Starting phenix.real_space_refine on Thu Jul 31 05:50:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xkt_22224/07_2025/6xkt_22224.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xkt_22224/07_2025/6xkt_22224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xkt_22224/07_2025/6xkt_22224.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xkt_22224/07_2025/6xkt_22224.map" model { file = "/net/cci-nas-00/data/ceres_data/6xkt_22224/07_2025/6xkt_22224.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xkt_22224/07_2025/6xkt_22224.cif" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 10 7.16 5 S 78 5.16 5 C 8578 2.51 5 N 2155 2.21 5 O 2258 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13079 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 3244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3244 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 393} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'HIS:plan': 3, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1} 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: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 20 Chain: "P" Number of atoms: 3244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3244 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 393} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'HIS:plan': 3, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1} 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: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1365 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 170} Chain: "R" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1365 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 170} Chain: "C" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11016 SG CYS E 133 30.987 63.086 26.275 0.25105.87 S ATOM 11162 SG CYS E 153 31.786 60.791 23.548 0.25107.21 S ATOM 12381 SG CYS R 133 82.986 37.981 26.362 0.25105.87 S ATOM 12527 SG CYS R 153 82.121 40.213 23.602 0.25107.21 S Residues with excluded nonbonded symmetry interactions: 54 residue: pdb=" N MET E 129 " occ=0.25 ... (6 atoms not shown) pdb=" CE MET E 129 " occ=0.25 residue: pdb=" N GLY E 131 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY E 131 " occ=0.25 residue: pdb=" N VAL E 132 " occ=0.25 ... (5 atoms not shown) pdb=" CG2 VAL E 132 " occ=0.25 residue: pdb=" N CYS E 133 " occ=0.25 ... (4 atoms not shown) pdb=" SG CYS E 133 " occ=0.25 residue: pdb=" N THR E 134 " occ=0.25 ... (5 atoms not shown) pdb=" CG2 THR E 134 " occ=0.25 residue: pdb=" N HIS E 135 " occ=0.25 ... (8 atoms not shown) pdb=" NE2 HIS E 135 " occ=0.25 residue: pdb=" N LEU E 136 " occ=0.25 ... (6 atoms not shown) pdb=" CD2 LEU E 136 " occ=0.25 residue: pdb=" N GLY E 137 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY E 137 " occ=0.25 residue: pdb=" N CYS E 138 " occ=0.25 ... (4 atoms not shown) pdb=" SG CYS E 138 " occ=0.25 residue: pdb=" N VAL E 139 " occ=0.25 ... (5 atoms not shown) pdb=" CG2 VAL E 139 " occ=0.25 residue: pdb=" N PRO E 140 " occ=0.25 ... (5 atoms not shown) pdb=" CD PRO E 140 " occ=0.25 residue: pdb=" N GLY E 142 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY E 142 " occ=0.25 ... (remaining 42 not shown) Time building chain proxies: 8.20, per 1000 atoms: 0.63 Number of scatterers: 13079 At special positions: 0 Unit cell: (115.6, 102, 110.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 10 26.01 S 78 16.00 O 2258 8.00 N 2155 7.00 C 8578 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 155 " distance=2.03 Simple disulfide: pdb=" SG CYS R 138 " - pdb=" SG CYS R 155 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.67 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 501 " pdb="FE2 FES E 501 " - pdb=" ND1 HIS E 135 " pdb="FE2 FES E 501 " - pdb=" ND1 HIS E 156 " pdb="FE1 FES E 501 " - pdb=" SG CYS E 153 " pdb="FE1 FES E 501 " - pdb=" SG CYS E 133 " pdb=" FES R 501 " pdb="FE2 FES R 501 " - pdb=" ND1 HIS R 156 " pdb="FE2 FES R 501 " - pdb=" ND1 HIS R 135 " pdb="FE1 FES R 501 " - pdb=" SG CYS R 153 " pdb="FE1 FES R 501 " - pdb=" SG CYS R 133 " Number of angles added : 6 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3056 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 8 sheets defined 51.8% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 33 removed outlier: 3.763A pdb=" N GLY C 27 " --> pdb=" O LEU C 23 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE C 33 " --> pdb=" O VAL C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 66 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 90 through 118 removed outlier: 3.757A pdb=" N SER C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 148 removed outlier: 3.860A pdb=" N TRP C 129 " --> pdb=" O ARG C 125 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL C 148 " --> pdb=" O PHE C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 169 removed outlier: 3.624A pdb=" N TRP C 157 " --> pdb=" O GLN C 153 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N PHE C 166 " --> pdb=" O ILE C 162 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY C 167 " --> pdb=" O THR C 163 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 182 removed outlier: 3.668A pdb=" N ILE C 176 " --> pdb=" O ILE C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 199 Processing helix chain 'C' and resid 200 through 219 removed outlier: 3.960A pdb=" N VAL C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE C 216 " --> pdb=" O HIS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 270 Processing helix chain 'C' and resid 276 through 281 Processing helix chain 'C' and resid 298 through 308 removed outlier: 4.405A pdb=" N PHE C 308 " --> pdb=" O ILE C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 321 Processing helix chain 'C' and resid 327 through 346 removed outlier: 3.848A pdb=" N MET C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 356 through 359 Processing helix chain 'C' and resid 360 through 381 Processing helix chain 'C' and resid 388 through 415 removed outlier: 5.576A pdb=" N LEU C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Proline residue: C 409 - end of helix Processing helix chain 'D' and resid 19 through 33 removed outlier: 3.629A pdb=" N LEU D 23 " --> pdb=" O ASP D 19 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU D 32 " --> pdb=" O GLN D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 37 Processing helix chain 'D' and resid 44 through 49 Processing helix chain 'D' and resid 57 through 67 Processing helix chain 'D' and resid 127 through 136 Processing helix chain 'D' and resid 201 through 218 Processing helix chain 'D' and resid 220 through 250 Processing helix chain 'P' and resid 14 through 19 Processing helix chain 'P' and resid 23 through 33 removed outlier: 3.762A pdb=" N GLY P 27 " --> pdb=" O LEU P 23 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE P 33 " --> pdb=" O VAL P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 66 Processing helix chain 'P' and resid 75 through 86 Processing helix chain 'P' and resid 90 through 118 removed outlier: 3.753A pdb=" N SER P 102 " --> pdb=" O ALA P 98 " (cutoff:3.500A) Processing helix chain 'P' and resid 125 through 148 removed outlier: 3.860A pdb=" N TRP P 129 " --> pdb=" O ARG P 125 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL P 148 " --> pdb=" O PHE P 144 " (cutoff:3.500A) Processing helix chain 'P' and resid 153 through 169 removed outlier: 3.623A pdb=" N TRP P 157 " --> pdb=" O GLN P 153 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N PHE P 166 " --> pdb=" O ILE P 162 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY P 167 " --> pdb=" O THR P 163 