restraints: 18520 Sorted by residual: angle pdb="FE1 FES R 501 " pdb=" S2 FES R 501 " pdb="FE2 FES R 501 " ideal model delta sigma weight residual 75.66 89.11 -13.45 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 89.09 -13.43 1.14e+00 7.69e-01 1.39e+02 angle pdb=" S1 FES R 501 " pdb="FE2 FES R 501 " pdb=" S2 FES R 501 " ideal model delta sigma weight residual 104.33 90.91 13.42 1.14e+00 7.69e-01 1.39e+02 angle pdb=" S1 FES E 501 " pdb="FE2 FES E 501 " pdb=" S2 FES E 501 " ideal model delta sigma weight residual 104.33 90.94 13.39 1.14e+00 7.69e-01 1.38e+02 angle pdb=" S1 FES E 501 " pdb="FE1 FES E 501 " pdb=" S2 FES E 501 " ideal model delta sigma weight residual 104.33 90.80 13.53 1.20e+00 6.94e-01 1.27e+02 ... (remaining 18515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 6979 17.90 - 35.79: 535 35.79 - 53.69: 79 53.69 - 71.58: 10 71.58 - 89.48: 22 Dihedral angle restraints: 7625 sinusoidal: 2835 harmonic: 4790 Sorted by residual: dihedral pdb=" C2B HEC P 501 " pdb=" C3B HEC P 501 " pdb=" CAB HEC P 501 " pdb=" CBB HEC P 501 " ideal model delta sinusoidal sigma weight residual 60.00 -22.29 82.29 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 -22.15 82.15 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 -17.14 77.14 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: 1912 0.146 - 0.292: 45 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 1.32e+01 chirality pdb=" CB THR Q 198 " pdb=" CA THR Q 198 " pdb=" OG1 THR Q 198 " pdb=" CG2 THR Q 198 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.52 2.00e-01 2.50e+01 6.87e+00 ... (remaining 1967 not shown) Planarity restraints: 2327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC Q 501 " 0.010 2.00e-02 2.50e+03 4.12e-02 3.82e+01 pdb=" C2C HEC Q 501 " -0.109 2.00e-02 2.50e+03 pdb=" C3C HEC Q 501 " 0.042 2.00e-02 2.50e+03 pdb=" C4C HEC Q 501 " 0.007 2.00e-02 2.50e+03 pdb=" CAC HEC Q 501 " 0.007 2.00e-02 2.50e+03 pdb=" CHC HEC Q 501 " 0.018 2.00e-02 2.50e+03 pdb=" CHD HEC Q 501 " -0.007 2.00e-02 2.50e+03 pdb=" CMC HEC Q 501 " 0.031 2.00e-02 2.50e+03 pdb=" NC HEC Q 501 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC D 501 " -0.010 2.00e-02 2.50e+03 4.10e-02 3.78e+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 4.27e-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: 160 2.57 - 3.15: 11764 3.15 - 3.73: 19511 3.73 - 4.32: 27440 4.32 - 4.90: 45711 Nonbonded interactions: 104586 Sorted by model distance: nonbonded pdb=" O THR E 186 " pdb=" OG1 THR E 187 " model vdw 1.987 3.040 nonbonded pdb=" O THR R 186 " pdb=" OG1 THR R 187 " model vdw 1.987 3.040 nonbonded pdb=" OG SER P 120 " pdb=" ND2 ASN P 222 " model vdw 1.988 3.120 nonbonded pdb=" NH2 ARG C 306 " pdb=" O MET C 383 " model vdw 2.007 3.120 nonbonded pdb=" NH2 ARG P 306 " pdb=" O MET P 383 " model vdw 2.007 3.120 ... (remaining 104581 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.600 Find NCS groups from input model: 0.220 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 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 : 1.046 23.217 18530 Z= 0.636 Chirality : 0.070 0.731 1970 Planarity : 0.007 0.082 2327 Dihedral : 13.757 89.475 4563 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 23.31 Ramachandran Plot: Outliers : 0.42 % Allowed : 16.34 % Favored : 83.23 % 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: -3.37 (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 P 85 TYR 0.010 0.001 TYR C 297 PHE 0.021 0.001 PHE P 104 TRP 0.012 0.001 TRP P 296 HIS 0.010 0.001 HIS P 111 Details of bonding type rmsd covalent geometry : bond 0.00944 (13509) covalent geometry : angle 1.01486 (18520) SS BOND : bond 0.00106 ( 2) SS BOND : angle 0.58186 ( 4) hydrogen bonds : bond 0.14334 ( 630) hydrogen bonds : angle 6.99174 ( 1815) metal coordination : bond 0.01153 ( 8) metal coordination : angle 14.22173 ( 6) Misc. bond : bond 0.14976 ( 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 217 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 81 ASP cc_start: 0.1777 (t70) cc_final: 0.1459 (t70) REVERT: E 113 ARG cc_start: 0.7350 (tpt90) cc_final: 0.7095 (ttt90) REVERT: D 218 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8111 (tp30) REVERT: P 305 LEU cc_start: 0.8858 (tp) cc_final: 0.8565 (tt) REVERT: Q 74 LYS cc_start: 0.7557 (ttpt) cc_final: 