Starting phenix.real_space_refine on Thu Jul 31 05:58:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xkv_22226/07_2025/6xkv_22226.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xkv_22226/07_2025/6xkv_22226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xkv_22226/07_2025/6xkv_22226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xkv_22226/07_2025/6xkv_22226.map" model { file = "/net/cci-nas-00/data/ceres_data/6xkv_22226/07_2025/6xkv_22226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xkv_22226/07_2025/6xkv_22226.cif" } resolution = 3.5 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 14 residue(s): 0.03s 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 31.625 67.838 38.027 0.25105.87 S ATOM 11162 SG CYS E 153 30.491 64.409 37.476 0.25107.21 S ATOM 12381 SG CYS R 133 82.719 27.940 38.570 0.25105.87 S ATOM 12527 SG CYS R 153 83.841 31.371 38.015 0.25107.21 S Residues with excluded nonbonded symmetry interactions: 52 residue: pdb=" N MET E 129 " occ=0.25 ... (6 atoms not shown) pdb=" CE MET E 129 " occ=0.25 residue: pdb=" N GLY E 131 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY E 131 " occ=0.25 residue: pdb=" N VAL E 132 " occ=0.25 ... (5 atoms not shown) pdb=" CG2 VAL E 132 " occ=0.25 residue: pdb=" N CYS E 133 " occ=0.25 ... (4 atoms not shown) pdb=" SG CYS E 133 " occ=0.25 residue: pdb=" N THR E 134 " occ=0.25 ... (5 atoms not shown) pdb=" CG2 THR E 134 " occ=0.25 residue: pdb=" N HIS E 135 " occ=0.25 ... (8 atoms not shown) pdb=" NE2 HIS E 135 " occ=0.25 residue: pdb=" N LEU E 136 " occ=0.25 ... (6 atoms not shown) pdb=" CD2 LEU E 136 " occ=0.25 residue: pdb=" N GLY E 137 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY E 137 " occ=0.25 residue: pdb=" N CYS E 138 " occ=0.25 ... (4 atoms not shown) pdb=" SG CYS E 138 " occ=0.25 residue: pdb=" N VAL E 139 " occ=0.25 ... (5 atoms not shown) pdb=" CG2 VAL E 139 " occ=0.25 residue: pdb=" N PRO E 140 " occ=0.25 ... (5 atoms not shown) pdb=" CD PRO E 140 " occ=0.25 residue: pdb=" N GLY E 142 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY E 142 " occ=0.25 ... (remaining 40 not shown) Time building chain proxies: 8.55, per 1000 atoms: 0.65 Number of scatterers: 13079 At special positions: 0 Unit cell: (115.6, 96.56, 107.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 10 26.01 S 78 16.00 O 2258 8.00 N 2155 7.00 C 8578 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 155 " distance=2.03 Simple disulfide: pdb=" SG CYS R 138 " - pdb=" SG CYS R 155 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.58 Conformation dependent library (CDL) restraints added in 1.7 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 135 " pdb="FE2 FES R 501 " - pdb=" ND1 HIS R 156 " pdb="FE1 FES R 501 " - pdb=" SG CYS R 133 " pdb="FE1 FES R 501 " - pdb=" SG CYS R 153 " Number of angles added : 6 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3056 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 8 sheets defined 51.8% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 33 removed outlier: 3.764A pdb=" N GLY C 27 " --> pdb=" O LEU C 23 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE C 33 " --> pdb=" O VAL C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 66 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 90 through 118 removed outlier: 3.757A pdb=" N SER C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 148 removed outlier: 3.860A pdb=" N TRP C 129 " --> pdb=" O ARG C 125 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL C 148 " --> pdb=" O PHE C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 169 removed outlier: 3.623A pdb=" N TRP C 157 " --> pdb=" O GLN C 153 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N PHE C 166 " --> pdb=" O ILE C 162 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY C 167 " --> pdb=" O THR C 163 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 182 removed outlier: 3.668A pdb=" N ILE C 176 " --> pdb=" O ILE C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 199 Processing helix chain 'C' and resid 200 through 219 removed outlier: 3.959A pdb=" N VAL C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE C 216 " --> pdb=" O HIS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 270 Processing helix chain 'C' and resid 276 through 281 Processing helix chain 'C' and resid 298 through 308 removed outlier: 4.405A pdb=" N PHE C 308 " --> pdb=" O ILE C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 321 Processing helix chain 'C' and resid 327 through 346 removed outlier: 3.848A pdb=" N MET C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 356 through 359 Processing helix chain 'C' and resid 360 through 381 Processing helix chain 'C' and resid 388 through 415 removed outlier: 5.577A pdb=" N LEU C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Proline residue: C 409 - end of helix Processing helix chain 'D' and resid 19 through 33 removed outlier: 3.629A pdb=" N LEU D 23 " --> pdb=" O ASP D 19 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU D 32 " --> pdb=" O GLN D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 37 Processing helix chain 'D' and resid 44 through 49 Processing helix chain 'D' and resid 57 through 67 Processing helix chain 'D' and resid 127 through 136 Processing helix chain 'D' and resid 164 through 168 Processing helix chain 'D' and resid 201 through 218 Processing helix chain 'D' and resid 220 through 250 Processing helix chain 'P' and resid 14 through 19 Processing helix chain 'P' and resid 23 through 33 removed outlier: 3.762A pdb=" N GLY P 27 " --> pdb=" O LEU P 23 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE P 33 " --> pdb=" O VAL P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 66 Processing helix chain 'P' and resid 75 through 86 Processing helix chain 'P' and resid 90 through 118 removed outlier: 3.754A pdb=" N SER P 102 " --> pdb=" O ALA P 98 " (cutoff:3.500A) Processing helix chain 'P' and resid 125 through 148 removed outlier: 3.859A pdb=" N TRP P 129 " --> pdb=" O ARG P 125 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL P 148 " --> pdb=" O PHE P 144 " (cutoff:3.500A) Processing helix chain 'P' and resid 153 through 169 removed outlier: 3.623A pdb=" N TRP P 157 " --> pdb=" O GLN P 153 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N