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE P 169 " --> pdb=" O LEU P 165 " (cutoff:3.500A) Processing helix chain 'P' and resid 172 through 182 removed outlier: 3.668A pdb=" N ILE P 176 " --> pdb=" O ILE P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 187 through 199 Processing helix chain 'P' and resid 200 through 219 removed outlier: 3.958A pdb=" N VAL P 204 " --> pdb=" O LEU P 200 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE P 216 " --> pdb=" O HIS P 212 " (cutoff:3.500A) Processing helix chain 'P' and resid 246 through 270 Processing helix chain 'P' and resid 276 through 281 Processing helix chain 'P' and resid 298 through 308 removed outlier: 4.405A pdb=" N PHE P 308 " --> pdb=" O ILE P 304 " (cutoff:3.500A) Processing helix chain 'P' and resid 316 through 321 Processing helix chain 'P' and resid 327 through 346 removed outlier: 3.848A pdb=" N MET P 343 " --> pdb=" O ALA P 339 " (cutoff:3.500A) Processing helix chain 'P' and resid 347 through 349 No H-bonds generated for 'chain 'P' and resid 347 through 349' Processing helix chain 'P' and resid 356 through 359 Processing helix chain 'P' and resid 360 through 381 Processing helix chain 'P' and resid 388 through 415 removed outlier: 5.575A pdb=" N LEU P 408 " --> pdb=" O PHE P 404 " (cutoff:3.500A) Proline residue: P 409 - end of helix Processing helix chain 'Q' and resid 19 through 33 removed outlier: 3.627A pdb=" N LEU Q 23 " --> pdb=" O ASP Q 19 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU Q 32 " --> pdb=" O GLN Q 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 34 through 37 Processing helix chain 'Q' and resid 44 through 49 removed outlier: 3.567A pdb=" N THR Q 47 " --> pdb=" O PRO Q 44 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU Q 48 " --> pdb=" O ILE Q 45 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA Q 49 " --> pdb=" O ARG Q 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 44 through 49' Processing helix chain 'Q' and resid 57 through 67 Processing helix chain 'Q' and resid 127 through 136 Processing helix chain 'Q' and resid 201 through 218 Processing helix chain 'Q' and resid 220 through 250 Processing helix chain 'E' and resid 12 through 37 Proline residue: E 33 - end of helix Processing helix chain 'E' and resid 41 through 49 removed outlier: 4.227A pdb=" N ALA E 46 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N MET E 47 " --> pdb=" O ASP E 43 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA E 48 " --> pdb=" O VAL E 44 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 87 Processing helix chain 'E' and resid 109 through 114 Processing helix chain 'R' and resid 12 through 37 Proline residue: R 33 - end of helix Processing helix chain 'R' and resid 41 through 49 removed outlier: 4.225A pdb=" N ALA R 46 " --> pdb=" O ALA R 42 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N MET R 47 " --> pdb=" O ASP R 43 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA R 48 " --> pdb=" O VAL R 44 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER R 49 " --> pdb=" O LYS R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 87 Processing helix chain 'R' and resid 109 through 114 Processing sheet with id=AA1, first strand: chain 'D' and resid 153 through 155 Processing sheet with id=AA2, first strand: chain 'Q' and resid 153 through 155 Processing sheet with id=AA3, first strand: chain 'E' and resid 50 through 52 removed outlier: 3.607A pdb=" N ALA E 181 " --> pdb=" O LYS E 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 64 through 67 Processing sheet with id=AA5, first strand: chain 'E' and resid 141 through 145 removed outlier: 4.683A pdb=" N ASP E 143 " --> pdb=" O GLY E 150 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N GLY E 150 " --> pdb=" O ASP E 143 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TRP E 151 " --> pdb=" O TYR E 160 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER E 158 " --> pdb=" O CYS E 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 50 through 52 removed outlier: 3.607A pdb=" N ALA R 181 " --> pdb=" O LYS R 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 64 through 67 Processing sheet with id=AA8, first strand: chain 'R' and resid 141 through 145 removed outlier: 4.683A pdb=" N ASP R 143 " --> pdb=" O GLY R 150 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N GLY R 150 " --> pdb=" O ASP R 143 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TRP R 151 " --> pdb=" O TYR R 160 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER R 158 " --> pdb=" O CYS R 153 " (cutoff:3.500A) 629 hydrogen bonds defined for protein. 1812 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.35 Time building geometry restraints manager: 4.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.41: 5787 1.41 - 1.61: 7560 1.61 - 1.80: 109 1.80 - 2.00: 25 2.00 - 2.20: 28 Bond restraints: 13509 Sorted by residual: bond pdb=" CAC HEC C 501 " pdb=" CBC HEC C 501 " ideal model delta sigma weight residual 1.544 1.324 0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" CAC HEC P 501 " pdb=" CBC HEC P 501 " ideal model delta sigma weight residual 1.544 1.325 0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" CAB HEC P 501 " pdb=" CBB HEC P 501 " ideal model delta sigma weight residual 1.544 1.336 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C2D HEC C 501 " pdb=" C3D HEC C 501 " ideal model delta sigma weight residual 1.544 1.336 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C2D HEC P 501 " pdb=" C3D HEC P 501 " ideal model delta sigma weight residual 1.544 1.337 0.207 2.00e-02 2.50e+03 1.08e+02 ... (remaining 13504 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 18203 3.15 - 6.31: 270 6.31 - 9.46: 28 9.46 - 12.61: 3 12.61 - 15.76: 16 Bond angle restraints: 18520 Sorted by residual: angle pdb="FE1 FES R 501 " pdb=" S2 FES R 501 " pdb="FE2 FES R 501 " ideal model delta sigma weight residual 75.66 89.10 -13.44 1.14e+00 7.69e-01 1.39e+02 angle pdb="FE1 FES E 501 " pdb=" S2 FES E 501 " pdb="FE2 FES E 501 " ideal model delta sigma weight residual 75.66 89.08 -13.42 1.14e+00 7.69e-01 1.39e+02 angle pdb=" S1 FES E 501 " pdb="FE2 FES E 501 " pdb=" S2 FES E 501 " ideal model delta sigma weight residual 104.33 90.92 13.41 1.14e+00 7.69e-01 1.38e+02 angle pdb=" S1 FES R 501 " pdb="FE2 FES R 501 " pdb=" S2 FES R 501 " ideal model delta sigma weight residual 104.33 90.92 13.41 1.14e+00 7.69e-01 1.38e+02 angle pdb=" S1 FES E 501 " pdb="FE1 FES E 501 " pdb=" S2 FES E 501 " ideal model delta sigma weight residual 104.33 90.78 13.55 1.20e+00 6.94e-01 1.27e+02 ... (remaining 18515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 6976 17.90 - 35.79: 536 35.79 - 53.69: 81 53.69 - 71.59: 10 71.59 - 89.48: 22 Dihedral angle restraints: 7625 sinusoidal: 2835 harmonic: 4790 Sorted by residual: dihedral pdb=" C2B HEC P 501 " pdb=" C3B HEC P 501 " pdb=" CAB HEC P 501 " pdb=" CBB HEC P 501 " ideal model delta sinusoidal sigma weight residual 60.00 -22.24 82.24 2 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" C2B HEC C 501 " pdb=" C3B HEC C 501 " pdb=" CAB HEC C 501 " pdb=" CBB HEC C 501 " ideal model delta sinusoidal sigma weight residual 60.00 -22.11 82.11 2 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" C2C HEC P 502 " pdb=" C3C HEC P 502 " pdb=" CAC HEC P 502 " pdb=" CBC HEC P 502 " ideal model delta sinusoidal sigma weight residual 60.00 -17.19 77.19 2 1.00e+01 1.00e-02 4.56e+01 ... (remaining 7622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 1925 0.146 - 0.293: 32 0.293 - 0.439: 1 0.439 - 0.585: 10 0.585 - 0.731: 2 Chirality restraints: 1970 Sorted by residual: chirality pdb=" CG LEU Q 244 " pdb=" CB LEU