0.7274 (tttt) REVERT: Q 218 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7917 (tp30) REVERT: Q 247 LYS cc_start: 0.7812 (tttt) cc_final: 0.7558 (tttt) REVERT: R 81 ASP cc_start: 0.1993 (t70) cc_final: 0.1619 (t70) REVERT: R 113 ARG cc_start: 0.7393 (tpt90) cc_final: 0.7085 (ttt90) outliers start: 1 outliers final: 1 residues processed: 217 average time/residue: 0.1411 time to fit residues: 42.0965 Evaluate side-chains 147 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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: 0.9980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 17 HIS E 100 ASN C 68 HIS C 82 HIS C 222 ASN C 223 ASN D 177 HIS P 68 HIS P 82 HIS P 222 ASN Q 159 GLN Q 177 HIS R 17 HIS R 100 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.173581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.138065 restraints weight = 15372.405| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.73 r_work: 0.3201 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.258 13529 Z= 0.158 Angle : 0.764 13.687 18530 Z= 0.356 Chirality : 0.045 0.191 1970 Planarity : 0.006 0.078 2327 Dihedral : 8.638 88.758 1861 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.46 % Favored : 88.42 % Rotamer: Outliers : 0.88 % Allowed : 8.97 % Favored : 90.15 % 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: -2.22 (0.19), residues: 1658 helix: 0.18 (0.17), residues: 820 sheet: -2.20 (0.57), residues: 70 loop : -3.43 (0.19), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 82 TYR 0.026 0.001 TYR P 199 PHE 0.022 0.001 PHE C 216 TRP 0.017 0.002 TRP E 67 HIS 0.006 0.001 HIS P 111 Details of bonding type rmsd covalent geometry : bond 0.00348 (13509) covalent geometry : angle 0.75289 (18520) SS BOND : bond 0.00097 ( 2) SS BOND : angle 0.42329 ( 4) hydrogen bonds : bond 0.05108 ( 630) hydrogen bonds : angle 4.79990 ( 1815) metal coordination : bond 0.00975 ( 8) metal coordination : angle 7.22113 ( 6) Misc. bond : bond 0.15194 ( 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 191 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 180 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: E 115 LEU cc_start: 0.6806 (pp) cc_final: 0.6525 (pt) REVERT: C 18 TRP cc_start: 0.6105 (t-100) cc_final: 0.5497 (t-100) REVERT: D 80 ARG cc_start: 0.8676 (mtm110) cc_final: 0.8388 (mtm-85) REVERT: D 155 ASN cc_start: 0.8669 (t0) cc_final: 0.8419 (t0) REVERT: D 248 ARG cc_start: 0.8426 (ttm170) cc_final: 0.7371 (ttt-90) REVERT: P 18 TRP cc_start: 0.6131 (t-100) cc_final: 0.5543 (t-100) REVERT: P 252 ASP cc_start: 0.8106 (m-30) cc_final: 0.7853 (m-30) REVERT: P 305 LEU cc_start: 0.9104 (tp) cc_final: 0.8833 (tt) REVERT: P 383 MET cc_start: 0.8475 (mmm) cc_final: 0.7954 (mmm) REVERT: Q 74 LYS cc_start: 0.7610 (ttpt) cc_final: 0.7348 (tttt) REVERT: Q 247 LYS cc_start: 0.8439 (tttt) cc_final: 0.8210 (tttt) REVERT: Q 248 ARG cc_start: 0.8518 (ttm170) cc_final: 0.7394 (ttt180) REVERT: R 66 LYS cc_start: 0.8045 (tptm) cc_final: 0.7696 (tptp) REVERT: R 100 ASN cc_start: 0.7527 (p0) cc_final: 0.7099 (p0) REVERT: R 115 LEU cc_start: 0.7546 (pp) cc_final: 0.7066 (pt) outliers start: 11 outliers final: 8 residues processed: 186 average time/residue: 0.1235 time to fit residues: 32.6146 Evaluate side-chains 165 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 157 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 187 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 145 optimal weight: 2.9990 chunk 70 optimal weight: 0.3980 chunk 2 optimal weight: 0.9980 chunk 144 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN C 272 ASN P 99 ASN P 272 ASN Q 155 ASN Q 159 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.165857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.129150 restraints weight = 15786.906| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.82 r_work: 0.2943 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.303 13529 Z= 0.159 Angle : 0.737 15.542 18530 Z= 0.332 Chirality : 0.045 0.188 1970 Planarity : 0.006 0.066 2327 Dihedral : 8.241 81.704 1858 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.46 % Favored : 88.48 % Rotamer: Outliers : 1.84 % Allowed : 11.37 % Favored : 86.79 % 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: -1.48 (0.20), residues: 1658 helix: 0.78 (0.18), residues: 