PHE P 166 " --> pdb=" O ILE P 162 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY P 167 " --> pdb=" O THR P 163 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE P 169 " --> pdb=" O LEU P 165 " (cutoff:3.500A) Processing helix chain 'P' and resid 172 through 182 removed outlier: 3.669A pdb=" N ILE P 176 " --> pdb=" O ILE P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 187 through 199 Processing helix chain 'P' and resid 200 through 219 removed outlier: 3.957A pdb=" N VAL P 204 " --> pdb=" O LEU P 200 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE P 216 " --> pdb=" O HIS P 212 " (cutoff:3.500A) Processing helix chain 'P' and resid 246 through 270 Processing helix chain 'P' and resid 276 through 281 Processing helix chain 'P' and resid 298 through 308 removed outlier: 4.405A pdb=" N PHE P 308 " --> pdb=" O ILE P 304 " (cutoff:3.500A) Processing helix chain 'P' and resid 316 through 321 Processing helix chain 'P' and resid 327 through 346 removed outlier: 3.847A pdb=" N MET P 343 " --> pdb=" O ALA P 339 " (cutoff:3.500A) Processing helix chain 'P' and resid 347 through 349 No H-bonds generated for 'chain 'P' and resid 347 through 349' Processing helix chain 'P' and resid 356 through 359 Processing helix chain 'P' and resid 360 through 381 Processing helix chain 'P' and resid 388 through 415 removed outlier: 5.576A pdb=" N LEU P 408 " --> pdb=" O PHE P 404 " (cutoff:3.500A) Proline residue: P 409 - end of helix Processing helix chain 'Q' and resid 19 through 33 removed outlier: 3.628A pdb=" N LEU Q 23 " --> pdb=" O ASP Q 19 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU Q 32 " --> pdb=" O GLN Q 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 34 through 37 Processing helix chain 'Q' and resid 44 through 49 removed outlier: 3.567A pdb=" N THR Q 47 " --> pdb=" O PRO Q 44 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU Q 48 " --> pdb=" O ILE Q 45 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA Q 49 " --> pdb=" O ARG Q 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 44 through 49' Processing helix chain 'Q' and resid 57 through 67 Processing helix chain 'Q' and resid 127 through 136 Processing helix chain 'Q' and resid 201 through 218 Processing helix chain 'Q' and resid 220 through 250 Processing helix chain 'E' and resid 12 through 37 Proline residue: E 33 - end of helix Processing helix chain 'E' and resid 41 through 46 removed outlier: 3.563A pdb=" N ALA E 46 " --> pdb=" O ALA E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 87 Processing helix chain 'E' and resid 109 through 114 Processing helix chain 'R' and resid 12 through 37 Proline residue: R 33 - end of helix Processing helix chain 'R' and resid 41 through 46 removed outlier: 3.563A pdb=" N ALA R 46 " --> pdb=" O ALA R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 87 Processing helix chain 'R' and resid 109 through 114 Processing sheet with id=AA1, first strand: chain 'D' and resid 153 through 155 Processing sheet with id=AA2, first strand: chain 'Q' and resid 153 through 155 Processing sheet with id=AA3, first strand: chain 'E' and resid 50 through 52 removed outlier: 3.606A pdb=" N ALA E 181 " --> pdb=" O LYS E 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 64 through 67 Processing sheet with id=AA5, first strand: chain 'E' and resid 141 through 145 removed outlier: 4.682A pdb=" N ASP E 143 " --> pdb=" O GLY E 150 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N GLY E 150 " --> pdb=" O ASP E 143 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TRP E 151 " --> pdb=" O TYR E 160 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER E 158 " --> pdb=" O CYS E 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 50 through 52 removed outlier: 3.607A pdb=" N ALA R 181 " --> pdb=" O LYS R 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 64 through 67 Processing sheet with id=AA8, first strand: chain 'R' and resid 141 through 145 removed outlier: 4.683A pdb=" N ASP R 143 " --> pdb=" O GLY R 150 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLY R 150 " --> pdb=" O ASP R 143 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TRP R 151 " --> pdb=" O TYR R 160 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER R 158 " --> pdb=" O CYS R 153 " (cutoff:3.500A) 631 hydrogen bonds defined for protein. 1812 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.48 Time building geometry restraints manager: 4.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.41: 5786 1.41 - 1.61: 7561 1.61 - 1.80: 99 1.80 - 2.00: 35 2.00 - 2.20: 28 Bond restraints: 13509 Sorted by residual: bond pdb=" CAC HEC C 501 " pdb=" CBC HEC C 501 " ideal model delta sigma weight residual 1.544 1.324 0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" CAC HEC P 501 " pdb=" CBC HEC P 501 " ideal model delta sigma weight residual 1.544 1.325 0.219 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C2D HEC C 501 " pdb=" C3D HEC C 501 " ideal model delta sigma weight residual 1.544 1.336 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" CAB HEC C 501 " pdb=" CBB HEC C 501 " ideal model delta sigma weight residual 1.544 1.336 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" CAB HEC P 501 " pdb=" CBB HEC P 501 " ideal model delta sigma weight residual 1.544 1.336 0.208 2.00e-02 2.50e+03 1.08e+02 ... (remaining 13504 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 18183 3.16 - 6.32: 288 6.32 - 9.48: 28 9.48 - 12.63: 4 12.63 - 15.79: 17 Bond angle restraints: 18520 Sorted by residual: angle pdb="FE1 FES R 501 " pdb=" S2 FES R 501 " pdb="FE2 FES R 501 " ideal model delta sigma weight residual 75.66 89.12 -13.46 1.14e+00 7.69e-01 1.39e+02 angle pdb="FE1 FES E 501 " pdb=" S2 FES E 501 " pdb="FE2 FES E 501 " ideal model delta sigma weight residual 75.66 89.10 -13.44 1.14e+00 7.69e-01 1.39e+02 angle pdb=" S1 FES E 501 " pdb="FE2 FES E 501 " pdb=" S2 FES E 501 " ideal model delta sigma weight residual 104.33 90.92 13.41 1.14e+00 7.69e-01 1.38e+02 angle pdb=" S1 FES R 501 " pdb="FE2 FES R 501 " pdb=" S2 FES R 501 " ideal model delta sigma weight residual 104.33 90.93 13.40 1.14e+00 7.69e-01 1.38e+02 angle pdb=" S1 FES R 501 " pdb="FE1 FES R 501 " pdb=" S2 FES R 501 " ideal model delta sigma weight residual 104.33 90.79 13.54 1.20e+00 6.94e-01 1.27e+02 ... (remaining 