Q 244 " pdb=" CD1 LEU Q 244 " pdb=" CD2 LEU Q 244 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" CG LEU D 244 " pdb=" CB LEU D 244 " pdb=" CD1 LEU D 244 " pdb=" CD2 LEU D 244 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" CB THR D 198 " pdb=" CA THR D 198 " pdb=" OG1 THR D 198 " pdb=" CG2 THR D 198 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.53 2.00e-01 2.50e+01 6.92e+00 ... (remaining 1967 not shown) Planarity restraints: 2327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC Q 501 " 0.009 2.00e-02 2.50e+03 4.12e-02 3.82e+01 pdb=" C2C HEC Q 501 " -0.109 2.00e-02 2.50e+03 pdb=" C3C HEC Q 501 " 0.042 2.00e-02 2.50e+03 pdb=" C4C HEC Q 501 " 0.007 2.00e-02 2.50e+03 pdb=" CAC HEC Q 501 " 0.007 2.00e-02 2.50e+03 pdb=" CHC HEC Q 501 " 0.018 2.00e-02 2.50e+03 pdb=" CHD HEC Q 501 " -0.007 2.00e-02 2.50e+03 pdb=" CMC HEC Q 501 " 0.031 2.00e-02 2.50e+03 pdb=" NC HEC Q 501 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC D 501 " -0.010 2.00e-02 2.50e+03 4.09e-02 3.76e+01 pdb=" C2C HEC D 501 " 0.109 2.00e-02 2.50e+03 pdb=" C3C HEC D 501 " -0.041 2.00e-02 2.50e+03 pdb=" C4C HEC D 501 " -0.007 2.00e-02 2.50e+03 pdb=" CAC HEC D 501 " -0.007 2.00e-02 2.50e+03 pdb=" CHC HEC D 501 " -0.017 2.00e-02 2.50e+03 pdb=" CHD HEC D 501 " 0.007 2.00e-02 2.50e+03 pdb=" CMC HEC D 501 " -0.031 2.00e-02 2.50e+03 pdb=" NC HEC D 501 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 222 " -0.021 2.00e-02 2.50e+03 4.26e-02 1.81e+01 pdb=" C ASN C 222 " 0.074 2.00e-02 2.50e+03 pdb=" O ASN C 222 " -0.028 2.00e-02 2.50e+03 pdb=" N ASN C 223 " -0.025 2.00e-02 2.50e+03 ... (remaining 2324 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 46 2.37 - 3.00: 8314 3.00 - 3.63: 18666 3.63 - 4.27: 28692 4.27 - 4.90: 48565 Nonbonded interactions: 104283 Sorted by model distance: nonbonded pdb=" CD2 LEU P 286 " pdb=" CD LYS R 70 " model vdw 1.732 3.860 nonbonded pdb=" CD2 LEU C 286 " pdb=" CD LYS E 70 " model vdw 1.797 3.860 nonbonded pdb=" NH2 ARG P 193 " pdb=" O MET R 38 " model vdw 1.949 3.120 nonbonded pdb=" OD1 ASP Q 75 " pdb=" NZ LYS E 66 " model vdw 1.962 3.120 nonbonded pdb=" O THR R 186 " pdb=" OG1 THR R 187 " model vdw 1.987 3.040 ... (remaining 104278 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'P' } ncs_group { reference = (chain 'D' and (resid 5 through 80 or (resid 81 and (name N or name CA or name C \ or name O or name CB )) or resid 82 or (resid 83 and (name N or name CA or name \ C or name O or name CB )) or resid 84 through 257 or resid 501)) selection = chain 'Q' } ncs_group { reference = chain 'E' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.25 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 34.170 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.220 13529 Z= 0.465 Angle : 1.023 23.199 18530 Z= 0.617 Chirality : 0.068 0.731 1970 Planarity : 0.006 0.083 2327 Dihedral : 13.782 89.483 4563 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 26.25 Ramachandran Plot: Outliers : 0.42 % Allowed : 16.47 % Favored : 83.11 % Rotamer: Outliers : 0.08 % Allowed : 2.72 % Favored : 97.20 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.20 (0.17), residues: 1658 helix: -1.61 (0.16), residues: 772 sheet: -2.87 (0.52), residues: 64 loop : -4.12 (0.18), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 296 HIS 0.010 0.001 HIS C 111 PHE 0.021 0.001 PHE P 104 TYR 0.010 0.001 TYR C 297 ARG 0.002 0.000 ARG P 85 Details of bonding type rmsd hydrogen bonds : bond 0.14686 ( 629) hydrogen bonds : angle 6.99060 ( 1812) metal coordination : bond 0.01169 ( 8) metal coordination : angle 14.20470 ( 6) SS BOND : bond 0.00126 ( 2) SS BOND : angle 0.54900 ( 4) covalent geometry : bond 0.00937 (13509) covalent geometry : angle 0.99033 (18520) Misc. bond : bond 0.14987 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 445 time to evaluate : 1.601 Fit side-chains Corrupt residue: chain: C residue: PRO 24 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: P residue: PRO 24 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 132 TYR cc_start: 0.7207 (t80) cc_final: 0.6488 (t80) REVERT: D 155 ASN cc_start: 0.9198 (t0) cc_final: 0.8869 (t0) REVERT: D 160 ILE cc_start: 0.7429 (mt) cc_final: 0.7031 (mt) REVERT: D 208 ASP cc_start: 0.8066 (m-30) cc_final: 0.7433 (m-30) REVERT: P 390 ASP cc_start: 0.7791 (p0) cc_final: 0.7496 (p0) REVERT: Q 132 TYR cc_start: 0.7233 (t80) cc_final: 0.6792 (t80) REVERT: Q 152 TYR cc_start: 0.7987 (m-80) cc_final: 0.7485 (m-10) REVERT: Q 160 ILE cc_start: 0.7502 (mt) cc_final: 0.6953 (mt) REVERT: Q 208 ASP cc_start: 0.7905 (m-30) cc_final: 0.7355 (m-30) REVERT: E 37 GLN cc_start: 0.8286 (pp30) cc_final: 0.7591 (pp30) REVERT: E 102 ASN cc_start: 0.8301 (p0) cc_final: 0.7565 (p0) REVERT: E 114 THR cc_start: 0.7319 (p) cc_final: 0.7054 (p) REVERT: E 134 THR cc_start: 0.4063 (p) cc_final: 0.3530 (t) REVERT: E 136 LEU cc_start: 0.5116 (mt) cc_final: 0.4658 (mt) REVERT: E 165 ARG cc_start: 0.7527 (mtm-85) cc_final: 0.7061 (mtm-85) REVERT: R 19 THR cc_start: 0.6601 (p) cc_final: 0.5897 (p) REVERT: R 136 LEU cc_start: 0.5207 (mt) cc_final: 0.4918 (mt) REVERT: R 140 PRO cc_start: 0.8183 (Cg_exo) cc_final: 0.7925 (Cg_endo) REVERT: R 165 ARG cc_start: 0.8366 (mtm-85) cc_final: 0.7976 (mtm180) outliers start: 1 outliers final: 0 residues processed: 446 average time/residue: 0.3376 time to fit residues: 213.6324 Evaluate side-chains 285 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 96 optimal weight: 9.9990 chunk 150 optimal weight: 0.0670 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 HIS ** P 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 217 HIS P 222 ASN P 291 HIS E 17 HIS R 100 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.145903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.113013 restraints weight = 21322.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.115922 restraints weight = 11180.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.117595 restraints weight = 7786.696| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.331 13529 Z= 0.164 Angle : 0.788 17.853 18530 Z= 0.370 Chirality : 0.047 0.188 1970 Planarity : 0.006 0.080 2327 Dihedral : 8.820 89.813 1858 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.30 % Favored : 87.64 % Rotamer: Outliers : 3.76 % Allowed : 12.41 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.19), residues: 1658 helix: 0.29 (0.17), residues: 802 sheet: -1.41 (0.67), residues: 60 loop : -3.33 (0.19), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 157 HIS 0.004 0.001 HIS C 217 PHE 0.022 0.001 PHE P 104 TYR 0.012 0.001 TYR R 160 ARG 0.007 0.001 ARG E 167 Details of bonding type rmsd hydrogen bonds : bond 0.04972 ( 629) hydrogen bonds : angle 4.75730 ( 1812) metal coordination : bond 0.01340 ( 8) metal coordination : angle 9.57147 ( 6) SS BOND : bond 0.00614 ( 2) SS BOND : angle 2.26756 ( 4) covalent geometry : bond 0.00367 (13509) covalent geometry : angle 0.76821 (18520) Misc. bond : bond 0.19017 ( 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 388 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 341 time to evaluate : 2.348 Fit side-chains Corrupt residue: chain: C residue: PRO 24 >>> skipping revert: symmetry clash Corrupt residue: chain: P residue: PRO 24 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7529 (mm-30) REVERT: C 93 MET cc_start: 0.8579 (mmt) cc_final: 0.7803 (mmt) REVERT: D 155 ASN cc_start: 0.9314 (t0) cc_final: 0.9012 (t0) REVERT: D 158 PHE cc_start: 0.8656 (t80) cc_final: 0.7879 (t80) REVERT: D 160 ILE cc_start: 0.8523 (mt) cc_final: 0.8319 (tp) REVERT: D 204 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.6597 (tm-30) REVERT: D 208 ASP