826 sheet: -1.20 (0.78), residues: 44 loop : -3.09 (0.19), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG Q 82 TYR 0.011 0.001 TYR P 199 PHE 0.018 0.001 PHE C 113 TRP 0.011 0.001 TRP E 126 HIS 0.006 0.001 HIS P 212 Details of bonding type rmsd covalent geometry : bond 0.00365 (13509) covalent geometry : angle 0.72683 (18520) SS BOND : bond 0.00163 ( 2) SS BOND : angle 0.30725 ( 4) hydrogen bonds : bond 0.05118 ( 630) hydrogen bonds : angle 4.61899 ( 1815) metal coordination : bond 0.00773 ( 8) metal coordination : angle 6.92336 ( 6) Misc. bond : bond 0.14491 ( 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 204 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 0.436 Fit side-chains REVERT: E 100 ASN cc_start: 0.7381 (p0) cc_final: 0.6976 (p0) REVERT: C 18 TRP cc_start: 0.6091 (t-100) cc_final: 0.5621 (t-100) REVERT: C 252 ASP cc_start: 0.8379 (m-30) cc_final: 0.8133 (m-30) REVERT: D 80 ARG cc_start: 0.8682 (mtm110) cc_final: 0.8191 (mtm-85) REVERT: D 218 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8734 (tp30) REVERT: D 248 ARG cc_start: 0.8599 (ttm170) cc_final: 0.7400 (ttt-90) REVERT: P 18 TRP cc_start: 0.6186 (t-100) cc_final: 0.5743 (t-100) REVERT: P 252 ASP cc_start: 0.8355 (m-30) cc_final: 0.8107 (m-30) REVERT: Q 74 LYS cc_start: 0.7667 (ttpt) cc_final: 0.7404 (tttt) REVERT: Q 143 GLU cc_start: 0.7163 (pp20) cc_final: 0.6946 (pp20) REVERT: Q 155 ASN cc_start: 0.9106 (t0) cc_final: 0.8898 (t0) REVERT: Q 174 LYS cc_start: 0.8062 (ptmm) cc_final: 0.7834 (ptmm) REVERT: Q 218 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8721 (tp30) REVERT: Q 248 ARG cc_start: 0.8572 (ttm170) cc_final: 0.7413 (ttt180) REVERT: R 66 LYS cc_start: 0.7980 (tptm) cc_final: 0.7557 (tptp) REVERT: R 100 ASN cc_start: 0.7470 (p0) cc_final: 0.7009 (p0) REVERT: R 129 MET cc_start: 0.7061 (ptp) cc_final: 0.6860 (mtm) outliers start: 23 outliers final: 20 residues processed: 193 average time/residue: 0.1049 time to fit residues: 29.8953 Evaluate side-chains 176 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 234 MET Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 186 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 144 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 124 optimal weight: 0.3980 chunk 42 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 ASN D 204 GLN Q 204 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.164948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.127544 restraints weight = 15810.404| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.84 r_work: 0.2920 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2835 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.246 13529 Z= 0.142 Angle : 0.689 13.917 18530 Z= 0.316 Chirality : 0.044 0.186 1970 Planarity : 0.005 0.062 2327 Dihedral : 8.216 88.696 1858 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.31 % Favored : 89.57 % Rotamer: Outliers : 2.24 % Allowed : 12.65 % Favored : 85.11 % 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: 1.17 (0.18), residues: 822 sheet: -0.97 (0.64), residues: 70 loop : -3.00 (0.20), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 231 TYR 0.010 0.001 TYR C 399 PHE 0.015 0.001 PHE C 113 TRP 0.010 0.001 TRP P 400 HIS 0.005 0.001 HIS P 212 Details of bonding type rmsd covalent geometry : bond 0.00329 (13509) covalent geometry : angle 0.67928 (18520) SS BOND : bond 0.00113 ( 2) SS BOND : angle 0.36194 ( 4) hydrogen bonds : bond 0.04836 ( 630) hydrogen bonds : angle 4.43894 ( 1815) metal coordination : bond 0.00710 ( 8) metal coordination : angle 6.53083 ( 6) Misc. bond : bond 0.11080 ( 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 199 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.468 Fit side-chains REVERT: E 100 ASN cc_start: 0.7411 (p0) cc_final: 0.6758 (p0) REVERT: C 18 TRP cc_start: 0.6133 (t-100) cc_final: 0.5747 (t-100) REVERT: C 252 ASP cc_start: 0.8443 (m-30) cc_final: 0.8174 (m-30) REVERT: D 28 GLN cc_start: 0.9040 (tt0) cc_final: 0.8783 (tt0) REVERT: D 248 ARG cc_start: 0.8641 (ttm170) cc_final: 0.7303 (ttt-90) REVERT: P 18 TRP cc_start: 0.6161 (t-100) cc_final: 0.5782 (t-100) REVERT: P 252 ASP cc_start: 0.8399 (m-30) cc_final: 0.8122 (m-30) REVERT: Q 79 GLU cc_start: 0.7400 (mt-10) cc_final: 0.6915 (mm-30) REVERT: Q 155 ASN cc_start: 