18515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 6978 17.90 - 35.80: 536 35.80 - 53.69: 79 53.69 - 71.59: 10 71.59 - 89.49: 22 Dihedral angle restraints: 7625 sinusoidal: 2835 harmonic: 4790 Sorted by residual: dihedral pdb=" C2B HEC P 501 " pdb=" C3B HEC P 501 " pdb=" CAB HEC P 501 " pdb=" CBB HEC P 501 " ideal model delta sinusoidal sigma weight residual 60.00 -22.24 82.24 2 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" C2B HEC C 501 " pdb=" C3B HEC C 501 " pdb=" CAB HEC C 501 " pdb=" CBB HEC C 501 " ideal model delta sinusoidal sigma weight residual 60.00 -22.11 82.11 2 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" C2C HEC P 502 " pdb=" C3C HEC P 502 " pdb=" CAC HEC P 502 " pdb=" CBC HEC P 502 " ideal model delta sinusoidal sigma weight residual 60.00 -17.15 77.15 2 1.00e+01 1.00e-02 4.56e+01 ... (remaining 7622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 1911 0.146 - 0.292: 46 0.292 - 0.439: 1 0.439 - 0.585: 10 0.585 - 0.731: 2 Chirality restraints: 1970 Sorted by residual: chirality pdb=" CG LEU Q 244 " pdb=" CB LEU Q 244 " pdb=" CD1 LEU Q 244 " pdb=" CD2 LEU Q 244 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" CG LEU D 244 " pdb=" CB LEU D 244 " pdb=" CD1 LEU D 244 " pdb=" CD2 LEU D 244 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" CB THR Q 198 " pdb=" CA THR Q 198 " pdb=" OG1 THR Q 198 " pdb=" CG2 THR Q 198 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.53 2.00e-01 2.50e+01 6.91e+00 ... (remaining 1967 not shown) Planarity restraints: 2327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC Q 501 " 0.009 2.00e-02 2.50e+03 4.12e-02 3.82e+01 pdb=" C2C HEC Q 501 " -0.110 2.00e-02 2.50e+03 pdb=" C3C HEC Q 501 " 0.042 2.00e-02 2.50e+03 pdb=" C4C HEC Q 501 " 0.007 2.00e-02 2.50e+03 pdb=" CAC HEC Q 501 " 0.007 2.00e-02 2.50e+03 pdb=" CHC HEC Q 501 " 0.018 2.00e-02 2.50e+03 pdb=" CHD HEC Q 501 " -0.007 2.00e-02 2.50e+03 pdb=" CMC HEC Q 501 " 0.031 2.00e-02 2.50e+03 pdb=" NC HEC Q 501 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC D 501 " -0.009 2.00e-02 2.50e+03 4.11e-02 3.79e+01 pdb=" C2C HEC D 501 " 0.109 2.00e-02 2.50e+03 pdb=" C3C HEC D 501 " -0.042 2.00e-02 2.50e+03 pdb=" C4C HEC D 501 " -0.007 2.00e-02 2.50e+03 pdb=" CAC HEC D 501 " -0.007 2.00e-02 2.50e+03 pdb=" CHC HEC D 501 " -0.018 2.00e-02 2.50e+03 pdb=" CHD HEC D 501 " 0.007 2.00e-02 2.50e+03 pdb=" CMC HEC D 501 " -0.031 2.00e-02 2.50e+03 pdb=" NC HEC D 501 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 222 " -0.021 2.00e-02 2.50e+03 4.28e-02 1.83e+01 pdb=" C ASN C 222 " 0.074 2.00e-02 2.50e+03 pdb=" O ASN C 222 " -0.028 2.00e-02 2.50e+03 pdb=" N ASN C 223 " -0.025 2.00e-02 2.50e+03 ... (remaining 2324 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 156 2.57 - 3.15: 11758 3.15 - 3.73: 19507 3.73 - 4.32: 27392 4.32 - 4.90: 45655 Nonbonded interactions: 104468 Sorted by model distance: nonbonded pdb=" O THR R 186 " pdb=" OG1 THR R 187 " model vdw 1.987 3.040 nonbonded pdb=" O THR E 186 " pdb=" OG1 THR E 187 " model vdw 1.987 3.040 nonbonded pdb=" OG SER P 120 " pdb=" ND2 ASN P 222 " model vdw 1.988 3.120 nonbonded pdb=" NH2 ARG C 306 " pdb=" O MET C 383 " model vdw 2.006 3.120 nonbonded pdb=" NH2 ARG P 306 " pdb=" O MET P 383 " model vdw 2.007 3.120 ... (remaining 104463 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'P' } ncs_group { reference = (chain 'D' and (resid 5 through 80 or (resid 81 and (name N or name CA or name C \ or name O or name CB )) or resid 82 or (resid 83 and (name N or name CA or name \ C or name O or name CB )) or resid 84 through 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: 0.010 Normalize map: mean=0, sd=1: 25.430 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: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 34.570 Find NCS groups from input model: 0.430 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.220 13529 Z= 0.474 Angle : 1.049 23.239 18530 Z= 0.637 Chirality : 0.070 0.731 1970 Planarity : 0.007 0.082 2327 Dihedral : 13.755 89.490 4563 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 23.35 Ramachandran Plot: Outliers : 0.42 % Allowed : 16.41 % Favored : 83.17 % Rotamer: Outliers : 0.08 % Allowed : 3.04 % Favored : 96.88 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.31 (0.17), residues: 1658 helix: -1.65 (0.16), residues: 784 sheet: -3.39 (0.48), residues: 64 loop : -4.22 (0.18), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 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 E 75 Details of bonding type rmsd hydrogen bonds : bond 0.14451 ( 631) hydrogen bonds : angle 6.99308 ( 1812) metal coordination : bond 0.01145 ( 8) metal coordination : angle 14.22020 ( 6) SS BOND : bond 0.00172 ( 2) SS BOND : angle 0.56970 ( 4) covalent geometry : bond 0.00945 (13509) covalent geometry : angle 1.01798 (18520) Misc. bond : bond 0.14979 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 291 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 231 ARG cc_start: 0.8472 (ptp-170) cc_final: 0.8212 (ptp-170) REVERT: C 351 THR cc_start: 0.8113 (p) cc_final: 0.7549 (p) REVERT: D 14 ILE cc_start: 0.8784 (mp) cc_final: 0.8577 (mt) REVERT: D 165 ASP cc_start: 0.6750 (m-30) cc_final: 0.6381 (m-30) REVERT: D 196 ASP cc_start: 0.8044 (p0) cc_final: 0.7757 (p0) REVERT: P 222 ASN cc_start: 0.7704 (t0) cc_final: 0.7276 (t0) REVERT: P 334 ILE cc_start: 0.8882 (mt) cc_final: 0.8667 (mt) REVERT: Q 14 ILE cc_start: 0.8568 (mp) cc_final: 0.8364 (mt) REVERT: E 13 ASP cc_start: 0.5978 (p0) cc_final: 0.5733 (m-30) REVERT: E 94 ARG cc_start: 0.6015 (ttm-80) cc_final: 0.5510 (mpt180) REVERT: E 118 PHE cc_start: 0.5907 (m-80) cc_final: 0.5507 (m-80) REVERT: E 119 ASP cc_start: 0.5752 (t0) cc_final: 0.4514 (m-30) REVERT: E 165 ARG cc_start: 0.5899 (mtm-85) cc_final: 0.5616 (mtm-85) REVERT: R 139 VAL cc_start: 0.6400 (t) cc_final: 0.5308 (t) REVERT: R 158 SER cc_start: 0.1845 (m) cc_final: 0.1597 (m) REVERT: R 161 ASP cc_start: 0.6263 (p0) cc_final: 0.6009 (p0) outliers start: 1 outliers final: 1 residues processed: 292 average time/residue: 0.2961 time to fit residues: 121.7139 Evaluate side-chains 190 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 9.9990 chunk 125 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 HIS C 153 GLN D 20 GLN D 159 GLN D 177 HIS P 68 HIS P 99 ASN P 153 GLN P 222 ASN E 17 HIS E 100 ASN R 17 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.156824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.123364 restraints weight = 17074.