cc_start: 0.8635 (m-30) cc_final: 0.8035 (m-30) REVERT: P 222 ASN cc_start: 0.8904 (t160) cc_final: 0.8464 (t0) REVERT: P 253 LEU cc_start: 0.9237 (mt) cc_final: 0.9004 (mp) REVERT: Q 96 MET cc_start: 0.8477 (mmt) cc_final: 0.8223 (mmt) REVERT: Q 155 ASN cc_start: 0.9280 (t0) cc_final: 0.9018 (t0) REVERT: Q 158 PHE cc_start: 0.8850 (t80) cc_final: 0.8601 (t80) REVERT: Q 160 ILE cc_start: 0.8716 (mt) cc_final: 0.8422 (mt) REVERT: Q 183 MET cc_start: 0.8789 (ttp) cc_final: 0.8524 (ttp) REVERT: Q 204 GLN cc_start: 0.7450 (mm-40) cc_final: 0.6397 (tm-30) REVERT: Q 208 ASP cc_start: 0.8617 (m-30) cc_final: 0.7886 (m-30) REVERT: E 37 GLN cc_start: 0.8744 (pp30) cc_final: 0.7977 (pp30) REVERT: E 78 ASP cc_start: 0.8449 (t0) cc_final: 0.7781 (m-30) REVERT: R 37 GLN cc_start: 0.9023 (pp30) cc_final: 0.7970 (pp30) REVERT: R 88 VAL cc_start: 0.6984 (t) cc_final: 0.6706 (p) outliers start: 47 outliers final: 32 residues processed: 362 average time/residue: 0.2798 time to fit residues: 147.5360 Evaluate side-chains 299 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 266 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 272 ASN Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 167 CYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 218 THR Chi-restraints excluded: chain P residue 272 ASN Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain Q residue 94 ASP Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 100 ASN Chi-restraints excluded: chain R residue 187 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 96 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 chunk 143 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 57 optimal weight: 0.4980 chunk 92 optimal weight: 2.9990 chunk 68 optimal weight: 0.0170 chunk 103 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.0420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 177 GLN C 217 HIS P 99 ASN P 177 GLN R 36 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.130969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.100664 restraints weight = 22295.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.099282 restraints weight = 14216.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.100313 restraints weight = 12136.190| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.270 13529 Z= 0.182 Angle : 0.756 18.217 18530 Z= 0.355 Chirality : 0.046 0.181 1970 Planarity : 0.006 0.071 2327 Dihedral : 8.483 89.840 1858 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.74 % Favored : 89.14 % Rotamer: Outliers : 5.20 % Allowed : 12.65 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.20), residues: 1658 helix: 0.66 (0.17), residues: 838 sheet: -0.25 (0.73), residues: 56 loop : -3.31 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 126 HIS 0.005 0.001 HIS P 111 PHE 0.020 0.002 PHE P 363 TYR 0.016 0.001 TYR R 160 ARG 0.006 0.001 ARG C 193 Details of bonding type rmsd hydrogen bonds : bond 0.05057 ( 629) hydrogen bonds : angle 4.65192 ( 1812) metal coordination : bond 0.01068 ( 8) metal coordination : angle 10.24898 ( 6) SS BOND : bond 0.00422 ( 2) SS BOND : angle 1.38124 ( 4) covalent geometry : bond 0.00433 (13509) covalent geometry : angle 0.73272 (18520) Misc. bond : bond 0.15302 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 277 time to evaluate : 1.740 Fit side-chains Corrupt residue: chain: C residue: PRO 24 >>> skipping revert: symmetry clash Corrupt residue: chain: P residue: PRO 24 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 LYS cc_start: 0.8713 (mttt) cc_final: 0.7302 (tttm) REVERT: C 122 LYS cc_start: 0.8807 (mmtp) cc_final: 0.8602 (mmmm) REVERT: C 253 LEU cc_start: 0.9352 (mt) cc_final: 0.9079 (mp) REVERT: D 103 MET cc_start: 0.9000 (mmm) cc_final: 0.8780 (tpt) REVERT: D 158 PHE cc_start: 0.9040 (t80) cc_final: 0.8490 (t80) REVERT: D 204 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.6561 (tm-30) REVERT: D 208 ASP cc_start: 0.8630 (m-30) cc_final: 0.8086 (m-30) REVERT: D 226 GLN cc_start: 0.7774 (mt0) cc_final: 0.7470 (mp10) REVERT: P 253 LEU cc_start: 0.9373 (mt) cc_final: 0.9093 (mp) REVERT: Q 80 ARG cc_start: 0.8760 (mtm-85) cc_final: 0.8485 (mtp-110) REVERT: Q 96 MET cc_start: 0.8595 (mmt) cc_final: 0.8347 (mmm) REVERT: Q 101 SER cc_start: 0.8740 (m) cc_final: 0.8497 (p) REVERT: Q 155 ASN cc_start: 0.9300 (t0) cc_final: 0.8930 (t0) REVERT: Q 158 PHE cc_start: 0.9156 (t80) cc_final: 0.8532 (t80) REVERT: Q 204 GLN cc_start: 0.7678 (mm-40) cc_final: 0.6720 (tm-30) REVERT: Q 208 ASP cc_start: 0.8604 (m-30) cc_final: 0.7949 (m-30) REVERT: Q 226 GLN cc_start: 0.7828 (mt0) cc_final: 0.7492 (mp10) REVERT: E 37 GLN cc_start: 0.8801 (pp30) cc_final: 0.8146 (pp30) REVERT: E 83 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8445 (tp30) REVERT: E 127 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8027 (tp) REVERT: R 37 GLN cc_start: 0.9241 (pp30) cc_final: 0.8451 (pp30) REVERT: R 38 MET cc_start: 0.9024 (mtp) cc_final: 0.8804 (mtp) REVERT: R 88 VAL cc_start: 0.7297 (t) cc_final: 0.7056 (p) outliers start: 65 outliers final: 50 residues processed: 307 average time/residue: 0.2545 time to fit residues: 113.8215 Evaluate side-chains 304 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 252 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 272 ASN Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 167 CYS Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 169 ILE Chi-restraints excluded: chain P residue 196 SER Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 218 THR Chi-restraints excluded: chain P residue 267 VAL Chi-restraints excluded: chain P residue 272 ASN Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 94 ASP Chi-restraints excluded: chain Q residue 167 CYS Chi-restraints excluded: chain Q residue 233 VAL Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 70 LYS Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain R residue 16 TYR Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 188 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 96 optimal weight: 10.0000 chunk 125 optimal weight: 0.6980 chunk 118 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 81 optimal weight: 0.0570 chunk 63 optimal weight: 2.9990 overall best weight: 1.1300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS C 217 HIS D 31 ASN P 177 GLN Q 31 ASN E 36 ASN R 36 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.127728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.096907 restraints weight = 21756.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.097664 restraints weight = 14194.