0.9071 (t0) cc_final: 0.8848 (t0) REVERT: Q 174 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7988 (ptmm) REVERT: Q 218 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8773 (tp30) REVERT: Q 248 ARG cc_start: 0.8642 (ttm170) cc_final: 0.7351 (ttt-90) REVERT: R 66 LYS cc_start: 0.8018 (tptm) cc_final: 0.7553 (tptp) REVERT: R 100 ASN cc_start: 0.7307 (p0) cc_final: 0.6815 (p0) outliers start: 28 outliers final: 19 residues processed: 186 average time/residue: 0.1065 time to fit residues: 29.5568 Evaluate side-chains 164 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 270 MET Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 174 LYS Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 234 MET Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 186 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 131 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 117 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.152273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.113135 restraints weight = 15943.196| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.06 r_work: 0.2856 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.244 13529 Z= 0.159 Angle : 0.712 15.339 18530 Z= 0.322 Chirality : 0.044 0.186 1970 Planarity : 0.005 0.062 2327 Dihedral : 8.145 85.946 1858 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.46 % Favored : 88.42 % Rotamer: Outliers : 2.48 % Allowed : 14.81 % Favored : 82.71 % 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: -0.91 (0.21), residues: 1658 helix: 1.25 (0.18), residues: 820 sheet: -0.57 (0.73), residues: 60 loop : -2.85 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 193 TYR 0.012 0.001 TYR C 399 PHE 0.017 0.001 PHE C 113 TRP 0.010 0.001 TRP C 400 HIS 0.006 0.001 HIS C 97 Details of bonding type rmsd covalent geometry : bond 0.00379 (13509) covalent geometry : angle 0.70203 (18520) SS BOND : bond 0.00110 ( 2) SS BOND : angle 0.38134 ( 4) hydrogen bonds : bond 0.05116 ( 630) hydrogen bonds : angle 4.48349 ( 1815) metal coordination : bond 0.00744 ( 8) metal coordination : angle 6.55438 ( 6) Misc. bond : bond 0.12137 ( 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 189 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.407 Fit side-chains REVERT: E 50 ILE cc_start: 0.3154 (OUTLIER) cc_final: 0.2626 (tt) REVERT: E 100 ASN cc_start: 0.7216 (p0) cc_final: 0.6435 (p0) REVERT: C 154 MET cc_start: 0.8772 (tpp) cc_final: 0.8489 (mpp) REVERT: C 252 ASP cc_start: 0.8220 (m-30) cc_final: 0.7918 (m-30) REVERT: D 28 GLN cc_start: 0.9029 (tt0) cc_final: 0.8755 (tt0) REVERT: D 132 TYR cc_start: 0.8973 (t80) cc_final: 0.8439 (t80) REVERT: D 248 ARG cc_start: 0.8625 (ttm170) cc_final: 0.7280 (ttt-90) REVERT: P 18 TRP cc_start: 0.6245 (t-100) cc_final: 0.5960 (t-100) REVERT: P 252 ASP cc_start: 0.8210 (m-30) cc_final: 0.7903 (m-30) REVERT: Q 174 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8249 (ptmm) REVERT: Q 191 GLN cc_start: 0.9092 (tt0) cc_final: 0.8789 (tt0) REVERT: Q 248 ARG cc_start: 0.8624 (ttm170) cc_final: 0.7283 (ttt-90) REVERT: R 50 ILE cc_start: 0.2453 (OUTLIER) cc_final: 0.2025 (tt) REVERT: R 66 LYS cc_start: 0.7996 (tptm) cc_final: 0.7751 (tptm) REVERT: R 100 ASN cc_start: 0.7238 (p0) cc_final: 0.6469 (p0) REVERT: R 115 LEU cc_start: 0.6480 (OUTLIER) cc_final: 0.6024 (pt) outliers start: 31 outliers final: 23 residues processed: 179 average time/residue: 0.1058 time to fit residues: 27.6251 Evaluate side-chains 178 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 270 MET Chi-restraints excluded: chain P residue 281 VAL Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 174 LYS Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 234 MET Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 179 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 77 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 157 optimal weight: 9.9990 chunk 28 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 119 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.152970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.113441 restraints weight = 15840.337| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.85 r_work: 0.2896 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.233 13529 Z= 0.138 Angle : 0.674 13.863 18530 Z= 0.308 