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.121822 restraints weight = 19632.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.122504 restraints weight = 17461.896| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.267 13529 Z= 0.192 Angle : 0.764 11.247 18530 Z= 0.369 Chirality : 0.047 0.199 1970 Planarity : 0.006 0.076 2327 Dihedral : 8.659 87.426 1861 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.70 % Favored : 88.12 % Rotamer: Outliers : 2.40 % Allowed : 11.05 % Favored : 86.55 % 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: -2.34 (0.19), residues: 1658 helix: 0.15 (0.17), residues: 812 sheet: -2.12 (0.59), residues: 70 loop : -3.55 (0.19), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP P 157 HIS 0.004 0.001 HIS P 111 PHE 0.025 0.002 PHE P 113 TYR 0.029 0.002 TYR C 199 ARG 0.005 0.001 ARG Q 82 Details of bonding type rmsd hydrogen bonds : bond 0.05380 ( 631) hydrogen bonds : angle 4.83978 ( 1812) metal coordination : bond 0.01116 ( 8) metal coordination : angle 7.56866 ( 6) SS BOND : bond 0.00161 ( 2) SS BOND : angle 0.43879 ( 4) covalent geometry : bond 0.00454 (13509) covalent geometry : angle 0.75240 (18520) Misc. bond : bond 0.14774 ( 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 256 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 226 time to evaluate : 1.794 Fit side-chains revert: symmetry clash REVERT: C 122 LYS cc_start: 0.9177 (mmtm) cc_final: 0.8974 (mmtm) REVERT: C 252 ASP cc_start: 0.7436 (m-30) cc_final: 0.7220 (m-30) REVERT: C 351 THR cc_start: 0.8509 (p) cc_final: 0.8137 (p) REVERT: D 50 ASP cc_start: 0.8044 (m-30) cc_final: 0.7540 (m-30) REVERT: D 79 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7560 (mm-30) REVERT: D 218 GLU cc_start: 0.8236 (mm-30) cc_final: 0.8009 (tp30) REVERT: Q 79 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7419 (mm-30) REVERT: Q 87 MET cc_start: 0.8926 (mtt) cc_final: 0.8408 (mtt) REVERT: Q 99 ASP cc_start: 0.8293 (t0) cc_final: 0.7774 (t70) REVERT: Q 218 GLU cc_start: 0.8232 (mm-30) cc_final: 0.8003 (tp30) REVERT: E 68 ARG cc_start: 0.7136 (ttt180) cc_final: 0.6768 (ttt180) REVERT: E 94 ARG cc_start: 0.6365 (ttm-80) cc_final: 0.5824 (mpt180) REVERT: R 53 ASP cc_start: 0.5585 (t70) cc_final: 0.5153 (m-30) outliers start: 30 outliers final: 19 residues processed: 245 average time/residue: 0.3091 time to fit residues: 108.2839 Evaluate side-chains 195 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 39 LYS Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 84 GLU Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain R residue 128 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 96 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 chunk 136 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 127 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 ASN C 82 HIS C 99 ASN C 276 HIS D 20 GLN D 159 GLN P 42 ASN P 82 HIS R 36 ASN R 100 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.144862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.109528 restraints weight = 17857.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.109664 restraints weight = 19144.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.110509 restraints weight = 15867.210| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.254 13529 Z= 0.225 Angle : 0.766 12.662 18530 Z= 0.368 Chirality : 0.048 0.196 1970 Planarity : 0.006 0.064 2327 Dihedral : 8.521 87.920 1858 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.94 % Favored : 87.94 % Rotamer: Outliers : 4.32 % Allowed : 12.65 % Favored : 83.03 % 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: -1.71 (0.20), residues: 1658 helix: 0.50 (0.17), residues: 844 sheet: -1.37 (0.64), residues: 68 loop : -3.20 (0.20), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 67 HIS 0.010 0.002 HIS C 97 PHE 0.025 0.002 PHE C 113 TYR 0.020 0.002 TYR D 153 ARG 0.006 0.001 ARG P 193 Details of bonding type rmsd hydrogen bonds : bond 0.05864 ( 631) hydrogen bonds : angle 4.83243 ( 1812) metal coordination : bond 0.01409 ( 8) metal coordination : angle 7.05100 ( 6) SS BOND : bond 0.00471 ( 2) SS BOND : angle 0.87577 ( 4) covalent geometry : bond 0.00557 (13509) covalent geometry : angle 0.75547 (18520) Misc. bond : bond 0.14171 ( 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 269 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 213 time to evaluate : 1.093 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: C 252 ASP cc_start: 0.7750 (m-30) cc_final: 0.7466 (m-30) REVERT: C 351 THR cc_start: 0.8763 (p) cc_final: 0.8412 (p) REVERT: D 50 ASP cc_start: 0.8357 (m-30) cc_final: 0.7960 (m-30) REVERT: D 79 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7505 (mm-30) REVERT: D 165 ASP cc_start: 0.7294 (m-30) cc_final: 0.7091 (m-30) REVERT: D 208 ASP cc_start: 0.8052 (m-30) cc_final: 0.7810 (m-30) REVERT: P 351 THR cc_start: 0.8676 (OUTLIER) cc_final: 0.8197 (p) REVERT: Q 79 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7407 (mm-30) REVERT: Q 87 MET cc_start: 0.8995 (mtt) cc_final: 0.8508 (mtt) REVERT: E 94 ARG cc_start: 0.6607 (ttm-80) cc_final: 0.6292 (mpt180) REVERT: E 173 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.6739 (mtm180) REVERT: R 113 ARG cc_start: 0.6553 (tpt90) cc_final: 0.5988 (tpt170) outliers start: 56 outliers final: 35 residues processed: 257 average time/residue: 0.2591 time to fit residues: 95.8657 Evaluate side-chains 219 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 182 time to evaluate : 1.369 ------------------------------------------------------------------------------- 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 165 LEU Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 167 CYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain P residue 24 PRO Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain P residue 229 VAL Chi-restraints excluded: chain P residue 334 ILE Chi-restraints excluded: chain P residue 351 THR Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 84 GLU Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 144 CYS Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain R residue 25 VAL Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 158 SER Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 186 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 96 optimal weight: 10.0000 chunk 125 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 21 optimal weight: 0.0980 chunk 91 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 59 optimal weight: 0.0980 chunk 111 optimal weight: 0.9980 chunk 81 optimal weight: 0.2980 chunk 63 optimal weight: 2.