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.098577 restraints weight = 10434.799| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.214 13529 Z= 0.182 Angle : 0.732 17.159 18530 Z= 0.344 Chirality : 0.046 0.182 1970 Planarity : 0.006 0.065 2327 Dihedral : 8.541 88.344 1858 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.86 % Favored : 89.02 % Rotamer: Outliers : 5.52 % Allowed : 16.09 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.20), residues: 1658 helix: 0.87 (0.17), residues: 824 sheet: -0.15 (0.77), residues: 56 loop : -2.95 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 126 HIS 0.005 0.001 HIS C 212 PHE 0.016 0.002 PHE C 104 TYR 0.016 0.001 TYR D 153 ARG 0.005 0.001 ARG C 193 Details of bonding type rmsd hydrogen bonds : bond 0.04973 ( 629) hydrogen bonds : angle 4.61288 ( 1812) metal coordination : bond 0.01241 ( 8) metal coordination : angle 9.76478 ( 6) SS BOND : bond 0.00305 ( 2) SS BOND : angle 1.07726 ( 4) covalent geometry : bond 0.00445 (13509) covalent geometry : angle 0.71081 (18520) Misc. bond : bond 0.11311 ( 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 333 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 262 time to evaluate : 1.333 Fit side-chains Corrupt residue: chain: C residue: PRO 24 >>> skipping revert: symmetry clash Corrupt residue: chain: P residue: PRO 24 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 122 LYS cc_start: 0.8862 (mmtp) cc_final: 0.8614 (mmtp) REVERT: D 96 MET cc_start: 0.8677 (mmt) cc_final: 0.8333 (mmm) REVERT: D 103 MET cc_start: 0.9118 (mmm) cc_final: 0.8852 (tpt) REVERT: D 158 PHE cc_start: 0.9235 (t80) cc_final: 0.8736 (t80) REVERT: D 183 MET cc_start: 0.8451 (ttm) cc_final: 0.8052 (ttm) REVERT: D 191 GLN cc_start: 0.8350 (mm-40) cc_final: 0.8137 (tp40) REVERT: D 204 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.6557 (tm-30) REVERT: D 208 ASP cc_start: 0.8650 (m-30) cc_final: 0.7942 (m-30) REVERT: D 226 GLN cc_start: 0.7514 (mt0) cc_final: 0.7208 (mt0) REVERT: Q 80 ARG cc_start: 0.8769 (mtm-85) cc_final: 0.8484 (mtp-110) REVERT: Q 155 ASN cc_start: 0.9321 (t0) cc_final: 0.8969 (t0) REVERT: Q 204 GLN cc_start: 0.7842 (mm-40) cc_final: 0.6672 (tm-30) REVERT: Q 208 ASP cc_start: 0.8612 (m-30) cc_final: 0.8031 (m-30) REVERT: Q 226 GLN cc_start: 0.7956 (mt0) cc_final: 0.7645 (mp10) REVERT: E 12 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.5906 (mmt-90) REVERT: E 37 GLN cc_start: 0.8813 (pp30) cc_final: 0.8131 (pp30) REVERT: E 66 LYS cc_start: 0.8528 (tppt) cc_final: 0.8178 (mmtm) REVERT: E 78 ASP cc_start: 0.8304 (t0) cc_final: 0.8018 (m-30) REVERT: R 37 GLN cc_start: 0.9251 (pp30) cc_final: 0.8476 (pp30) REVERT: R 45 LYS cc_start: 0.9014 (mmmm) cc_final: 0.8703 (mtpt) REVERT: R 88 VAL cc_start: 0.7660 (t) cc_final: 0.7201 (p) REVERT: R 129 MET cc_start: 0.7583 (ptp) cc_final: 0.7355 (ptp) outliers start: 71 outliers final: 60 residues processed: 298 average time/residue: 0.2280 time to fit residues: 101.0786 Evaluate side-chains 307 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 245 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 PRO Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 217 HIS Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 272 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 167 CYS Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain P residue 24 PRO Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 196 SER Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 218 THR Chi-restraints excluded: chain P residue 267 VAL Chi-restraints excluded: chain P residue 272 ASN Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain Q residue 94 ASP Chi-restraints excluded: chain Q residue 160 ILE Chi-restraints excluded: chain Q residue 188 VAL Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 70 LYS Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain R residue 16 TYR Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 83 GLU Chi-restraints excluded: chain R residue 110 ASP Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 188 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 109 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 54 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 34 optimal weight: 0.0980 chunk 141 optimal weight: 0.3980 chunk 29 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 217 HIS P 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.129589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.098570 restraints weight = 21948.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.100015 restraints weight = 14547.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.100745 restraints weight = 9922.734| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.5199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.152 13529 Z= 0.131 Angle : 0.668 15.663 18530 Z= 0.321 Chirality : 0.044 0.171 1970 Planarity : 0.005 0.060 2327 Dihedral : 8.375 88.245 1858 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.92 % Favored : 88.96 % Rotamer: Outliers : 4.72 % Allowed : 17.85 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.21), residues: 1658 helix: 1.05 (0.18), residues: 828 sheet: -0.65 (0.75), residues: 60 loop : -2.74 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 126 HIS 0.020 0.001 HIS C 217 PHE 0.014 0.001 PHE C 216 TYR 0.014 0.001 TYR Q 153 ARG 0.004 0.000 ARG C 193 Details of bonding type rmsd hydrogen bonds : bond 0.04519 ( 629) hydrogen bonds : angle 4.41437 ( 1812) metal coordination : bond 0.01414 ( 8) metal coordination : angle 9.16432 ( 6) SS BOND : bond 0.00965 ( 2) SS BOND : angle 1.84167 ( 4) covalent geometry : bond 0.00312 (13509) covalent geometry : angle 0.64717 (18520) Misc. bond : bond 0.08221 ( 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 334 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 275 time to evaluate : 1.308 Fit side-chains Corrupt residue: chain: C residue: PRO 24 >>> skipping Corrupt residue: chain: P residue: PRO 24 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 93 MET cc_start: 0.8461 (mmt) cc_final: 0.8159 (mmt) REVERT: C 104 PHE cc_start: 0.8935 (t80) cc_final: 0.8714 (t80) REVERT: C 122 LYS cc_start: 0.8687 (mmtp) cc_final: 0.8439 (mmtp) REVERT: C 222 ASN cc_start: 0.8695 (t0) cc_final: 0.8218 (t0) REVERT: C 337 PHE cc_start: 0.7716 (m-10) cc_final: 0.7489 (m-10) REVERT: D 31 ASN cc_start: 0.8533 (t0) cc_final: 0.8212 (t0) REVERT: D 158 PHE cc_start: 0.9142 (t80) cc_final: 0.8631 (t80) REVERT: D 191 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8162 (tp40) REVERT: D 204 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.6766 (tm-30) REVERT: D 208 ASP cc_start: 0.8631 (m-30) cc_final: 0.7920 (m-30) REVERT: D 226 GLN cc_start: 0.7596 (mt0) cc_final: 0.7238 (mp10) REVERT: P 104 PHE cc_start: 0.8943 (t80) cc_final: 0.8674 (t80) REVERT: P 177 GLN cc_start: 0.8251 (tt0) cc_final: 0.8051 (mt0) REVERT: P 372 LEU cc_start: 0.8805 (tp) cc_final: 0.8581 (tt) REVERT: Q 80 ARG cc_start: 0.8695 (mtm-85) cc_final: 0.8379 (mtp-110) REVERT: Q 96 MET cc_start: 0.8851 (mmt) cc_final: 0.8537 (mmm) REVERT: Q 155 ASN cc_start: 0.9193 (t0) cc_final: 0.8863 (t0) REVERT: Q 204 GLN cc_start: 0.7831 (mm-40) cc_final: 0.6718 (tm-30) REVERT: Q 208 ASP cc_start: 0.8625 (m-30) cc_final: 0.8061 (m-30) REVERT: Q 226 GLN cc_start: 0.7959 (mt0) cc_final: 0.7564 (mp10) REVERT: E 12 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.5947 (mmm-85) REVERT: E 37 GLN cc_start: 0.8781 (pp30) cc_final: 0.8094 (pp30) REVERT: E 66 LYS cc_start: 0.8208 (tppt) cc_final: 0.7993 (mmtm) REVERT: E 129 MET cc_start: 0.7456 (ptp) cc_final: 0.7198 (ptm) REVERT: R 37 GLN cc_start: 0.9190 (pp30) cc_final: 0.8408 (pp30) REVERT: R 45 LYS cc_start: 0.8989 (mmmm) cc_final: 0.8660 (mtpt) REVERT: R 66 LYS cc_start: 0.8517 (tppt) cc_final: 0.8264 (mmtm) REVERT: R 88 VAL cc_start: 0.7661 (t) cc_final: 0.7342 (p) outliers start: 59 outliers final: 43 residues processed: 308 average time/residue: 0.2251 time to fit residues: 104.4416 Evaluate side-chains 307 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 262 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 272 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 272 ASN Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 94 ASP Chi-restraints excluded: chain Q residue 160 ILE Chi-restraints excluded: chain Q residue 188 VAL Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 188 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 29 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 119 optimal weight: 0.2980 chunk 86 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 156 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.128722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.098070 restraints weight = 22267.