Chirality : 0.043 0.187 1970 Planarity : 0.005 0.060 2327 Dihedral : 8.072 82.470 1858 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.31 % Favored : 89.57 % Rotamer: Outliers : 2.56 % Allowed : 15.77 % Favored : 81.67 % 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: -0.70 (0.21), residues: 1658 helix: 1.34 (0.18), residues: 826 sheet: -0.64 (0.66), residues: 76 loop : -2.68 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 193 TYR 0.012 0.001 TYR Q 134 PHE 0.013 0.001 PHE C 113 TRP 0.010 0.001 TRP P 400 HIS 0.005 0.001 HIS P 212 Details of bonding type rmsd covalent geometry : bond 0.00323 (13509) covalent geometry : angle 0.66424 (18520) SS BOND : bond 0.00084 ( 2) SS BOND : angle 0.33475 ( 4) hydrogen bonds : bond 0.04809 ( 630) hydrogen bonds : angle 4.40139 ( 1815) metal coordination : bond 0.00748 ( 8) metal coordination : angle 6.40364 ( 6) Misc. bond : bond 0.11940 ( 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 192 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: E 50 ILE cc_start: 0.3250 (OUTLIER) cc_final: 0.2700 (tt) REVERT: E 100 ASN cc_start: 0.7353 (p0) cc_final: 0.6550 (p0) REVERT: C 252 ASP cc_start: 0.8417 (m-30) cc_final: 0.8121 (m-30) REVERT: C 351 THR cc_start: 0.8668 (p) cc_final: 0.8383 (p) REVERT: D 28 GLN cc_start: 0.9083 (tt0) cc_final: 0.8854 (tt0) REVERT: D 183 MET cc_start: 0.8881 (ttt) cc_final: 0.8127 (ttt) REVERT: D 248 ARG cc_start: 0.8682 (ttm170) cc_final: 0.7368 (ttt-90) REVERT: P 252 ASP cc_start: 0.8391 (m-30) cc_final: 0.8101 (m-30) REVERT: P 351 THR cc_start: 0.8649 (p) cc_final: 0.8335 (p) REVERT: Q 73 ASP cc_start: 0.6479 (OUTLIER) cc_final: 0.5789 (t70) REVERT: Q 174 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8293 (ptmm) REVERT: Q 191 GLN cc_start: 0.9062 (tt0) cc_final: 0.8710 (tt0) REVERT: Q 248 ARG cc_start: 0.8702 (ttm170) cc_final: 0.7411 (ttt-90) REVERT: R 50 ILE cc_start: 0.2540 (OUTLIER) cc_final: 0.2071 (tt) REVERT: R 66 LYS cc_start: 0.8060 (tptm) cc_final: 0.7579 (tptp) REVERT: R 100 ASN cc_start: 0.7290 (p0) cc_final: 0.6504 (p0) REVERT: R 175 LEU cc_start: 0.7294 (mt) cc_final: 0.7067 (mt) outliers start: 32 outliers final: 22 residues processed: 182 average time/residue: 0.1184 time to fit residues: 31.2880 Evaluate side-chains 183 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 270 MET Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 73 ASP Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 174 LYS Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 179 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 161 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 165 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 123 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 147 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN R 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.153575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.115197 restraints weight = 15839.798| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.89 r_work: 0.2892 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.275 13529 Z= 0.148 Angle : 0.694 14.955 18530 Z= 0.311 Chirality : 0.044 0.184 1970 Planarity : 0.005 0.059 2327 Dihedral : 8.027 79.545 1858 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.92 % Favored : 88.96 % Rotamer: Outliers : 2.96 % Allowed : 15.29 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.21), residues: 1658 helix: 1.45 (0.18), residues: 818 sheet: -0.50 (0.66), residues: 76 loop : -2.56 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 193 TYR 0.013 0.001 TYR C 399 PHE 0.015 0.001 PHE C 113 TRP 0.018 0.001 TRP P 18 HIS 0.005 0.001 HIS P 212 Details of bonding type rmsd covalent geometry : bond 0.00351 (13509) covalent geometry : angle 0.68494 (18520) SS BOND : bond 0.00088 ( 2) SS BOND : angle 0.33744 ( 4) hydrogen bonds : bond 0.04935 ( 630) hydrogen bonds : angle 4.41495 ( 1815) metal coordination : bond 0.00912 ( 8) metal coordination : angle 6.22580 ( 6) Misc. bond : bond 0.13538 ( 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 196 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 159 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: E 12 ARG cc_start: 0.1056 (OUTLIER) cc_final: 0.0514 (tpm170) REVERT: E 50 ILE cc_start: 0.3221 (OUTLIER) cc_final: 