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 HIS R 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.149483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.114954 restraints weight = 17347.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.113707 restraints weight = 21962.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.115252 restraints weight = 17147.830| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.180 13529 Z= 0.130 Angle : 0.663 10.378 18530 Z= 0.320 Chirality : 0.044 0.185 1970 Planarity : 0.005 0.064 2327 Dihedral : 8.185 80.944 1858 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.43 % Favored : 89.45 % Rotamer: Outliers : 2.80 % Allowed : 15.93 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.07 (0.21), residues: 1658 helix: 1.14 (0.18), residues: 814 sheet: -1.04 (0.73), residues: 54 loop : -2.87 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 296 HIS 0.004 0.001 HIS P 212 PHE 0.017 0.001 PHE C 216 TYR 0.015 0.001 TYR D 153 ARG 0.009 0.001 ARG E 77 Details of bonding type rmsd hydrogen bonds : bond 0.04684 ( 631) hydrogen bonds : angle 4.44312 ( 1812) metal coordination : bond 0.00789 ( 8) metal coordination : angle 6.96490 ( 6) SS BOND : bond 0.00127 ( 2) SS BOND : angle 0.16936 ( 4) covalent geometry : bond 0.00291 (13509) covalent geometry : angle 0.65129 (18520) Misc. bond : bond 0.11391 ( 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 235 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 200 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 193 ARG cc_start: 0.8287 (mtt90) cc_final: 0.8019 (mtt90) REVERT: C 252 ASP cc_start: 0.7654 (m-30) cc_final: 0.7445 (m-30) REVERT: C 351 THR cc_start: 0.8684 (p) cc_final: 0.8320 (p) REVERT: D 50 ASP cc_start: 0.8226 (m-30) cc_final: 0.7844 (m-30) REVERT: D 159 GLN cc_start: 0.7916 (mm110) cc_final: 0.7715 (mm110) REVERT: D 208 ASP cc_start: 0.7948 (m-30) cc_final: 0.7711 (m-30) REVERT: D 248 ARG cc_start: 0.8472 (ttm170) cc_final: 0.7271 (ttt180) REVERT: Q 79 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7308 (mm-30) REVERT: Q 87 MET cc_start: 0.8974 (mtt) cc_final: 0.8568 (mtt) REVERT: Q 160 ILE cc_start: 0.8841 (mm) cc_final: 0.8626 (mm) REVERT: Q 208 ASP cc_start: 0.7951 (m-30) cc_final: 0.7711 (m-30) REVERT: Q 218 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8119 (tp30) REVERT: Q 227 MET cc_start: 0.8256 (ttp) cc_final: 0.8050 (tmm) REVERT: Q 248 ARG cc_start: 0.8411 (ttm170) cc_final: 0.7204 (ttt180) REVERT: E 94 ARG cc_start: 0.6813 (ttm-80) cc_final: 0.6437 (mpt180) REVERT: E 99 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6460 (mp0) outliers start: 35 outliers final: 20 residues processed: 226 average time/residue: 0.2703 time to fit residues: 86.8715 Evaluate side-chains 200 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 167 CYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain P residue 351 THR Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 84 GLU Chi-restraints excluded: chain Q residue 167 CYS Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 158 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 109 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 54 optimal weight: 0.0870 chunk 36 optimal weight: 0.5980 chunk 136 optimal weight: 0.6980 chunk 143 optimal weight: 0.0980 chunk 101 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 ASN P 42 ASN E 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.149774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.114477 restraints weight = 17727.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.114545 restraints weight = 18632.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.115100 restraints weight = 14917.555| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.155 13529 Z= 0.123 Angle : 0.640 9.449 18530 Z= 0.308 Chirality : 0.043 0.175 1970 Planarity : 0.005 0.062 2327 Dihedral : 8.033 79.001 1858 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.49 % Favored : 89.38 % Rotamer: Outliers : 1.92 % Allowed : 17.61 % Favored : 80.46 % 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: -0.79 (0.21), residues: 1658 helix: 1.32 (0.18), residues: 814 sheet: -0.74 (0.68), residues: 68 loop : -2.71 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 151 HIS 0.004 0.001 HIS P 212 PHE 0.017 0.001 PHE P 216 TYR 0.014 0.001 TYR D 153 ARG 0.008 0.000 ARG P 193 Details of bonding type rmsd hydrogen bonds : bond 0.04522 ( 631) hydrogen bonds : angle 4.31549 ( 1812) metal coordination : bond 0.00713 ( 8) metal coordination : angle 6.56071 ( 6) SS BOND : bond 0.00158 ( 2) SS BOND : angle 0.25184 ( 4) covalent geometry : bond 0.00283 (13509) covalent geometry : angle 0.62944 (18520) Misc. bond : bond 0.08972 ( 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 226 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 1.490 Fit side-chains revert: symmetry clash REVERT: C 180 LEU cc_start: 0.9391 (tp) cc_final: 0.9071 (mt) REVERT: C 193 ARG cc_start: 0.8225 (mtt90) cc_final: 0.7971 (mtt90) REVERT: C 252 ASP cc_start: 0.8045 (m-30) cc_final: 0.7661 (m-30) REVERT: D 50 ASP cc_start: 0.8129 (m-30) cc_final: 0.7704 (m-30) REVERT: D 79 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7516 (mm-30) REVERT: D 183 MET cc_start: 0.8245 (ttp) cc_final: 0.7912 (ttm) REVERT: D 208 ASP cc_start: 0.8054 (m-30) cc_final: 0.7827 (m-30) REVERT: D 248 ARG cc_start: 0.8480 (ttm170) cc_final: 0.7255 (ttt180) REVERT: Q 79 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7304 (mm-30) REVERT: Q 87 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8397 (mtt) REVERT: Q 160 ILE cc_start: 0.9035 (mm) cc_final: 0.8824 (mm) REVERT: Q 208 ASP cc_start: 0.8085 (m-30) cc_final: 0.7818 (m-30) REVERT: Q 218 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8184 (tp30) REVERT: Q 227 MET cc_start: 