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.098891 restraints weight = 14455.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.099916 restraints weight = 11981.641| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.133 13529 Z= 0.145 Angle : 0.697 22.060 18530 Z= 0.327 Chirality : 0.044 0.174 1970 Planarity : 0.005 0.058 2327 Dihedral : 8.365 89.136 1858 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.98 % Favored : 88.90 % Rotamer: Outliers : 4.88 % Allowed : 18.73 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.21), residues: 1658 helix: 1.24 (0.18), residues: 816 sheet: -0.30 (0.74), residues: 56 loop : -2.61 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 126 HIS 0.004 0.001 HIS C 111 PHE 0.014 0.001 PHE C 263 TYR 0.012 0.001 TYR Q 153 ARG 0.009 0.001 ARG C 193 Details of bonding type rmsd hydrogen bonds : bond 0.04530 ( 629) hydrogen bonds : angle 4.38787 ( 1812) metal coordination : bond 0.01143 ( 8) metal coordination : angle 11.30441 ( 6) SS BOND : bond 0.00277 ( 2) SS BOND : angle 1.23298 ( 4) covalent geometry : bond 0.00356 (13509) covalent geometry : angle 0.66707 (18520) Misc. bond : bond 0.07144 ( 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 339 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 277 time to evaluate : 1.445 Fit side-chains Corrupt residue: chain: C residue: PRO 24 >>> skipping Corrupt residue: chain: P residue: PRO 24 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 MET cc_start: 0.9443 (mmm) cc_final: 0.9226 (mmm) REVERT: C 104 PHE cc_start: 0.8929 (t80) cc_final: 0.8695 (t80) REVERT: C 222 ASN cc_start: 0.8665 (t0) cc_final: 0.8213 (t0) REVERT: C 337 PHE cc_start: 0.7675 (m-10) cc_final: 0.7445 (m-10) REVERT: D 158 PHE cc_start: 0.9181 (t80) cc_final: 0.8586 (t80) REVERT: D 160 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8502 (pt) REVERT: D 191 GLN cc_start: 0.8472 (mm-40) cc_final: 0.8176 (tp40) REVERT: D 204 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.6803 (tm-30) REVERT: D 208 ASP cc_start: 0.8598 (m-30) cc_final: 0.7946 (m-30) REVERT: D 226 GLN cc_start: 0.7623 (mt0) cc_final: 0.7184 (mp10) REVERT: D 241 MET cc_start: 0.8113 (tmm) cc_final: 0.7729 (tmm) REVERT: P 40 ASN cc_start: 0.8108 (t0) cc_final: 0.7560 (t0) REVERT: P 104 PHE cc_start: 0.8936 (t80) cc_final: 0.8671 (t80) REVERT: P 372 LEU cc_start: 0.8871 (tp) cc_final: 0.8621 (tt) REVERT: Q 80 ARG cc_start: 0.8715 (mtm-85) cc_final: 0.8372 (mtp-110) REVERT: Q 96 MET cc_start: 0.8885 (mmt) cc_final: 0.8558 (mmm) REVERT: Q 204 GLN cc_start: 0.7927 (mm-40) cc_final: 0.6831 (tm-30) REVERT: Q 208 ASP cc_start: 0.8653 (m-30) cc_final: 0.8098 (m-30) REVERT: Q 226 GLN cc_start: 0.7778 (mt0) cc_final: 0.7351 (mp10) REVERT: E 12 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.5920 (mmm-85) REVERT: E 37 GLN cc_start: 0.8849 (pp30) cc_final: 0.8127 (pp30) REVERT: E 45 LYS cc_start: 0.8854 (mmmm) cc_final: 0.8483 (ttpt) REVERT: E 66 LYS cc_start: 0.8263 (tppt) cc_final: 0.8012 (mmtm) REVERT: R 37 GLN cc_start: 0.9216 (pp30) cc_final: 0.8423 (pp30) REVERT: R 45 LYS cc_start: 0.8964 (mmmm) cc_final: 0.8647 (mtpt) REVERT: R 66 LYS cc_start: 0.8460 (tppt) cc_final: 0.8213 (mmtm) REVERT: R 88 VAL cc_start: 0.7723 (t) cc_final: 0.7417 (p) REVERT: R 89 PRO cc_start: 0.8240 (Cg_endo) cc_final: 0.8038 (Cg_exo) outliers start: 62 outliers final: 46 residues processed: 315 average time/residue: 0.3541 time to fit residues: 168.4766 Evaluate side-chains 315 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 266 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 272 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain P residue 24 PRO Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 169 ILE Chi-restraints excluded: chain P residue 196 SER Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 229 VAL Chi-restraints excluded: chain P residue 272 ASN Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 94 ASP Chi-restraints excluded: chain Q residue 188 VAL Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 187 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 7 optimal weight: 0.9990 chunk 75 optimal weight: 0.1980 chunk 100 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 chunk 110 optimal weight: 0.0370 chunk 137 optimal weight: 5.9990 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 177 GLN ** R 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.129278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.098625 restraints weight = 22162.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.100177 restraints weight = 14970.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.100948 restraints weight = 10123.065| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 13529 Z= 0.137 Angle : 0.690 18.942 18530 Z= 0.327 Chirality : 0.044 0.167 1970 Planarity : 0.005 0.056 2327 Dihedral : 8.404 88.625 1858 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.10 % Favored : 88.78 % Rotamer: Outliers : 4.72 % Allowed : 19.30 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.21), residues: 1658 helix: 1.21 (0.18), residues: 830 sheet: -1.23 (0.60), residues: 76 loop : -2.50 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 126 HIS 0.003 0.001 HIS P 111 PHE 0.013 0.001 PHE C 216 TYR 0.012 0.001 TYR D 153 ARG 0.010 0.001 ARG C 193 Details of bonding type rmsd hydrogen bonds : bond 0.04440 ( 629) hydrogen bonds : angle 4.32794 ( 1812) metal coordination : bond 0.00954 ( 8) metal coordination : angle 10.70099 ( 6) SS BOND : bond 0.00186 ( 2) SS BOND : angle 0.87433 ( 4) covalent geometry : bond 0.00332 (13509) covalent geometry : angle 0.66305 (18520) Misc. bond : bond 0.06486 ( 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 334 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 274 time to evaluate : 2.456 Fit side-chains Corrupt residue: chain: C residue: PRO 24 >>> skipping Corrupt residue: chain: P residue: PRO 24 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 MET cc_start: 0.9441 (mmm) cc_final: 0.9189 (mmm) REVERT: C 222 ASN cc_start: 0.8638 (t0) cc_final: 0.8228 (t0) REVERT: C 337 PHE cc_start: 0.7559 (m-10) cc_final: 0.7296 (m-10) REVERT: D 90 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8519 (t) REVERT: D 143 GLU cc_start: 0.8010 (pm20) cc_final: 0.7803 (tp30) REVERT: D 158 PHE cc_start: 0.9169 (t80) cc_final: 0.8561 (t80) REVERT: D 160 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8516 (pt) REVERT: D 191 GLN cc_start: 0.8446 (mm-40) cc_final: 0.8132 (tp40) REVERT: D 204 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.6799 (tm-30) REVERT: D 208 ASP cc_start: 0.8591 (m-30) cc_final: 0.7932 (m-30) REVERT: D 226 GLN cc_start: 0.7628 (mt0) cc_final: 0.7181 (mp10) REVERT: P 40 ASN cc_start: 0.8093 (t0) cc_final: 0.7561 (t0) REVERT: P 104 PHE cc_start: 0.8935 (t80) cc_final: 0.8694 (t80) REVERT: P 372 LEU cc_start: 0.8837 (tp) cc_final: 0.8589 (tt) REVERT: Q 80 ARG cc_start: 0.8679 (mtm-85) cc_final: 0.8313 (mtp-110) REVERT: Q 96 MET cc_start: 0.8859 (mmt) cc_final: 0.8566 (mmm) REVERT: Q 182 ARG cc_start: 0.7876 (ttp-110) cc_final: 0.7373 (ttm-80) REVERT: Q 183 MET cc_start: 0.8352 (ttm) cc_final: 0.8145 (ttm) REVERT: Q 204 GLN cc_start: 0.7889 (mm-40) cc_final: 0.6726 (tm-30) REVERT: Q 208 ASP cc_start: 0.8603 (m-30) cc_final: 0.8056 (m-30) REVERT: Q 226 GLN cc_start: 0.7725 (mt0) cc_final: 0.7246 (mp10) REVERT: E 12 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.5792 (mmt-90) REVERT: E 37 GLN cc_start: 0.8795 (pp30) cc_final: 0.8040 (pp30) REVERT: E 45 LYS cc_start: 0.8808 (mmmm) cc_final: 0.8506 (ttpt) REVERT: E 66 LYS cc_start: 0.8235 (tppt) cc_final: 0.8021 (mmtm) REVERT: E 103 LYS cc_start: 0.7353 (ptpp) cc_final: 0.6995 (ptpt) REVERT: R 37 GLN cc_start: 0.9202 (pp30) cc_final: 0.8396 (pp30) REVERT: R 45 LYS cc_start: 0.8980 (mmmm) cc_final: 0.8674 (mtpt) REVERT: R 66 LYS cc_start: 0.8481 (tppt) cc_final: 0.8202 (mmtm) REVERT: R 88 VAL cc_start: 0.7749 (t) cc_final: 0.7468 (p) outliers start: 60 outliers final: 49 residues processed: 309 average time/residue: 0.3818 time to fit residues: 179.0328 Evaluate side-chains 308 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 255 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 272 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain P residue 24 PRO Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 169 ILE Chi-restraints excluded: chain P residue 196 SER Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 229 VAL Chi-restraints excluded: chain P residue 272 ASN Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 72 ILE Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 94 ASP Chi-restraints excluded: chain Q residue 188 VAL Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 188 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 4 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 113 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 88 optimal weight: 0.3980 chunk 94 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.125050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.094916 restraints weight = 22457.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.095735 restraints weight = 14186.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.096462 restraints weight = 11354.359| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.5802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.157 13529 Z= 0.187 Angle : 0.750 19.595 18530 Z= 0.353 Chirality : 0.045 0.174 1970 Planarity : 0.005 0.058 2327 Dihedral : 8.459 88.150 1858 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.86 % Favored : 89.02 % Rotamer: Outliers : 5.28 % Allowed : 19.46 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.21), residues: 1658 helix: 1.01 (0.18), residues: 840 sheet: -1.18 (0.61), residues: 76 loop : -2.49 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 126 HIS 0.005 0.001 HIS D 38 PHE 0.014 0.002 PHE P 105 TYR 0.012 0.001 TYR Q 153 ARG 0.010 0.001 ARG C 193 Details of bonding type rmsd hydrogen bonds : bond 0.04966 ( 629) hydrogen bonds : angle 4.56901 ( 1812) metal coordination : bond 0.00956 ( 8) metal coordination : angle 11.18654 ( 6) SS BOND : bond 0.00270 ( 2) SS BOND : angle 1.09094 ( 4) covalent geometry : bond 0.00465 (13509) covalent geometry : angle 0.72212 (18520) Misc. bond : bond 0.09397 ( 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 327 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 259 time to evaluate : 4.131 Fit side-chains Corrupt residue: chain: C residue: PRO 24 >>> skipping Corrupt residue: chain: P residue: PRO 24 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 337 PHE cc_start: 0.7721 (m-10) cc_final: 0.7456 (m-10) REVERT: D 99 ASP cc_start: 0.8301 (t0) cc_final: 0.7845 (m-30) REVERT: D 143 GLU cc_start: 0.8059 (pm20) cc_final: 0.7782 (tp30) REVERT: D 191 GLN cc_start: 0.8396 (mm-40) cc_final: 0.8071 (tp40) REVERT: D 204 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.6739 (tm-30) REVERT: D 208 ASP cc_start: 0.8598 (m-30) cc_final: 0.7959 (m-30) REVERT: D 226 GLN cc_start: 0.7595 (mt0) cc_final: 0.7096 (mp10) REVERT: P 40 ASN cc_start: 0.8380 (t0) cc_final: 0.7721 (t0) REVERT: Q 96 MET cc_start: 0.8891 (mmt) cc_final: 0.8590 (mmm) REVERT: Q 99 ASP cc_start: 0.8309 (t0) cc_final: 0.8087 (t0) REVERT: Q 182 ARG cc_start: 0.7881 (ttp-110) cc_final: 0.7436 (ttm-80) REVERT: Q 204 GLN cc_start: 0.8013 (mm-40) cc_final: 0.7339 (tm-30) REVERT: Q 226 GLN cc_start: 0.7659 (mt0) cc_final: 0.7151 (mp10) REVERT: E 12 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.5817 (mmt-90) REVERT: E 37 GLN cc_start: 0.9036 (pp30) cc_final: 0.8743 (pp30) REVERT: E 66 LYS cc_start: 0.8336 (tppt) cc_final: 0.8134 (mmtm) REVERT: E 83 GLU cc_start: 0.8294 (mp0) cc_final: 0.7981 (tp30) REVERT: E 103 LYS cc_start: 0.7315 (ptpp) cc_final: 0.6973 (ptpt) REVERT: E 168 LYS cc_start: 0.7823 (tttp) cc_final: 0.7557 (ttmm) REVERT: R 37 GLN cc_start: 0.9259 (pp30) cc_final: 0.8411 (pp30) REVERT: R 45 LYS cc_start: 0.8949 (mmmm) cc_final: 0.8590 (mtpt) REVERT: R 66 LYS cc_start: 0.8412 (tppt) cc_final: 0.8147 (mmtm) REVERT: R 88 VAL cc_start: 0.7849 (t) cc_final: 0.7561 (p) outliers start: 68 outliers final: 54 residues processed: 300 average time/residue: 0.3569 time to fit residues: 166.0822 Evaluate side-chains 304 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 248 time to evaluate : 2.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 PRO Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 272 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain P residue 24 PRO Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 169 ILE Chi-restraints excluded: chain P residue 196 SER Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 267 VAL Chi-restraints excluded: chain P residue 272 ASN Chi-restraints excluded: chain P residue 288 THR Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 94 ASP Chi-restraints excluded: chain Q residue 188 VAL Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 97 SER Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 188 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 49 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 58 GLN P 72 HIS ** R 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.126065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.095781 restraints weight = 22261.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.096409 restraints weight = 14625.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.096996 restraints weight = 11974.706| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.5934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.143 13529 Z= 0.165 Angle : 0.725 18.531 18530 Z= 0.343 Chirality : 0.045 0.169 1970 Planarity : 0.005 0.056 2327 Dihedral : 8.535 86.733 1858 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.80 % Favored : 89.08 % Rotamer: Outliers : 4.88 % Allowed : 20.02 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.21), residues: 1658 helix: 1.01 (0.18), residues: 840 sheet: -1.33 (0.60), residues: 76 loop : -2.43 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 126 HIS 0.005 0.001 HIS C 111 PHE 0.013 0.001 PHE C 104 TYR 0.010 0.001 TYR Q 153 ARG 0.008 0.001 ARG C 193 Details of bonding type rmsd hydrogen bonds : bond 0.04760 ( 629) hydrogen bonds : angle 4.50401 ( 1812) metal coordination : bond 0.01236 ( 8) metal coordination : angle 11.56549 ( 6) SS BOND : bond 0.00238 ( 2) SS BOND : angle 0.99884 ( 4) covalent geometry : bond 0.00410 (13509) covalent geometry : angle 0.69423 (18520) Misc. bond : bond 0.08188 ( 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 325 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 263 time to evaluate : 1.299 Fit side-chains Corrupt residue: chain: C residue: PRO 24 >>> skipping Corrupt residue: chain: P residue: PRO 24 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 222 ASN cc_start: 0.8578 (t0) cc_final: 0.8244 (t0) REVERT: C 337 PHE cc_start: 0.7712 (m-10) cc_final: 0.7455 (m-10) REVERT: D 191 GLN cc_start: 0.8399 (mm-40) cc_final: 0.8082 (tp40) REVERT: D 204 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.6746 (tm-30) REVERT: D 208 ASP cc_start: 0.8601 (m-30) cc_final: 0.7966 (m-30) REVERT: D 226 GLN cc_start: 0.7575 (mt0) cc_final: 0.7099 (mp10) REVERT: P 40 ASN cc_start: 0.8401 (t0) cc_final: 0.7763 (t0) REVERT: P 372 LEU cc_start: 0.8871 (tp) cc_final: 0.8621 (tt) REVERT: P 383 MET cc_start: 0.8493 (mmm) cc_final: 0.8206 (mmm) REVERT: Q 96 MET cc_start: 0.8912 (mmt) cc_final: 0.8607 (mmm) REVERT: Q 182 ARG cc_start: 0.7779 (ttp-110) cc_final: 0.7448 (ttm-80) REVERT: Q 204 GLN cc_start: 0.7849 (mm-40) cc_final: 0.7143 (tm-30) REVERT: Q 226 GLN cc_start: 0.7664 (mt0) cc_final: 0.7184 (mp10) REVERT: E 12 ARG cc_start: 0.6874 (OUTLIER) cc_final: 0.5650 (mmt-90) REVERT: E 37 GLN cc_start: 0.8954 (pp30) cc_final: 0.8657 (pp30) REVERT: E 83 GLU cc_start: 0.8206 (mp0) cc_final: 0.7881 (tp30) REVERT: E 103 LYS cc_start: 0.7312 (ptpp) cc_final: 0.7006 (ptpt) REVERT: R 37 GLN cc_start: 0.9212 (pp30) cc_final: 0.8344 (pp30) REVERT: R 45 LYS cc_start: 0.8953 (mmmm) cc_final: 0.8551 (mtpt) REVERT: R 66 LYS cc_start: 0.8383 (tppt) cc_final: 0.8134 (mmtm) outliers start: 62 outliers final: 51 residues processed: 300 average time/residue: 0.2162 time to fit residues: 98.6608 Evaluate side-chains 299 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 246 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 272 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain P residue 24 PRO Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 169 ILE Chi-restraints excluded: chain P residue 196 SER Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 267 VAL Chi-restraints excluded: chain P residue 272 ASN Chi-restraints excluded: chain P residue 288 THR Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain Q residue 188 VAL Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 188 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 152 optimal weight: 0.7980 chunk 67 optimal weight: 0.0370 chunk 82 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 0.1980 chunk 30 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.129205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.099085 restraints weight = 22454.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.099861 restraints weight = 14434.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.100622 restraints weight = 11791.468| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.6072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 13529 Z= 0.136 Angle : 0.711 17.703 18530 Z= 0.337 Chirality : 0.043 0.164 1970 Planarity : 0.005 0.058 2327 Dihedral : 8.362 84.000 1858 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.74 % Favored : 89.14 % Rotamer: Outliers : 4.00 % Allowed : 21.46 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.21), residues: 1658 helix: 1.27 (0.18), residues: 828 sheet: -1.43 (0.58), residues: 76 loop : -2.35 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 126 HIS 0.004 0.001 HIS C 111 PHE 0.015 0.001 PHE P 104 TYR 0.009 0.001 TYR Q 153 ARG 0.009 0.000 ARG C 193 Details of bonding type rmsd hydrogen bonds : bond 0.04445 ( 629) hydrogen bonds : angle 4.35776 ( 1812) metal coordination : bond 0.01117 ( 8) metal coordination : angle 11.17173 ( 6) SS BOND : bond 0.00204 ( 2) SS BOND : angle 0.78908 ( 4) covalent geometry : bond 0.00326 (13509) covalent geometry : angle 0.68256 (18520) Misc. bond : bond 0.06138 ( 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 312 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 261 time to evaluate : 1.404 Fit side-chains Corrupt residue: chain: C residue: PRO 24 >>> skipping Corrupt residue: chain: P residue: PRO 24 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 MET cc_start: 0.9264 (mmm) cc_final: 0.8857 (mmm) REVERT: D 191 GLN cc_start: 0.8328 (mm-40) cc_final: 0.8046 (tp40) REVERT: D 204 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.6819 (tm-30) REVERT: D 208 ASP cc_start: 0.8586 (m-30) cc_final: 0.7944 (m-30) REVERT: D 226 GLN cc_start: 0.7496 (mt0) cc_final: 0.7050 (mp10) REVERT: P 40 ASN cc_start: 0.8162 (t0) cc_final: 0.7616 (t0) REVERT: P 104 PHE cc_start: 0.8823 (t80) cc_final: 0.8521 (t80) REVERT: P 372 LEU cc_start: 0.8807 (tp) cc_final: 0.8576 (tt) REVERT: Q 96 MET cc_start: 0.8866 (mmt) cc_final: 0.8610 (mmm) REVERT: Q 99 ASP cc_start: 0.8045 (t70) cc_final: 0.7717 (t0) REVERT: Q 182 ARG cc_start: 0.7677 (ttp-110) cc_final: 0.7370 (ttm-80) REVERT: Q 204 GLN cc_start: 0.7929 (mm-40) cc_final: 0.6774 (tm-30) REVERT: Q 208 ASP cc_start: 0.8529 (m-30) cc_final: 0.7946 (m-30) REVERT: Q 226 GLN cc_start: 0.7593 (mt0) cc_final: 0.7089 (mp10) REVERT: E 12 ARG cc_start: 0.6877 (OUTLIER) cc_final: 0.5712 (mmt-90) REVERT: E 37 GLN cc_start: 0.8904 (pp30) cc_final: 0.8617 (pp30) REVERT: E 83 GLU cc_start: 0.8286 (mp0) cc_final: 0.7932 (tp30) REVERT: E 89 PRO cc_start: 0.7795 (Cg_endo) cc_final: 0.7406 (Cg_exo) REVERT: E 103 LYS cc_start: 0.7219 (ptpp) cc_final: 0.7011 (ptpt) REVERT: R 37 GLN cc_start: 0.9153 (pp30) cc_final: 0.8264 (pp30) REVERT: R 45 LYS cc_start: 0.8912 (mmmm) cc_final: 0.8508 (mtpt) REVERT: R 47 MET cc_start: 0.8365 (mmt) cc_final: 0.8157 (mmt) REVERT: R 66 LYS cc_start: 0.8369 (tppt) cc_final: 0.8071 (mmtm) outliers start: 51 outliers final: 45 residues processed: 289 average time/residue: 0.2281 time to fit residues: 99.5225 Evaluate side-chains 293 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 246 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 272 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain P residue 24 PRO Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 169 ILE Chi-restraints excluded: chain P residue 196 SER Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 229 VAL Chi-restraints excluded: chain P residue 272 ASN Chi-restraints excluded: chain P residue 288 THR Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain Q residue 94 ASP Chi-restraints excluded: chain Q residue 101 SER Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 97 SER Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 83 GLU Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 188 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 41 optimal weight: 0.7980 chunk 143 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 138 optimal weight: 8.9990 chunk 136 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 28 optimal weight: 0.0970 chunk 156 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.124578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.094612 restraints weight = 22693.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.095097 restraints weight = 15152.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.095835 restraints weight = 12859.608| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.6159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.155 13529 Z= 0.207 Angle : 0.759 16.274 18530 Z= 0.362 Chirality : 0.046 0.172 1970 Planarity : 0.005 0.058 2327 Dihedral : 8.517 89.890 1858 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.98 % Favored : 88.90 % Rotamer: Outliers : 4.32 % Allowed : 21.14 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.21), residues: 1658 helix: 1.09 (0.18), residues: 828 sheet: -1.56 (0.58), residues: 76 loop : -2.42 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 126 HIS 0.007 0.001 HIS D 38 PHE 0.017 0.002 PHE P 104 TYR 0.013 0.001 TYR C 199 ARG 0.007 0.001 ARG C 193 Details of bonding type rmsd hydrogen bonds : bond 0.05136 ( 629) hydrogen bonds : angle 4.62213 ( 1812) metal coordination : bond 0.01322 ( 8) metal coordination : angle 10.47348 ( 6) SS BOND : bond 0.00314 ( 2) SS BOND : angle 1.13825 ( 4) covalent geometry : bond 0.00522 (13509) covalent geometry : angle 0.73486 (18520) Misc. bond : bond 0.10011 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5012.86 seconds wall clock time: 92 minutes 41.98 seconds (5561.98 seconds total)