0.2674 (tt) REVERT: E 100 ASN cc_start: 0.7398 (p0) cc_final: 0.6579 (p0) REVERT: C 252 ASP cc_start: 0.8437 (m-30) cc_final: 0.8156 (m-30) REVERT: C 351 THR cc_start: 0.8722 (p) cc_final: 0.8472 (p) REVERT: D 28 GLN cc_start: 0.9127 (tt0) cc_final: 0.8902 (tt0) REVERT: D 248 ARG cc_start: 0.8679 (ttm170) cc_final: 0.7349 (ttt-90) REVERT: P 351 THR cc_start: 0.8683 (p) cc_final: 0.8365 (p) REVERT: Q 174 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8339 (ptmm) REVERT: Q 191 GLN cc_start: 0.9067 (tt0) cc_final: 0.8661 (tt0) REVERT: R 50 ILE cc_start: 0.3222 (OUTLIER) cc_final: 0.2735 (tt) REVERT: R 66 LYS cc_start: 0.8101 (tptm) cc_final: 0.7674 (tptp) REVERT: R 100 ASN cc_start: 0.7316 (p0) cc_final: 0.6539 (p0) REVERT: R 115 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6651 (pt) REVERT: R 175 LEU cc_start: 0.7356 (mt) cc_final: 0.7105 (mt) outliers start: 37 outliers final: 25 residues processed: 187 average time/residue: 0.1192 time to fit residues: 32.1954 Evaluate side-chains 182 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 270 MET Chi-restraints excluded: chain P residue 281 VAL Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 174 LYS Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain R residue 47 MET Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 179 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 62 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 162 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 chunk 143 optimal weight: 0.6980 chunk 165 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.153798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.116118 restraints weight = 15770.305| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.86 r_work: 0.2918 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.233 13529 Z= 0.146 Angle : 0.680 14.519 18530 Z= 0.309 Chirality : 0.043 0.186 1970 Planarity : 0.005 0.059 2327 Dihedral : 8.002 77.415 1858 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.92 % Favored : 88.96 % Rotamer: Outliers : 2.88 % Allowed : 15.61 % Favored : 81.51 % 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: 1.41 (0.18), residues: 824 sheet: -0.33 (0.68), residues: 72 loop : -2.50 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 193 TYR 0.012 0.001 TYR P 399 PHE 0.014 0.001 PHE C 113 TRP 0.019 0.001 TRP C 18 HIS 0.005 0.001 HIS P 212 Details of bonding type rmsd covalent geometry : bond 0.00347 (13509) covalent geometry : angle 0.67124 (18520) SS BOND : bond 0.00093 ( 2) SS BOND : angle 0.31179 ( 4) hydrogen bonds : bond 0.04898 ( 630) hydrogen bonds : angle 4.39693 ( 1815) metal coordination : bond 0.00761 ( 8) metal coordination : angle 6.23625 ( 6) Misc. bond : bond 0.12412 ( 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 195 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: E 12 ARG cc_start: 0.0936 (OUTLIER) cc_final: 0.0445 (tpm170) REVERT: E 50 ILE cc_start: 0.3319 (OUTLIER) cc_final: 0.2757 (tt) REVERT: E 100 ASN cc_start: 0.7377 (p0) cc_final: 0.6544 (p0) REVERT: C 351 THR cc_start: 0.8664 (p) cc_final: 0.8412 (p) REVERT: D 28 GLN cc_start: 0.9028 (tt0) cc_final: 0.8795 (tt0) REVERT: D 183 MET cc_start: 0.8801 (ttt) cc_final: 0.7934 (ttt) REVERT: D 248 ARG cc_start: 0.8662 (ttm170) cc_final: 0.7330 (ttt-90) REVERT: P 351 THR cc_start: 0.8638 (p) cc_final: 0.8346 (p) REVERT: Q 90 THR cc_start: 0.8954 (OUTLIER) cc_final: 0.8659 (p) REVERT: Q 174 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8394 (ptmm) REVERT: Q 191 GLN cc_start: 0.9093 (tt0) cc_final: 0.8691 (tt0) REVERT: R 50 ILE cc_start: 0.3226 (OUTLIER) cc_final: 0.2746 (tt) REVERT: R 66 LYS cc_start: 0.8091 (tptm) cc_final: 0.7644 (tptp) REVERT: R 100 ASN cc_start: 0.7305 (p0) cc_final: 0.6503 (p0) REVERT: R 115 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6662 (pt) REVERT: R 175 LEU cc_start: 0.7202 (mt) cc_final: 0.6998 (mt) outliers start: 36 outliers final: 27 residues processed: 186 average time/residue: 0.1073 time to fit residues: 29.2977 Evaluate side-chains 185 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 270 MET Chi-restraints excluded: chain P residue 281 VAL Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 174 LYS Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 234 MET Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain R residue 47 MET Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 179 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 72 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 153 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 162 optimal weight: 10.0000 chunk 157 optimal weight: 0.0030 chunk 14 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 19 optimal weight: 0.1980 chunk 112 optimal weight: 0.4980 chunk 142 optimal weight: 10.0000 overall best weight: 0.4790 ------------------------------------------------------------------------------- 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 = 0.3736 r_free = 0.3736 target = 0.158178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.121032 restraints weight = 15875.807| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.92 r_work: 0.2945 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.209 13529 Z= 0.124 Angle : 0.646 12.330 18530 Z= 0.297 Chirality : 0.042 0.179 1970 Planarity : 0.005 0.058 2327 Dihedral : 7.919 77.141 1858 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.86 % Favored : 89.02 % Rotamer: Outliers : 2.56 % Allowed : 16.33 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.21), residues: 1658 helix: 1.52 (0.18), residues: 826 sheet: 0.47 (0.82), residues: 52 loop : -2.37 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 193 TYR 0.010 0.001 TYR C 399 PHE 0.013 0.001 PHE C 216 TRP 0.024 0.001 TRP C 18 HIS 0.004 0.001 HIS P 212 Details of bonding type rmsd covalent geometry : bond 0.00283 (13509) covalent geometry : angle 0.63741 (18520) SS BOND : bond 0.00048 ( 2) SS BOND : angle 0.28727 ( 4) hydrogen bonds : bond 0.04463 ( 630) hydrogen bonds : angle 4.25511 ( 1815) metal coordination : bond 0.00543 ( 8) metal coordination : angle 5.84538 ( 6) Misc. bond : bond 0.10979 ( 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 189 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: E 12 ARG cc_start: 0.0701 (OUTLIER) cc_final: 0.0463 (mmm160) REVERT: E 47 MET cc_start: 0.3010 (ppp) cc_final: 0.2762 (ppp) REVERT: E 50 ILE cc_start: 0.3121 (OUTLIER) cc_final: 0.2653 (tt) REVERT: E 100 ASN cc_start: 0.7298 (p0) cc_final: 0.6456 (p0) REVERT: C 351 THR cc_start: 0.8605 (p) cc_final: 0.8375 (p) REVERT: D 183 MET cc_start: 0.8557 (ttt) cc_final: 0.7892 (ttt) REVERT: D 248 ARG cc_start: 0.8653 (ttm170) cc_final: 0.7532 (tmm160) REVERT: P 351 THR cc_start: 0.8678 (p) cc_final: 0.8396 (p) REVERT: Q 73 ASP cc_start: 0.6549 (OUTLIER) cc_final: 0.5748 (t70) REVERT: Q 191 GLN cc_start: 0.9011 (tt0) cc_final: 0.8622 (tt0) REVERT: R 50 ILE cc_start: 0.3284 (OUTLIER) cc_final: 0.2798 (tt) REVERT: R 66 LYS cc_start: 0.8027 (tptm) cc_final: 0.7609 (tptp) REVERT: R 100 ASN cc_start: 0.7222 (p0) cc_final: 0.6419 (p0) REVERT: R 115 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6675 (pt) REVERT: R 175 LEU cc_start: 0.7333 (mt) cc_final: 0.7105 (mt) outliers start: 32 outliers final: 24 residues processed: 180 average time/residue: 0.1102 time to fit residues: 29.1492 Evaluate side-chains 179 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 270 MET Chi-restraints excluded: chain P residue 281 VAL Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 73 ASP Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain R residue 47 MET Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 179 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 112 optimal weight: 0.9980 chunk 117 optimal weight: 0.0870 chunk 107 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 65 optimal weight: 0.2980 chunk 103 optimal weight: 0.9990 chunk 135 optimal weight: 0.5980 chunk 146 optimal weight: 1.9990 chunk 149 optimal weight: 0.0980 chunk 31 optimal weight: 0.7980 overall best weight: 0.3558 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.160030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.122411 restraints weight = 15876.963| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.85 r_work: 0.2989 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.177 13529 Z= 0.116 Angle : 0.630 11.237 18530 Z= 0.292 Chirality : 0.042 0.176 1970 Planarity : 0.005 0.056 2327 Dihedral : 7.800 77.526 1858 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.83 % Favored : 90.05 % Rotamer: Outliers : 2.08 % Allowed : 