0.8199 (ttp) cc_final: 0.7954 (tmm) REVERT: Q 248 ARG cc_start: 0.8371 (ttm170) cc_final: 0.7510 (ttt180) REVERT: E 94 ARG cc_start: 0.6868 (ttm-80) cc_final: 0.6060 (mpt180) REVERT: R 36 ASN cc_start: 0.8829 (t0) cc_final: 0.8092 (t0) outliers start: 24 outliers final: 17 residues processed: 222 average time/residue: 0.3039 time to fit residues: 94.7555 Evaluate side-chains 195 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 167 CYS Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain P residue 334 ILE Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 87 MET Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain R residue 128 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 29 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 155 optimal weight: 0.3980 chunk 119 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 chunk 25 optimal weight: 0.6980 chunk 1 optimal weight: 0.0980 chunk 156 optimal weight: 0.0020 chunk 142 optimal weight: 0.5980 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 72 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.151485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.115580 restraints weight = 17791.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.117633 restraints weight = 18780.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.117611 restraints weight = 14538.923| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.177 13529 Z= 0.121 Angle : 0.644 14.121 18530 Z= 0.308 Chirality : 0.042 0.176 1970 Planarity : 0.005 0.061 2327 Dihedral : 7.952 77.480 1858 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.13 % Favored : 89.75 % Rotamer: Outliers : 2.56 % Allowed : 18.09 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.48 (0.21), residues: 1658 helix: 1.58 (0.18), residues: 804 sheet: -0.58 (0.67), residues: 68 loop : -2.49 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 296 HIS 0.004 0.001 HIS P 212 PHE 0.018 0.001 PHE P 104 TYR 0.013 0.001 TYR D 153 ARG 0.004 0.000 ARG E 77 Details of bonding type rmsd hydrogen bonds : bond 0.04336 ( 631) hydrogen bonds : angle 4.25271 ( 1812) metal coordination : bond 0.00747 ( 8) metal coordination : angle 5.81707 ( 6) SS BOND : bond 0.00289 ( 2) SS BOND : angle 0.32520 ( 4) covalent geometry : bond 0.00279 (13509) covalent geometry : angle 0.63592 (18520) Misc. bond : bond 0.09393 ( 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 213 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 3.154 Fit side-chains REVERT: C 180 LEU cc_start: 0.9358 (tp) cc_final: 0.9059 (mt) REVERT: C 252 ASP cc_start: 0.8035 (m-30) cc_final: 0.7656 (m-30) REVERT: D 50 ASP cc_start: 0.8184 (m-30) cc_final: 0.7731 (m-30) REVERT: D 183 MET cc_start: 0.8377 (ttp) cc_final: 0.8088 (ttm) REVERT: D 208 ASP cc_start: 0.8073 (m-30) cc_final: 0.7833 (m-30) REVERT: D 227 MET cc_start: 0.8170 (ttp) cc_final: 0.7887 (tmm) REVERT: D 248 ARG cc_start: 0.8431 (ttm170) cc_final: 0.7532 (ttt180) REVERT: P 180 LEU cc_start: 0.9330 (tp) cc_final: 0.9080 (mt) REVERT: Q 79 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7270 (mm-30) REVERT: Q 87 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8355 (mtt) REVERT: Q 140 GLU cc_start: 0.7995 (mp0) cc_final: 0.7747 (mp0) REVERT: Q 183 MET cc_start: 0.8396 (ttp) cc_final: 0.8067 (ttm) REVERT: Q 208 ASP cc_start: 0.8126 (m-30) cc_final: 0.7859 (m-30) REVERT: Q 227 MET cc_start: 0.8125 (ttp) cc_final: 0.7855 (tmm) REVERT: Q 248 ARG cc_start: 0.8410 (ttm170) cc_final: 0.7551 (ttt180) REVERT: E 47 MET cc_start: 0.3067 (tmm) cc_final: 0.2818 (tmm) REVERT: E 94 ARG cc_start: 0.6798 (ttm-80) cc_final: 0.5659 (ttm170) REVERT: E 152 PHE cc_start: 0.7281 (t80) cc_final: 0.6673 (t80) REVERT: R 36 ASN cc_start: 0.8835 (t0) cc_final: 0.8068 (t0) outliers start: 32 outliers final: 16 residues processed: 209 average time/residue: 0.4296 time to fit residues: 131.4209 Evaluate side-chains 184 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 167 CYS Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 87 MET Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain R residue 128 VAL 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: 0.9980 chunk 100 optimal weight: 1.9990 chunk 155 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 0.4980 chunk 110 optimal weight: 0.0970 chunk 137 optimal weight: 0.1980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 36 ASN E 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.150733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.114986 restraints weight = 17710.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.115761 restraints weight = 18886.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.116564 restraints weight = 14942.729| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.156 13529 Z= 0.126 Angle : 0.658 13.285 18530 Z= 0.313 Chirality : 0.043 0.210 1970 Planarity : 0.005 0.059 2327 Dihedral : 7.921 77.635 1858 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.25 % Favored : 89.63 % Rotamer: Outliers : 1.68 % Allowed : 18.25 % Favored : 80.06 % 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: -0.39 (0.21), residues: 1658 helix: 1.64 (0.18), residues: 806 sheet: -0.72 (0.59), residues: 84 loop : -2.45 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 179 HIS 0.004 0.001 HIS P 212 PHE 0.023 0.001 PHE C 104 TYR 0.013 0.001 TYR D 153 ARG 0.009 0.000 ARG C 193 Details of bonding type rmsd hydrogen bonds : bond 0.04359 ( 631) hydrogen bonds : angle 4.24620 ( 1812) metal coordination : bond 0.00669 ( 8) metal coordination : angle 6.26308 ( 6) SS BOND : bond 0.00210 ( 2) SS BOND : angle 0.21552 ( 4) covalent geometry : bond 0.00292 (13509) covalent geometry : angle 0.64833 (18520) Misc. bond : bond 0.08606 ( 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 201 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 2.862 Fit side-chains REVERT: C 180 LEU cc_start: 0.9378 (tp) cc_final: 0.9055 (mt) REVERT: C 231 ARG cc_start: 0.8232 (ptp-170) cc_final: 0.7706 (mtt-85) REVERT: C 252 ASP cc_start: 0.7986 (m-30) cc_final: 0.7602 (m-30) REVERT: C 351 THR cc_start: 0.8755 (p) cc_final: 0.8360 (t) REVERT: D 50 ASP cc_start: 0.8133 (m-30) cc_final: 0.7677 (m-30) REVERT: D 87 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8538 (mmm) REVERT: D 140 GLU cc_start: 0.7932 (mp0) cc_final: 