16.97 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.21), residues: 1658 helix: 1.64 (0.18), residues: 824 sheet: 0.52 (0.82), residues: 52 loop : -2.30 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 193 TYR 0.010 0.001 TYR C 399 PHE 0.013 0.001 PHE C 216 TRP 0.030 0.001 TRP P 18 HIS 0.004 0.001 HIS P 212 Details of bonding type rmsd covalent geometry : bond 0.00265 (13509) covalent geometry : angle 0.62223 (18520) SS BOND : bond 0.00031 ( 2) SS BOND : angle 0.27068 ( 4) hydrogen bonds : bond 0.04269 ( 630) hydrogen bonds : angle 4.16489 ( 1815) metal coordination : bond 0.00357 ( 8) metal coordination : angle 5.51873 ( 6) Misc. bond : bond 0.09977 ( 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 180 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: E 12 ARG cc_start: 0.0269 (OUTLIER) cc_final: -0.0054 (tpp-160) REVERT: E 47 MET cc_start: 0.3326 (ppp) cc_final: 0.3091 (ppp) REVERT: E 50 ILE cc_start: 0.3171 (OUTLIER) cc_final: 0.2654 (tt) REVERT: E 100 ASN cc_start: 0.7248 (p0) cc_final: 0.6402 (p0) REVERT: C 252 ASP cc_start: 0.8037 (m-30) cc_final: 0.7746 (m-30) REVERT: C 406 VAL cc_start: 0.8316 (OUTLIER) cc_final: 0.8101 (m) REVERT: D 183 MET cc_start: 0.8412 (ttt) cc_final: 0.7768 (ttt) REVERT: D 248 ARG cc_start: 0.8620 (ttm170) cc_final: 0.7584 (tmm160) REVERT: P 252 ASP cc_start: 0.7960 (m-30) cc_final: 0.7665 (m-30) REVERT: P 351 THR cc_start: 0.8417 (p) cc_final: 0.8176 (p) REVERT: P 406 VAL cc_start: 0.8296 (OUTLIER) cc_final: 0.8054 (m) REVERT: Q 73 ASP cc_start: 0.6527 (OUTLIER) cc_final: 0.5752 (t70) REVERT: Q 191 GLN cc_start: 0.9019 (tt0) cc_final: 0.8628 (tt0) REVERT: R 50 ILE cc_start: 0.3180 (OUTLIER) cc_final: 0.2785 (tt) REVERT: R 66 LYS cc_start: 0.7925 (tptm) cc_final: 0.7477 (tptp) REVERT: R 100 ASN cc_start: 0.7135 (p0) cc_final: 0.6336 (p0) REVERT: R 115 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7204 (pt) REVERT: R 175 LEU cc_start: 0.7272 (mt) cc_final: 0.7052 (mt) outliers start: 26 outliers final: 16 residues processed: 174 average time/residue: 0.1103 time to fit residues: 28.3713 Evaluate side-chains 174 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 270 MET Chi-restraints excluded: chain P residue 281 VAL Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 73 ASP Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain R residue 47 MET Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 115 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 135 optimal weight: 1.9990 chunk 113 optimal weight: 0.0060 chunk 146 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 99 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 107 optimal weight: 0.0870 chunk 68 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 108 optimal weight: 0.5980 overall best weight: 0.3374 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.158884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.119747 restraints weight = 15731.991| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.85 r_work: 0.2990 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2815 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2815 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 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 0.172 13529 Z= 0.114 Angle : 0.619 11.007 18530 Z= 0.288 Chirality : 0.042 0.173 1970 Planarity : 0.005 0.054 2327 Dihedral : 7.730 77.415 1858 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.49 % Favored : 89.45 % Rotamer: Outliers : 1.92 % Allowed : 17.69 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.21), residues: 1658 helix: 1.68 (0.18), residues: 826 sheet: 0.44 (0.81), residues: 52 loop : -2.24 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 193 TYR 0.010 0.001 TYR C 399 PHE 0.013 0.001 PHE C 216 TRP 0.028 0.001 TRP C 18 HIS 0.004 0.001 HIS P 212 Details of bonding type rmsd covalent geometry : bond 0.00260 (13509) covalent geometry : angle 0.61209 (18520) SS BOND : bond 0.00022 ( 2) SS BOND : angle 0.31002 ( 4) hydrogen bonds : bond 0.04179 ( 630) hydrogen bonds : angle 4.11647 ( 1815) metal coordination : bond 0.00282 ( 8) metal coordination : angle 5.27023 ( 6) Misc. bond : bond 0.09709 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3272.12 seconds wall clock time: 56 minutes 31.43 seconds (3391.43 seconds total)