0.7583 (mp0) REVERT: D 183 MET cc_start: 0.8384 (ttp) cc_final: 0.7973 (ttm) REVERT: D 208 ASP cc_start: 0.8048 (m-30) cc_final: 0.7809 (m-30) REVERT: D 227 MET cc_start: 0.8157 (ttp) cc_final: 0.7876 (tmm) REVERT: D 248 ARG cc_start: 0.8394 (ttm170) cc_final: 0.7544 (ttt180) REVERT: P 180 LEU cc_start: 0.9353 (tp) cc_final: 0.9051 (mt) REVERT: Q 79 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7227 (mm-30) REVERT: Q 87 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8364 (mtt) REVERT: Q 183 MET cc_start: 0.8430 (ttp) cc_final: 0.7868 (ttm) REVERT: Q 208 ASP cc_start: 0.8097 (m-30) cc_final: 0.7829 (m-30) REVERT: Q 227 MET cc_start: 0.8178 (ttp) cc_final: 0.7878 (tmm) REVERT: Q 248 ARG cc_start: 0.8394 (ttm170) cc_final: 0.7597 (ttt180) REVERT: R 36 ASN cc_start: 0.8790 (t0) cc_final: 0.8042 (t0) outliers start: 21 outliers final: 15 residues processed: 198 average time/residue: 0.3836 time to fit residues: 118.1859 Evaluate side-chains 177 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 3.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 87 MET Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 186 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 4 optimal weight: 0.8980 chunk 96 optimal weight: 9.9990 chunk 92 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 88 optimal weight: 0.0980 chunk 94 optimal weight: 0.3980 chunk 107 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.148940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.111927 restraints weight = 17765.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.112406 restraints weight = 17585.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.113196 restraints weight = 13290.684| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.164 13529 Z= 0.136 Angle : 0.663 13.686 18530 Z= 0.316 Chirality : 0.043 0.181 1970 Planarity : 0.005 0.058 2327 Dihedral : 7.951 78.927 1858 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.80 % Favored : 89.08 % Rotamer: Outliers : 1.84 % Allowed : 18.98 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.37 (0.21), residues: 1658 helix: 1.64 (0.18), residues: 806 sheet: -0.65 (0.60), residues: 82 loop : -2.43 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 126 HIS 0.005 0.001 HIS P 212 PHE 0.021 0.001 PHE C 104 TYR 0.014 0.001 TYR D 153 ARG 0.008 0.000 ARG C 193 Details of bonding type rmsd hydrogen bonds : bond 0.04582 ( 631) hydrogen bonds : angle 4.30229 ( 1812) metal coordination : bond 0.00701 ( 8) metal coordination : angle 5.86342 ( 6) SS BOND : bond 0.00205 ( 2) SS BOND : angle 0.26768 ( 4) covalent geometry : bond 0.00331 (13509) covalent geometry : angle 0.65454 (18520) Misc. bond : bond 0.08640 ( 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 196 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 1.383 Fit side-chains REVERT: C 180 LEU cc_start: 0.9351 (tp) cc_final: 0.9001 (mt) REVERT: C 187 ASP cc_start: 0.8143 (t0) cc_final: 0.7882 (t0) REVERT: C 231 ARG cc_start: 0.8323 (ptp-170) cc_final: 0.7801 (mtt-85) REVERT: C 252 ASP cc_start: 0.8169 (m-30) cc_final: 0.7757 (m-30) REVERT: C 351 THR cc_start: 0.8744 (p) cc_final: 0.8357 (t) REVERT: D 50 ASP cc_start: 0.8196 (m-30) cc_final: 0.7746 (m-30) REVERT: D 87 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8590 (mmm) REVERT: D 140 GLU cc_start: 0.8043 (mp0) cc_final: 0.7701 (mp0) REVERT: D 183 MET cc_start: 0.8505 (ttp) cc_final: 0.7927 (ttm) REVERT: D 208 ASP cc_start: 0.8070 (m-30) cc_final: 0.7808 (m-30) REVERT: D 248 ARG cc_start: 0.8403 (ttm170) cc_final: 0.7551 (ttt180) REVERT: P 180 LEU cc_start: 0.9331 (tp) cc_final: 0.9066 (mt) REVERT: Q 79 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7314 (mm-30) REVERT: Q 87 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8272 (mtt) REVERT: Q 96 MET cc_start: 0.8562 (mtm) cc_final: 0.8278 (ptp) REVERT: Q 183 MET cc_start: 0.8559 (ttp) cc_final: 0.7809 (ttm) REVERT: Q 208 ASP cc_start: 0.8102 (m-30) cc_final: 0.7842 (m-30) REVERT: Q 227 MET cc_start: 0.8249 (ttp) cc_final: 0.7958 (tmm) REVERT: Q 248 ARG cc_start: 0.8400 (ttm170) cc_final: 0.7580 (ttt180) REVERT: R 36 ASN cc_start: 0.8783 (t0) cc_final: 0.8024 (t0) REVERT: R 38 MET cc_start: 0.8583 (mtp) cc_final: 0.8252 (mtp) outliers start: 23 outliers final: 17 residues processed: 190 average time/residue: 0.2387 time to fit residues: 66.6897 Evaluate side-chains 177 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 84 GLU Chi-restraints excluded: chain Q residue 87 MET Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 186 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 49 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 127 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.147204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.109970 restraints weight = 17738.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.110096 restraints weight = 17843.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.111300 restraints weight = 13619.815| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.177 13529 Z= 0.151 Angle : 0.678 13.684 18530 Z= 0.323 Chirality : 0.043 0.182 1970 Planarity : 0.005 0.058 2327 Dihedral : 7.972 79.108 1858 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.80 % Favored : 89.08 % Rotamer: Outliers : 1.84 % Allowed : 19.30 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.43 (0.21), residues: 1658 helix: 1.56 (0.18), residues: 810 sheet: -0.56 (0.60), residues: 82 loop : -2.45 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 179 HIS 0.005 0.001 HIS C 212 PHE 0.020 0.002 PHE C 104 TYR 0.013 0.001 TYR D 153 ARG 0.002 0.000 ARG E 77 Details of bonding type rmsd hydrogen bonds : bond 0.04728 ( 631) hydrogen bonds : angle 4.34503 ( 1812) metal coordination : bond 0.00941 ( 8) metal coordination : angle 5.58119 ( 6) SS BOND : bond 0.00275 ( 2) SS BOND : angle 0.32876 ( 4) covalent geometry : bond 0.00373 (13509) covalent geometry : angle 0.67103 (18520) Misc. bond : bond 0.09319 ( 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 190 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 1.270 Fit side-chains REVERT: C 180 LEU cc_start: 0.9378 (tp) cc_final: 0.9077 (mt) REVERT: C 187 ASP cc_start: 0.8199 (t0) cc_final: 0.7915 (t0) REVERT: C 252 ASP cc_start: 0.8090 (m-30) cc_final: 0.7690 (m-30) REVERT: C 351 THR cc_start: 0.8693 (p) cc_final: 0.8357 (t) REVERT: D 50 ASP cc_start: 0.8254 (m-30) cc_final: 0.7811 (m-30) REVERT: D 87 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8616 (mmm) REVERT: D 140 GLU cc_start: 0.8047 (mp0) cc_final: 0.7744 (mp0) REVERT: D 183 MET cc_start: 0.8539 (ttp) cc_final: 0.7940 (ttm) REVERT: D 208 ASP cc_start: 0.7992 (m-30) cc_final: 0.7739 (m-30) REVERT: D 248 ARG cc_start: 0.8396 (ttm170) cc_final: 0.7583 (ttt180) REVERT: P 180 LEU cc_start: 0.9376 (tp) cc_final: 0.9121 (mt) REVERT: P 187 ASP cc_start: 0.8164 (t0) cc_final: 0.7888 (t0) REVERT: Q 87 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8289 (mtt) REVERT: Q 183 MET cc_start: 0.8588 (ttp) cc_final: 0.7809 (ttm) REVERT: Q 208 ASP cc_start: 0.8038 (m-30) cc_final: 0.7774 (m-30) REVERT: Q 248 ARG cc_start: 0.8395 (ttm170) cc_final: 0.7603 (ttt180) REVERT: R 36 ASN cc_start: 0.8783 (t0) cc_final: 0.8029 (t0) REVERT: R 38 MET cc_start: 0.8709 (mtp) cc_final: 0.8403 (mtp) outliers start: 23 outliers final: 19 residues processed: 188 average time/residue: 0.2403 time to fit residues: 66.4010 Evaluate side-chains 177 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 84 GLU Chi-restraints excluded: chain Q residue 87 MET Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain R residue 128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 152 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 HIS P 276 HIS E 36 ASN R 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.143856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.107410 restraints weight = 17965.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.107908 restraints weight = 20498.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.108759 restraints weight = 15420.724| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.229 13529 Z= 0.201 Angle : 0.733 14.758 18530 Z= 0.348 Chirality : 0.045 0.193 1970 Planarity : 0.005 0.058 2327 Dihedral : 8.136 79.515 1858 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.46 % Favored : 88.42 % Rotamer: Outliers : 1.60 % Allowed : 19.94 % Favored : 78.46 % 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: -0.57 (0.21), residues: 1658 helix: 1.36 (0.18), residues: 814 sheet: -0.41 (0.61), residues: 82 loop : -2.46 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 151 HIS 0.006 0.001 HIS P 97 PHE 0.023 0.002 PHE C 104 TYR 0.014 0.001 TYR Q 153 ARG 0.004 0.000 ARG C 193 Details of bonding type rmsd hydrogen bonds : bond 0.05371 ( 631) hydrogen bonds : angle 4.53715 ( 1812) metal coordination : bond 0.01069 ( 8) metal coordination : angle 5.83637 ( 6) SS BOND : bond 0.00393 ( 2) SS BOND : angle 0.56302 ( 4) covalent geometry : bond 0.00501 (13509) covalent geometry : angle 0.72528 (18520) Misc. bond : bond 0.12401 ( 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 192 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 1.308 Fit side-chains REVERT: C 187 ASP cc_start: 0.8222 (t0) cc_final: 0.7962 (t0) REVERT: C 252 ASP cc_start: 0.7890 (m-30) cc_final: 0.7558 (m-30) REVERT: C 351 THR cc_start: 0.8662 (p) cc_final: 0.8424 (t) REVERT: D 55 GLN cc_start: 0.8392 (mp10) cc_final: 0.8120 (mp10) REVERT: D 87 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8713 (mmm) REVERT: D 183 MET cc_start: 0.8738 (ttp) cc_final: 0.8007 (ttm) REVERT: D 208 ASP cc_start: 0.7984 (m-30) cc_final: 0.7746 (m-30) REVERT: D 248 ARG cc_start: 0.8407 (ttm170) cc_final: 0.7570 (ttt180) REVERT: P 187 ASP cc_start: 0.8215 (t0) cc_final: 0.7929 (t0) REVERT: P 222 ASN cc_start: 0.8602 (t0) cc_final: 0.8392 (t0) REVERT: P 351 THR cc_start: 0.8801 (p) cc_final: 0.8433 (t) REVERT: Q 87 MET cc_start: 0.8965 (mtt) cc_final: 0.8304 (mtt) REVERT: Q 96 MET cc_start: 0.8585 (mtm) cc_final: 0.8360 (ptp) REVERT: Q 183 MET cc_start: 0.8697 (ttp) cc_final: 0.7811 (ttm) REVERT: Q 208 ASP cc_start: 0.8054 (m-30) cc_final: 0.7797 (m-30) REVERT: Q 248 ARG cc_start: 0.8361 (ttm170) cc_final: 0.7517 (ttt180) REVERT: R 38 MET cc_start: 0.8697 (mtp) cc_final: 0.8479 (mtp) outliers start: 20 outliers final: 18 residues processed: 190 average time/residue: 0.2266 time to fit residues: 64.3586 Evaluate side-chains 179 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 84 GLU Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain R residue 128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 41 optimal weight: 0.7980 chunk 143 optimal weight: 0.0980 chunk 8 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 136 optimal weight: 0.0870 chunk 100 optimal weight: 2.9990 chunk 49 optimal weight: 0.0870 chunk 88 optimal weight: 0.0010 chunk 28 optimal weight: 0.0770 chunk 156 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 overall best weight: 0.0700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 36 ASN R 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.151961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.117533 restraints weight = 17772.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.116351 restraints weight = 18995.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.117054 restraints weight = 17070.642| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.5285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.154 13529 Z= 0.124 Angle : 0.664 16.472 18530 Z= 0.315 Chirality : 0.042 0.170 1970 Planarity : 0.005 0.058 2327 Dihedral : 7.870 79.307 1858 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.13 % Favored : 89.75 % Rotamer: Outliers : 1.20 % Allowed : 21.14 % Favored : 77.66 % 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: -0.16 (0.21), residues: 1658 helix: 1.74 (0.18), residues: 808 sheet: 0.42 (0.70), residues: 62 loop : -2.29 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 157 HIS 0.003 0.001 HIS P 212 PHE 0.019 0.001 PHE E 152 TYR 0.012 0.001 TYR D 153 ARG 0.003 0.000 ARG C 193 Details of bonding type rmsd hydrogen bonds : bond 0.04185 ( 631) hydrogen bonds : angle 4.21108 ( 1812) metal coordination : bond 0.01130 ( 8) metal coordination : angle 5.63034 ( 6) SS BOND : bond 0.00108 ( 2) SS BOND : angle 0.22341 ( 4) covalent geometry : bond 0.00285 (13509) covalent geometry : angle 0.65596 (18520) Misc. bond : bond 0.08450 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4814.03 seconds wall clock time: 89 minutes 1.41 seconds (5341.41 seconds total)